@article {pmid37246713, year = {2023}, author = {Jowsey, WJ and Morris, CRP and Hall, DA and Sullivan, JT and Fagerlund, RD and Eto, KY and Solomon, PD and Mackay, JP and Bond, CS and Ramsay, JP and Ronson, CW}, title = {DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad457}, pmid = {37246713}, issn = {1362-4962}, abstract = {Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.}, }
@article {pmid37246198, year = {2023}, author = {Shafique, MS and Guo, W and Chen, X and Zhao, K and Liu, Y and Wang, C and Ji, Z}, title = {Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {189}, pmid = {37246198}, issn = {1438-7948}, }
@article {pmid37243281, year = {2023}, author = {Arnau, V and Díaz-Villanueva, W and Mifsut Benet, J and Villasante, P and Beamud, B and Mompó, P and Sanjuan, R and González-Candelas, F and Domingo-Calap, P and Džunková, M}, title = {Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/v15051196}, pmid = {37243281}, issn = {1999-4915}, abstract = {The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.}, }
@article {pmid37239594, year = {2023}, author = {Tuvo, B and Scarpaci, M and Bracaloni, S and Esposito, E and Costa, AL and Ioppolo, M and Casini, B}, title = {Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {10}, pages = {}, doi = {10.3390/ijerph20105868}, pmid = {37239594}, issn = {1660-4601}, abstract = {The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.}, }
@article {pmid37239483, year = {2023}, author = {Alim, NTB and Koppenhöfer, S and Lang, AS and Beatty, JT}, title = {Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/genes14051124}, pmid = {37239483}, issn = {2073-4425}, abstract = {A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.}, }
@article {pmid37239397, year = {2023}, author = {Dey, S and Gaur, M and Sykes, EME and Prusty, M and Elangovan, S and Dixit, S and Pati, S and Kumar, A and Subudhi, E}, title = {Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/genes14051037}, pmid = {37239397}, issn = {2073-4425}, abstract = {BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.<br><br>METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.<br><br>RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.<br><br>CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.}, }
@article {pmid37237011, year = {2023}, author = {Negeri, AA and Mamo, H and Gahlot, DK and Gurung, JM and Seyoum, ET and Francis, MS}, title = {Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8595}, pmid = {37237011}, issn = {2045-2322}, abstract = {CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.}, }
@article {pmid37236960, year = {2023}, author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H}, title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {5}, pages = {1415-1429}, doi = {10.13287/j.1001-9332.202305.032}, pmid = {37236960}, issn = {1001-9332}, abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.}, }
@article {pmid37236388, year = {2023}, author = {Song, D and Tang, X and Tariq, A and Pan, K and Li, D}, title = {Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116233}, doi = {10.1016/j.envres.2023.116233}, pmid = {37236388}, issn = {1096-0953}, abstract = {Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 10[5] to 6.22 × 10[7] copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.}, }
@article {pmid37232518, year = {2023}, author = {Burch, CL and Romanchuk, A and Kelly, M and Wu, Y and Jones, CD}, title = {Empirical evidence that complexity limits horizontal gene transfer.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad089}, pmid = {37232518}, issn = {1759-6653}, abstract = {Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein-protein interactions in which the gene participates, i.e., its connectivity. Two non-exclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the Complexity Hypothesis (Jain, Rivera, &amp; Lake, 1999) and the Balance Hypothesis (Papp, Pál, &amp; Hurst, 2003). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologues to make normal protein-protein interactions or from gene mis-expression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into E. coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the Complexity Hypotheses explains all three of these observations, the Balance Hypothesis explains only the first one.}, }
@article {pmid37115189, year = {2023}, author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR}, title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37115189}, issn = {2057-5858}, support = {U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.}, }
@article {pmid37227565, year = {2023}, author = {Chettri, U and Nongkhlaw, M and Joshi, SR}, title = {Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.}, journal = {Current microbiology}, volume = {80}, number = {7}, pages = {226}, pmid = {37227565}, issn = {1432-0991}, abstract = {Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.}, }
@article {pmid37227251, year = {2023}, author = {Tonkin-Hill, G and Corander, J and Parkhill, J}, title = {Challenges in prokaryote pangenomics.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001021}, pmid = {37227251}, issn = {2057-5858}, abstract = {Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.}, }
@article {pmid37223257, year = {2021}, author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P}, title = {Extracellular membrane vesicles and nanotubes in Archaea.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab007}, pmid = {37223257}, issn = {2633-6693}, abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.}, }
@article {pmid37223255, year = {2021}, author = {Afonina, I and Tien, B and Nair, Z and Matysik, A and Lam, LN and Veleba, M and Jie, AKJ and Rashid, R and Cazenave-Gassiot, A and Wenk, M and Wai, SN and Kline, KA}, title = {The composition and function of Enterococcus faecalis membrane vesicles.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab002}, pmid = {37223255}, issn = {2633-6693}, abstract = {Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.}, }
@article {pmid37221009, year = {2023}, author = {Shaferman, M and Gencel, M and Alon, N and Alasad, K and Rotblat, B and Serohijos, AWR and Alfonta, L and Bershtein, S}, title = {The fitness effects of codon composition of the horizontally transferred antibiotic resistance genes intensify at sub-lethal antibiotic levels.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad123}, pmid = {37221009}, issn = {1537-1719}, abstract = {The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced E. coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5'-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5'-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.}, }
@article {pmid37219457, year = {2023}, author = {Murthy, AC and Aleksanyan, N and Morton, GM and Toyoda, HC and Kalashyan, M and Chen, S and Ragucci, AE and Broulidakis, MP and Swerdlow, KJ and Bui, MNN and Muccioli, M and Berkmen, MB}, title = {Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0003323}, doi = {10.1128/jb.00033-23}, pmid = {37219457}, issn = {1098-5530}, abstract = {Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.}, }
@article {pmid37218693, year = {2023}, author = {Bejenari, M and Sondergaard, TE and Sørensen, JL}, title = {6-MSA, a secondary metabolite distribution hub with multiple fungal destinations.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad107}, pmid = {37218693}, issn = {1365-2672}, abstract = {6-methylsalicylic acid is a small, simple polyketide produced by a broad spectrum of fungal species. Since fungi obtained the ability to synthesize 6-MSA from bacteria through a horizontal gene transfer event, it has developed into a multipurpose metabolic hub from where numerous complex compounds are produced. The most relevant metabolite from a human perspective is the small lactone patulin as it is one of the most potent mycotoxins. Other important end products derived from 6-MSA include the small quinone epoxide terreic acid and the prenylated yanuthones. The most advanced modification of 6-MSA is observed in the aculin biosynthetic pathway, which is mediated by a non-ribosomal peptide synthase and a terpene cyclase. In this short review, we summarize for the first time all the possible pathways that takes their onset from 6-MSA and provide a synopsis of the responsible gene clusters and derive the resulting biosynthetic pathways.}, }
@article {pmid37078595, year = {2023}, author = {Botelho, J}, title = {Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance.}, journal = {Nucleic acids research}, volume = {51}, number = {9}, pages = {4385-4397}, pmid = {37078595}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents ; Virulence/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.}, }
@article {pmid37217185, year = {2023}, author = {Maruyama, M and Kagamoto, T and Matsumot, Y and Onum, R and Miyagishima, SY and Tanifuj, G and Nakazawa, M and Kashiyama, Y}, title = {Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcad044}, pmid = {37217185}, issn = {1471-9053}, abstract = {While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified the gene RvNaRL, which had sequence similarity to nitrate reductases found in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify its function of the protein product RvNaRL, we established a RNAi mediated knockdown and a CRISPR-Cas9-mediated knockout experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knockdown and knockout cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to acquisition of the nitrate assimilation by the horizontal gene transfer.}, }
@article {pmid37215039, year = {2023}, author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J}, title = {Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.11.540415}, pmid = {37215039}, abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ∼2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.}, }
@article {pmid37213501, year = {2023}, author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X}, title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1145315}, pmid = {37213501}, issn = {1664-302X}, abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.}, }
@article {pmid37213168, year = {2023}, author = {Youngblom, MA and Shockey, AC and Callaghan, MM and Dillard, JP and Pepperell, CS}, title = {The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.000985}, pmid = {37213168}, issn = {2057-5858}, abstract = {The incidence of gonorrhoea is increasing at an alarming pace, and therapeutic options continue to narrow as a result of worsening drug resistance. Neisseria gonorrhoeae is naturally competent, allowing the organism to adapt rapidly to selection pressures including antibiotics. A sub-population of N. gonorrhoeae carries the Gonococcal Genetic Island (GGI), which encodes a type IV secretion system (T4SS) that secretes chromosomal DNA. Previous research has shown that the GGI increases transformation efficiency in vitro, but the extent to which it contributes to horizontal gene transfer (HGT) during infection is unknown. Here we analysed genomic data from clinical isolates of N. gonorrhoeae to better characterize GGI+ and GGI- sub-populations and to delineate patterns of variation at the locus itself. We found the element segregating at an intermediate frequency (61%), and it appears to act as a mobile genetic element with examples of gain, loss, exchange and intra-locus recombination within our sample. We further found evidence suggesting that GGI+ and GGI- sub-populations preferentially inhabit distinct niches with different opportunities for HGT. Previously, GGI+ isolates were reported to be associated with more severe clinical infections, and our results suggest this could be related to metal-ion trafficking and biofilm formation. The co-segregation of GGI+ and GGI- isolates despite mobility of the element suggests that both niches inhabited by N. gonorrhoeae remain important to its overall persistence as has been demonstrated previously for cervical- and urethral-adapted sub-populations. These data emphasize the complex population structure of N. gonorrhoeae and its capacity to adapt to diverse niches.}, }
@article {pmid37213139, year = {2023}, author = {C Silva-de-Jesus, A and Rossi, CC and Pereira-Ribeiro, PM and Guaraldi, AL and Giambiagi-deMarval, M}, title = {Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2022-0225}, pmid = {37213139}, issn = {1746-0921}, abstract = {Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials &amp; methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.}, }
@article {pmid37210032, year = {2023}, author = {Yin, Y and Lou, T and Song, W and Wang, C and Wang, J}, title = {Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129180}, doi = {10.1016/j.biortech.2023.129180}, pmid = {37210032}, issn = {1873-2976}, abstract = {The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.}, }
@article {pmid37209559, year = {2023}, author = {Yuan, B and Zhang, Y and Zhang, Z and Lin, Z and Ma, Y and Sun, Y}, title = {Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131659}, doi = {10.1016/j.jhazmat.2023.131659}, pmid = {37209559}, issn = {1873-3336}, abstract = {Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.}, }
@article {pmid37204585, year = {2023}, author = {Lü, W and Ren, H and Ding, W and Li, H and Yao, X and Jiang, X}, title = {Rapid shifts in pond sediment microbiota in response to high ambient temperature in a water-sediment microcosm.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-023-26823-7}, pmid = {37204585}, issn = {1614-7499}, abstract = {Unlike the extensive research on the response of soil microorganisms to high ambient temperature (HTA), the response of sediment microorganisms to HTA remains unclear. Understanding the response of sediment microorganisms to HTA is important to forecast their impacts on ecosystems and climate warming under projected climate change scenarios. Against the background of climate warming and frequent high ambient temperatures in summer, we conducted a laboratory incubation experiment to clarify the unique assembly characteristics of pond sediment bacterial communities at different temperatures (4, 10, 15, 25, 30 and 35 °C). The results showed that the structure and function of the microbial community in pond sediments at 35 °C were different from those under other temperatures; the microbial community structure at 35 °C had the most large modules and an average module size. Temperature and dissolved oxygen influenced the microbial community network modularity. The CO2 emission rates of pond sediments at 35 °C were significantly higher than those at other temperatures. At 35 °C, heterogeneous selection was the most important assembly process. Additionally, warming altered the microbial network structure and ecosystem functioning but not the microbial diversity or community composition, which may be related to horizontal gene transfer. Revealing the rapid response of pond sediment microorganisms to HTA is important for identifying their role in nutrient cycling and assessing the ecological impacts of climate warming and high ambient temperatures on inland water sediments.}, }
@article {pmid37201375, year = {2023}, author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC}, title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.}, journal = {Water research}, volume = {239}, number = {}, pages = {120061}, doi = {10.1016/j.watres.2023.120061}, pmid = {37201375}, issn = {1879-2448}, abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.}, }
@article {pmid37196739, year = {2023}, author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y}, title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129190}, doi = {10.1016/j.biortech.2023.129190}, pmid = {37196739}, issn = {1873-2976}, abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.}, }
@article {pmid37191574, year = {2023}, author = {Zhu, Q and Gao, S and Xiao, B and He, Z and Hu, S}, title = {Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0464522}, doi = {10.1128/spectrum.04645-22}, pmid = {37191574}, issn = {2165-0497}, abstract = {Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.}, }
@article {pmid37187278, year = {2023}, author = {Zhou, Q and Zhang, J and Fang, Q and Zhang, M and Wang, X and Zhang, D and Pan, X}, title = {Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121828}, doi = {10.1016/j.envpol.2023.121828}, pmid = {37187278}, issn = {1873-6424}, abstract = {MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.}, }
@article {pmid37185344, year = {2023}, author = {Riccardi, C and Koper, P and Innocenti, G and diCenzo, GC and Fondi, M and Mengoni, A and Perrin, E}, title = {Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001025}, pmid = {37185344}, issn = {2057-5858}, abstract = {Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.}, }
@article {pmid37178001, year = {2023}, author = {Vesel, N and Iseli, C and Guex, N and Lemopoulos, A and Blokesch, M}, title = {DNA modifications impact natural transformation of Acinetobacter baumannii.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad377}, pmid = {37178001}, issn = {1362-4962}, support = {407240_167061/SNSF_/Swiss National Science Foundation/Switzerland ; 55008726/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.}, }
@article {pmid37177929, year = {2023}, author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F}, title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2551-2561}, doi = {10.13227/j.hjkx.202206267}, pmid = {37177929}, issn = {0250-3301}, abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.}, }
@article {pmid37173437, year = {2023}, author = {Feng, SY and Hauck, Y and Morgene, F and Mohammedi, R and Mirouze, N}, title = {The complex regulation of competence in Staphylococcus aureus under microaerobic conditions.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {512}, pmid = {37173437}, issn = {2399-3642}, abstract = {To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.}, }
@article {pmid37173063, year = {2023}, author = {Ayllón, MA and Vainio, EJ}, title = {Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle.}, journal = {Advances in virus research}, volume = {115}, number = {}, pages = {1-86}, doi = {10.1016/bs.aivir.2023.02.002}, pmid = {37173063}, issn = {1557-8399}, abstract = {Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.}, }
@article {pmid37172383, year = {2023}, author = {Liu, YJ and Li, ZH and He, YT and Yuan, L and Sheng, GP}, title = {Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131587}, doi = {10.1016/j.jhazmat.2023.131587}, pmid = {37172383}, issn = {1873-3336}, abstract = {Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.}, }
@article {pmid37172034, year = {2023}, author = {Green, VE and Klancher, CA and Yamamoto, S and Dalia, AB}, title = {The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae.}, journal = {PLoS genetics}, volume = {19}, number = {5}, pages = {e1010767}, doi = {10.1371/journal.pgen.1010767}, pmid = {37172034}, issn = {1553-7404}, abstract = {Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.}, }
@article {pmid37168121, year = {2023}, author = {Tao, S and Zhou, D and Chen, H and Li, N and Zheng, L and Fang, Y and Xu, Y and Jiang, Q and Liang, W}, title = {Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177841}, doi = {10.3389/fmicb.2023.1177841}, pmid = {37168121}, issn = {1664-302X}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.}, }
@article {pmid37167868, year = {2023}, author = {Cai, P and Chen, Q and Du, W and Yang, S and Li, J and Cai, H and Zhao, X and Sun, W and Xu, N and Wang, J}, title = {Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131567}, doi = {10.1016/j.jhazmat.2023.131567}, pmid = {37167868}, issn = {1873-3336}, abstract = {Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.}, }
@article {pmid37166501, year = {2023}, author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A}, title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37166501}, issn = {1432-184X}, abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.}, }
@article {pmid37164096, year = {2023}, author = {Gao, Y and Luo, W and Zhang, H and Chen, Y and Li, Z and Wei, G and Chen, W}, title = {Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163933}, doi = {10.1016/j.scitotenv.2023.163933}, pmid = {37164096}, issn = {1879-1026}, abstract = {Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.}, }
@article {pmid37158891, year = {2023}, author = {Tapia, SM and Macías, LG and Pérez-Torrado, R and Daroqui, N and Manzanares, P and Querol, A and Barrio, E}, title = {A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {102}, pmid = {37158891}, issn = {1741-7007}, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.<br><br>RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.<br><br>CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.}, }
@article {pmid37156983, year = {2023}, author = {Calderón-Franco, D and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG}, title = {Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, pmid = {37156983}, issn = {1572-9699}, abstract = {The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L[-1]). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L[-1]). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.}, }
@article {pmid37156401, year = {2023}, author = {Gartzonika, K and Politi, L and Mavroidi, A and Tsantes, AG and Spanakis, N and Priavali, E and Vrioni, G and Tsakris, A}, title = {High prevalence of clonally-related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {106837}, doi = {10.1016/j.ijantimicag.2023.106837}, pmid = {37156401}, issn = {1872-7913}, abstract = {NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were consecutively recovered. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined-disk tests for carbapenemase production, PCR and sequencing for resistance genes, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments, genotyping by multilocus sequence typing, whole genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST ST (ST182), whereas single isolates belonged to different STs (ST190, ST269, ST443, ST743). PFGE analysis has revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates of the study period. All ST182 blaNDM-1-carrying isolates also harbored the blaACT-16 AmpC gene, while blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most of the cases. In all clonal isolates the blaNDM-1 gene was located on an IncA/C-type plasmid and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. Our study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.}, }
@article {pmid37156383, year = {2023}, author = {Tyrrell, C and Do, TT and Leigh, RJ and Burgess, CM and Brennan, FP and Walsh, F}, title = {Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163926}, doi = {10.1016/j.scitotenv.2023.163926}, pmid = {37156383}, issn = {1879-1026}, abstract = {Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus. We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.}, }
@article {pmid37155884, year = {2023}, author = {Kinsella, CM and van der Hoek, L}, title = {Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {20}, pages = {e2303844120}, doi = {10.1073/pnas.2303844120}, pmid = {37155884}, issn = {1091-6490}, abstract = {Among cressdnaviruses, only the family Circoviridae is recognized to infect vertebrates, while many others have unknown hosts. Detection of virus-to-host horizontal gene transfer is useful for solving such virus-host relationships. Here, we extend this utility to an unusual case of virus-to-virus horizontal transfer, showing multiple ancient captures of cressdnavirus Rep genes by avipoxviruses-large dsDNA pathogens of birds and other saurians. As gene transfers must have occurred during virus coinfections, saurian hosts were implied for the cressdnavirus donor lineage. Surprisingly, phylogenetic analysis revealed that donors were not members of the vertebrate-infecting Circoviridae, instead belonging to a previously unclassified family that we name Draupnirviridae. While draupnirviruses still circulate today, we show that those in the genus Krikovirus infected saurian vertebrates at least 114 Mya, leaving endogenous viral elements inside snake, lizard, and turtle genomes throughout the Cretaceous Period. Endogenous krikovirus elements in some insect genomes and frequent detection in mosquitoes imply that spillover to vertebrates was arthropod mediated, while ancestral draupnirviruses likely infected protists before their emergence in animals. A modern krikovirus sampled from an avipoxvirus-induced lesion shows that their interaction with poxviruses is ongoing. Captured Rep genes in poxvirus genomes often have inactivated catalytic motifs, yet near-total presence across the Avipoxvirus genus, and evidence of both expression and purifying selection on them suggests currently unknown functions.}, }
@article {pmid37155541, year = {2023}, author = {Jiang, Y and Zhao, L and Li, JD and Sun, J and Miao, R and Shao, B and Wu, P}, title = {The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer.}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {1}, pages = {103-112}, doi = {10.5455/javar.2023.j658}, pmid = {37155541}, issn = {2311-7710}, abstract = {OBJECTIVES: This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts.<br><br>MATERIALS AND METHODS: Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed.<br><br>RESULTS: The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs.<br><br>CONCLUSIONS: The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.}, }
@article {pmid37154532, year = {2023}, author = {Cai, L}, title = {Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e16174}, doi = {10.1002/ajb2.16174}, pmid = {37154532}, issn = {1537-2197}, abstract = {The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.}, }
@article {pmid37152757, year = {2023}, author = {Nie, Z and Tang, K and Wang, W and Wang, P and Guo, Y and Wang, Y and Kao, SJ and Yin, J and Wang, X}, title = {Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138751}, pmid = {37152757}, issn = {1664-302X}, abstract = {Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.}, }
@article {pmid37071810, year = {2023}, author = {Paulat, NS and Storer, JM and Moreno-Santillán, DD and Osmanski, AB and Sullivan, KAM and Grimshaw, JR and Korstian, J and Halsey, M and Garcia, CJ and Crookshanks, C and Roberts, J and Smit, AFA and Hubley, R and Rosen, J and Teeling, EC and Vernes, SC and Myers, E and Pippel, M and Brown, T and Hiller, M and ,  and Rojas, D and Dávalos, LM and Lindblad-Toh, K and Karlsson, EK and Ray, DA}, title = {Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37071810}, issn = {1537-1719}, mesh = {Animals ; *DNA Transposable Elements/genetics ; *Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny ; }, abstract = {Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.}, }
@article {pmid37149187, year = {2023}, author = {Li, LG and Zhang, T}, title = {Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163870}, doi = {10.1016/j.scitotenv.2023.163870}, pmid = {37149187}, issn = {1879-1026}, abstract = {Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.}, }
@article {pmid37148762, year = {2023}, author = {Jiang, H and Zhang, L and Wang, X and Gu, J and Song, Z and Wei, S and Guo, H and Xu, L and Qian, X}, title = {Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118071}, doi = {10.1016/j.jenvman.2023.118071}, pmid = {37148762}, issn = {1095-8630}, abstract = {Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.}, }
@article {pmid37146969, year = {2023}, author = {Takada, H and Katoh, T and Sakanaka, M and Odamaki, T and Katayama, T}, title = {GH20 and GH84 β-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {104781}, doi = {10.1016/j.jbc.2023.104781}, pmid = {37146969}, issn = {1083-351X}, abstract = {Intestinal mucus layers mediate symbiosis and dysbiosis of host-microbe interactions. These interactions are influenced by the mucin O-glycan degrading ability of several gut microbes. The identities and prevalence of many glycoside hydrolyses (GHs) involved in microbial mucin O-glycan breakdown have been previously reported; however, the exact mechanisms and extent to which these GHs are dedicated to mucin O-glycan degradation pathways warrant further research. Here, using Bifidobacterium bifidum as a model mucinolytic bacterium, we revealed that two β-N-acetylglucosaminidases belonging to the GH20 (BbhI) and GH84 (BbhIV) families play important roles in mucin O-glycan degradation. Using substrate specificity analysis of natural oligosaccharides and O-glycomic analysis of porcine gastric mucin (PGM) incubated with purified enzymes or B. bifidum carrying bbhI and/or bbhIV mutations, we showed that BbhI and BbhIV are highly specific for β-(1→3)- and β-(1→6)-GlcNAc linkages of mucin core structures, respectively. Interestingly, we found that efficient hydrolysis of the β-(1→3)-linkage by BbhI of the mucin core 4 structure [GlcNAcβ1-3(GlcNAcβ1-6)GalNAcα-O-Thr] required prior removal of the β-(1→6)-GlcNAc linkage by BbhIV. Consistent with this, inactivation of bbhIV markedly decreased the ability of B. bifidum to release GlcNAc from PGM. When combined with a bbhI mutation, we observed that the growth of the strain on PGM was reduced. Finally, phylogenetic analysis suggests that GH84 members may have gained diversified functions through microbe-microbe and host-microbe horizontal gene transfer events. Taken together, these data strongly suggest GH84 family members in host glycan breakdown.}, }
@article {pmid37144438, year = {2023}, author = {Hu, X and Xu, Y and Liu, S and Gudda, FO and Ling, W and Qin, C and Gao, Y}, title = {Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2301177}, doi = {10.1002/smll.202301177}, pmid = {37144438}, issn = {1613-6829}, abstract = {Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.}, }
@article {pmid36933870, year = {2023}, author = {Yang, Q and Zhu, Y and Schwarz, S and Wang, L and Liu, W and Yang, W and Liu, S and Zhang, W}, title = {Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E.}, journal = {International journal of antimicrobial agents}, volume = {61}, number = {5}, pages = {106793}, doi = {10.1016/j.ijantimicag.2023.106793}, pmid = {36933870}, issn = {1872-7913}, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Streptococcus/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; }, abstract = {Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.}, }
@article {pmid37143068, year = {2023}, author = {Valach, M and Moreira, S and Petitjean, C and Benz, C and Butenko, A and Flegontova, O and Nenarokova, A and Prokopchuk, G and Batstone, T and Lapébie, P and Lemogo, L and Sarrasin, M and Stretenowich, P and Tripathi, P and Yazaki, E and Nara, T and Henrissat, B and Lang, BF and Gray, MW and Williams, TA and Lukeš, J and Burger, G}, title = {Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {99}, pmid = {37143068}, issn = {1741-7007}, support = {BB/R016437/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.<br><br>RESULTS: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The&#x2009;~&#x2009;280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.<br><br>CONCLUSIONS: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.}, }
@article {pmid37138596, year = {2023}, author = {Zhao, Y and Wei, HM and Yuan, JL and Xu, L and Sun, JQ}, title = {A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177951}, pmid = {37138596}, issn = {1664-302X}, abstract = {Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.}, }
@article {pmid37137974, year = {2023}, author = {Ikhimiukor, OO and Souza, SSR and Marcovici, MM and Nye, GJ and Gibson, R and Andam, CP}, title = {Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {482}, pmid = {37137974}, issn = {2399-3642}, abstract = {Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.}, }
@article {pmid37133439, year = {2023}, author = {Tran, NN and Morrisette, T and Jorgensen, SCJ and Orench-Benvenutti, JM and Kebriaei, R}, title = {Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections.}, journal = {Pharmacotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1002/phar.2806}, pmid = {37133439}, issn = {1875-9114}, abstract = {Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies and reported alternatives are discussed.}, }
@article {pmid37126651, year = {2023}, author = {Akmal, M and Akatsuka, M and Nishiki, I and Yoshida, T}, title = {Resistance and genomic characterization of a plasmid pkh2101 harbouring erm(B) isolated from emerging fish pathogen Lactococcus garvieae serotype II in Japan.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.13793}, pmid = {37126651}, issn = {1365-2761}, abstract = {The emergence of antibiotic-resistant pathogenic strains of Lactococcus garvieae serotype II isolated from fish in Japan has become a growing concern in recent years. The data on drug susceptibility and its associated resistance mechanism are limited. Therefore, the present study was conducted to determine the minimum inhibitory concentrations (MICs) of chemotherapeutic agents against 98 pathogenic strains of emerging Lactococcus garvieae serotype II isolated from fish from six different prefectures in Japan from 2018 to 2021. The tested strains were resistant to erythromycin, lincomycin and tiamulin. PCR amplification revealed the presence of erm(B) in all erythromycin-resistant strains, while a conjugation experiment confirmed that these strains carried erm(B) that could be transferred to recipient Enterococcus faecalis OG1RF with frequencies from 10[-4] to 10[-6] per donor cells. Nucleotide sequencing of the representative isolated plasmid pkh2101 from an erythromycin-resistant strain showed that it was a 26,850 bp molecule with an average GC content of 33.49%, comprising 31 CDSs, 13 of which remained without any functional annotation. Comparative genomic analysis suggested that pkh2101 shared the highest similarity (97.57% identity) with the plasmid pAMbeta1, which was previously isolated clinically from Enterococcus faecalis DS-5. This study provides potential evidence that the plasmid harbouring erm(B) could be a source of antibiotic resistance transmission in emerging L. garvieae infection in aquaculture.}, }
@article {pmid37125932, year = {2023}, author = {Quan, J and Hu, H and Zhang, H and Meng, Y and Liao, W and Zhou, J and Han, X and Shi, Q and Zhao, D and Wang, Q and Jiang, Y and Yu, Y}, title = {Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0355422}, doi = {10.1128/spectrum.03554-22}, pmid = {37125932}, issn = {2165-0497}, abstract = {The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.}, }
@article {pmid37125466, year = {2023}, author = {Castanheira, M and Mendes, RE and Gales, AC}, title = {Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {Supplement_2}, pages = {S166-S178}, doi = {10.1093/cid/ciad109}, pmid = {37125466}, issn = {1537-6591}, abstract = {Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.}, }
@article {pmid37121291, year = {2023}, author = {Kosterlitz, O and Huisman, JS}, title = {Guidelines for the estimation and reporting of plasmid conjugation rates.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102685}, doi = {10.1016/j.plasmid.2023.102685}, pmid = {37121291}, issn = {1095-9890}, abstract = {Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.}, }
@article {pmid37120693, year = {2023}, author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K}, title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {42}, pmid = {37120693}, issn = {2730-6151}, abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.}, }
@article {pmid37120212, year = {2023}, author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P}, title = {Lebanese fermented goat milk products: From tradition to meta-omics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {168}, number = {}, pages = {112762}, doi = {10.1016/j.foodres.2023.112762}, pmid = {37120212}, issn = {1873-7145}, abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.}, }
@article {pmid37120023, year = {2023}, author = {Adomako, MO and Yu, FH}, title = {Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163760}, doi = {10.1016/j.scitotenv.2023.163760}, pmid = {37120023}, issn = {1879-1026}, abstract = {Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.}, }
@article {pmid37119017, year = {2023}, author = {Shin, NR and Okamura, Y and Kirsch, R and Pauchet, Y}, title = {Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12844}, pmid = {37119017}, issn = {1365-2583}, abstract = {With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.}, }
@article {pmid37116631, year = {2023}, author = {Garcillán-Barcia, MP and Redondo-Salvo, S and de la Cruz, F}, title = {Plasmid classifications.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102684}, doi = {10.1016/j.plasmid.2023.102684}, pmid = {37116631}, issn = {1095-9890}, abstract = {Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).}, }
@article {pmid37110299, year = {2023}, author = {Qi, Q and Kamruzzaman, M and Iredell, JR}, title = {A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040878}, pmid = {37110299}, issn = {2076-2607}, abstract = {Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.}, }
@article {pmid37110264, year = {2023}, author = {Vittorakis, E and Vică, ML and Zervaki, CO and Vittorakis, E and Maraki, S and Mavromanolaki, VE and Schürger, ME and Neculicioiu, VS and Papadomanolaki, E and Sinanis, T and Giannoulaki, G and Xydaki, E and Kastanakis, SG and Junie, LM}, title = {Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040841}, pmid = {37110264}, issn = {2076-2607}, abstract = {S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020-2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections.}, }
@article {pmid37110261, year = {2023}, author = {Karnachuk, OV and Beletsky, AV and Rakitin, AL and Ikkert, OP and Avakyan, MR and Zyusman, VS and Napilov, A and Mardanov, AV and Ravin, NV}, title = {Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040838}, pmid = {37110261}, issn = {2076-2607}, abstract = {Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.}, }
@article {pmid37107701, year = {2023}, author = {Wu, L and Fan, P and Zhou, J and Li, Y and Xu, Z and Lin, Y and Wang, Y and Song, J and Yao, H}, title = {Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/genes14040943}, pmid = {37107701}, issn = {2073-4425}, abstract = {Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.}, }
@article {pmid37104544, year = {2023}, author = {Brual, T and Effantin, G and Baltenneck, J and Attaiech, L and Grosbois, C and Royer, M and Cigna, J and Faure, D and Hugouvieux-Cotte-Pattat, N and Gueguen, E}, title = {A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria.}, journal = {PLoS genetics}, volume = {19}, number = {4}, pages = {e1010725}, doi = {10.1371/journal.pgen.1010725}, pmid = {37104544}, issn = {1553-7404}, abstract = {The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.}, }
@article {pmid37102089, year = {2023}, author = {Shao, M and Liu, L and Liu, B and Zheng, H and Meng, W and Liu, Y and Zhang, X and Ma, X and Sun, C and Luo, X and Li, F and Xing, B}, title = {Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus.}, journal = {ACS environmental Au}, volume = {3}, number = {2}, pages = {105-120}, pmid = {37102089}, issn = {2694-2518}, abstract = {Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.}, }
@article {pmid37099912, year = {2023}, author = {Sun, X and Kong, T and Huang, D and Chen, Z and Kolton, M and Yang, J and Huang, Y and Cao, Y and Gao, P and Yang, N and Li, B and Liu, H and Sun, W}, title = {Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots.}, journal = {Journal of hazardous materials}, volume = {454}, number = {}, pages = {131458}, doi = {10.1016/j.jhazmat.2023.131458}, pmid = {37099912}, issn = {1873-3336}, abstract = {Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.}, }
@article {pmid37095096, year = {2023}, author = {Ahmad, M and Prensky, H and Balestrieri, J and ElNaggar, S and Gomez-Simmonds, A and Uhlemann, AC and Traxler, B and Singh, A and Lopatkin, AJ}, title = {Tradeoff between lag time and growth rate drives the plasmid acquisition cost.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2343}, pmid = {37095096}, issn = {2041-1723}, mesh = {Plasmids ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.}, }
@article {pmid37062264, year = {2023}, author = {Jin, C and Cao, J and Zhang, K and Zhang, X and Cao, Z and Zou, W}, title = {Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil.}, journal = {Ecotoxicology and environmental safety}, volume = {256}, number = {}, pages = {114913}, doi = {10.1016/j.ecoenv.2023.114913}, pmid = {37062264}, issn = {1090-2414}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Molybdenum/pharmacology ; Genes, Bacterial ; Soil ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Plasmids ; }, abstract = {The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5-10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.}, }
@article {pmid37098416, year = {2023}, author = {Gong, H and Huang, X and Zhu, W and Chen, J and Huang, Y and Zhao, Z and Weng, J and Che, Y and Wang, J and Wang, X}, title = {Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104249}, doi = {10.1016/j.fm.2023.104249}, pmid = {37098416}, issn = {1095-9998}, abstract = {Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.}, }
@article {pmid37098287, year = {2023}, author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J}, title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.}, journal = {Water research}, volume = {237}, number = {}, pages = {119986}, doi = {10.1016/j.watres.2023.119986}, pmid = {37098287}, issn = {1879-2448}, abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.}, }
@article {pmid37097444, year = {2023}, author = {Bibi, S and Weis, K and Kaur, A and Bhandari, R and Goss, EM and Jones, JB and Potnis, N}, title = {A Brief Evaluation of Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen, Xanthomonas euvesicatoria pv. perforans.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-02-23-0077-SC}, pmid = {37097444}, issn = {0031-949X}, abstract = {Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple Xanthomonas euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility including both phage related genes and transposase. Among copper tolerant strains of Xanthomonas euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid borne resistance.}, }
@article {pmid37097343, year = {2023}, author = {Francis, A and Steel, M}, title = {Labellable Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {85}, number = {6}, pages = {46}, pmid = {37097343}, issn = {1522-9602}, abstract = {Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations) and non-tree-like 'reticulate' processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper, we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of 'expanding covers' of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.}, }
@article {pmid36778249, year = {2023}, author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE}, title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778249}, support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; }, abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species and recently demonstrated to occur in rare instances from one human generation to the next. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeatedmeasures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous 2 numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.}, }
@article {pmid37094448, year = {2023}, author = {Zhu, S and Yang, B and Jia, Y and Yu, F and Wang, Z and Liu, Y}, title = {Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131428}, doi = {10.1016/j.jhazmat.2023.131428}, pmid = {37094448}, issn = {1873-3336}, abstract = {The propagation of antimicrobial resistance (AMR) is constantly paralyzing our healthcare systems. In addition to the pressure of antibiotic selection, the roles of non-antibiotic compounds in disseminating antibiotic resistance genes (ARGs) are a matter of great concerns. This study aimed to explore the impact of different disinfectants on the horizontal transfer of ARGs and their underlying mechanisms. First, the effects of different kinds of disinfectants on the conjugative transfer of RP4-7 plasmid were evaluated. Results showed that quaternary ammonium salt, organic halogen, alcohol and guanidine disinfectants significantly facilitated the conjugative transfer. Conversely, heavy-metals, peroxides and phenols otherwise displayed an inhibitory effect. Furthermore, we deciphered the mechanism by which guanidine disinfectants promoted conjugation, which includes increased cell membrane permeability, over-production of ROS, enhanced SOS response, and altered expression of conjugative transfer-related genes. More critically, we also revealed that guanidine disinfectants promoted bacterial energy metabolism by enhancing the activity of electron transport chain (ETC) and proton force motive (PMF), thus promoting ATP synthesis and flagellum motility. Overall, our findings reveal the promotive effects of disinfectants on the transmission of ARGs and highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.}, }
@article {pmid37093956, year = {2023}, author = {Baumdicker, F and Kupczok, A}, title = {Tackling the pangenome dilemma requires the concerted analysis of multiple population genetic processes.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad067}, pmid = {37093956}, issn = {1759-6653}, abstract = {The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory genes of low and intermediate frequencies. Different population genetics processes contribute to the shape of these pangenomes, namely selection and fitness-independent-processes such as gene transfer, gene loss, and migration. However, their relative importance is unknown and highly debated. Here we argue that the debate around prokaryotic pangenomes arose due to the imprecise application of population genetics models. Most importantly, two different processes of horizontal gene transfer act on prokaryotic populations, which are frequently confused, despite their fundamentally different behavior. Genes acquired from distantly related organisms (termed here acquiring gene transfer, AGT) is most comparable to mutation in nucleotide sequences. In contrast, gene gain within the population (termed here spreading gene transfer, SGT) has an effect on gene frequencies that is identical to the effect of positive selection on single genes. We thus show that selection and fitness-independent population genetic processes affecting pangenomes are indistinguishable at the level of single gene dynamics. Nevertheless, population genetics processes are fundamentally different when considering the joint distribution of all accessory genes across individuals of a population. We propose that, to understand to which degree the different processes shaped pangenome diversity, the development of comprehensive models and simulation tools is mandatory. Furthermore, we need to identify summary statistics and measurable features that can distinguish between the processes, where considering the joint distribution of accessory genes across individuals of a population will be particularly relevant.}, }
@article {pmid37092000, year = {2023}, author = {Han, Z and Xu, S and Gao, T}, title = {Unexpected complex horizontal gene transfer in teleost fish.}, journal = {Current zoology}, volume = {69}, number = {2}, pages = {222-223}, pmid = {37092000}, issn = {1674-5507}, }
@article {pmid37091576, year = {2022}, author = {Varner, PM and Allemann, MN and Michener, JK and Gunsch, CK}, title = {The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation.}, journal = {Environmental technology &amp; innovation}, volume = {28}, number = {}, pages = {}, pmid = {37091576}, issn = {2352-1864}, abstract = {Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.}, }
@article {pmid37087920, year = {2023}, author = {Zheng, CW and Luo, YH and Long, X and Gu, H and Cheng, J and Zhang, L and Lai, YJS and Rittmann, BE}, title = {The structure of biodegradable surfactants shaped the microbial community, antimicrobial resistance, and potential for horizontal gene transfer.}, journal = {Water research}, volume = {236}, number = {}, pages = {119944}, doi = {10.1016/j.watres.2023.119944}, pmid = {37087920}, issn = {1879-2448}, abstract = {While most household surfactants are biodegradable in aerobic conditions, their biodegradability may obscure their environmental risks. The presence of surfactants in a biological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in the biomass. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation ARG. Cationic hexadecyltrimethyl-ammonium (CTAB), anionic sodium dodecyl sulfate (SDS), and zwitterionic 3-(decyldimethylammonio)-propanesulfonate inner salt (DAPS) were used to represent the three classes of surfactants in domestic household clean-up products. This study focused on the removal of these surfactants by the O2-based Membrane Biofilm Reactor (O2-MBfR) for hotspot scenarios (∼1 mM) and how the three classes of surfactants affected the microbial community's structure and ARG. Given sufficient O2 delivery, the MBfR provided at least 98% surfactant removal. The presence and biodegradation for each surfactant uniquely shaped the biofilms' microbial communities and the presence of ARG. CTAB had by far the strongest impact and the higher ARG abundance. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also led to more functional genes relevant to the Type-IV secretion system and protection against oxidative stress, which also could encourage horizontal gene transfer. Our findings highlight that the biodegradation of quaternary ammonium surfactants, while beneficial, can pose public health concerns from its ability to promote the proliferation of ARG.}, }
@article {pmid37083586, year = {2023}, author = {Maphosa, S and Moleleki, LN and Motaung, TE}, title = {Bacterial secretion system functions: evidence of interactions and downstream implications.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {4}, pages = {}, doi = {10.1099/mic.0.001326}, pmid = {37083586}, issn = {1465-2080}, abstract = {Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.}, }
@article {pmid37083356, year = {2023}, author = {Wu, J and Zhou, JH and Liu, DF and Wu, J and He, RL and Cheng, ZH and Li, HH and Li, WW}, title = {Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c09491}, pmid = {37083356}, issn = {1520-5851}, abstract = {Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.}, }
@article {pmid37079454, year = {2023}, author = {Gulliver, EL and Adams, V and Marcelino, VR and Gould, J and Rutten, EL and Powell, DR and Young, RB and D'Adamo, GL and Hemphill, J and Solari, SM and Revitt-Mills, SA and Munn, S and Jirapanjawat, T and Greening, C and Boer, JC and Flanagan, KL and Kaldhusdal, M and Plebanski, M and Gibney, KB and Moore, RJ and Rood, JI and Forster, SC}, title = {Extensive genome analysis identifies novel plasmid families in Clostridium perfringens.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000995}, pmid = {37079454}, issn = {2057-5858}, abstract = {Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfringens strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464 C. perfringens genomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported from Clostridium botulinum. We sequenced and archived 102 new C. perfringens genomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11 C. perfringens strains representing all toxinotypes (A-G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across the C. perfringens isolates. Plasmids and plasmid diversity play an essential role in C. perfringens pathogenicity and broader biology. We have expanded the C. perfringens genome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novel C. perfringens plasmids whilst providing a comprehensive understanding of species diversity.}, }
@article {pmid37072776, year = {2023}, author = {Hernández, M and Roy, S and Keevil, CW and Dumont, MG}, title = {Identification of diverse antibiotic resistant bacteria in agricultural soil with H2[18]O stable isotope probing combined with high-throughput sequencing.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {34}, pmid = {37072776}, issn = {2524-6372}, abstract = {BACKGROUND: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in [18]O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.<br><br>RESULTS: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with [18]O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.<br><br>CONCLUSIONS: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.}, }
@article {pmid37072330, year = {2023}, author = {Fokina, AS and Karyagina, AS and Rusinov, IS and Moshensky, DM and Spirin, SA and Alexeevski, AV}, title = {Evolution of Restriction-Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {2}, pages = {253-261}, doi = {10.1134/S0006297923020086}, pmid = {37072330}, issn = {1608-3040}, abstract = {Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.}, }
@article {pmid37070987, year = {2023}, author = {Dai, X and Sun, J and Zhu, B and Lv, M and Chen, L and Chen, L and Wang, X and Huang, J and Wang, L}, title = {Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0487522}, doi = {10.1128/spectrum.04875-22}, pmid = {37070987}, issn = {2165-0497}, abstract = {The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.}, }
@article {pmid37070984, year = {2023}, author = {Wu, HY and Wei, ZL and Shi, DY and Li, HB and Li, XM and Yang, D and Zhou, SQ and Peng, XX and Yang, ZW and Yin, J and Chen, TJ and Li, JW and Jin, M}, title = {Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0482022}, doi = {10.1128/spectrum.04820-22}, pmid = {37070984}, issn = {2165-0497}, abstract = {The assessment of factors that can promote the transmission of antibiotic resistance genes (ARGs) across bacteria in the gastrointestinal tract is in great demand to understand the occurrence of infections related to antibiotic-resistant bacteria (ARB) in humans. However, whether acid-resistant enteric bacteria can promote ARG transmission in gastric fluid under high-pH conditions remains unknown. This study assessed the effects of simulated gastric fluid (SGF) at different pH levels on the RP4 plasmid-mediated conjugative transfer of ARGs. Moreover, transcriptomic analysis, measurement of reactive oxygen species (ROS) levels, assessment of cell membrane permeability, and real-time quantitative assessment of the expression of key genes were performed to identify the underlying mechanisms. The frequency of conjugative transfer was the highest in SGF at pH 4.5. Antidepressant consumption and certain dietary factors further negatively impacted this situation, with 5.66-fold and 4.26-fold increases in the conjugative transfer frequency being noted upon the addition of sertraline and 10% glucose, respectively, compared with that in the control group without any additives. The induction of ROS generation, the activation of cellular antioxidant systems, increases in cell membrane permeability, and the promotion of adhesive pilus formation were factors potentially contributing to the increased transfer frequency. These findings indicate that conjugative transfer could be enhanced under certain circumstances in SGF at elevated pH levels, thereby facilitating ARG transmission in the gastrointestinal tract. IMPORTANCE The low pH of gastric acid kills unwanted microorganisms, in turn affecting their inhabitation in the intestine. Hence, studies on the factors that influence antibiotic resistance gene (ARG) propagation in the gastrointestinal tract and on the underlying mechanisms are limited. In this study, we constructed a conjugative transfer model in the presence of simulated gastric fluid (SGF) and found that SGF could promote the dissemination of ARGs under high-pH conditions. Furthermore, antidepressant consumption and certain dietary factors could negatively impact this situation. Transcriptomic analysis and a reactive oxygen species assay revealed the overproduction of reactive oxygen species as a potential mechanism by which SGF could promote conjugative transfer. This finding can help provide a comprehensive understanding of the bloom of antibiotic-resistant bacteria in the body and create awareness regarding the risk of ARG transmission due to certain diseases or an improper diet and the subsequent decrease in gastric acid levels.}, }
@article {pmid37065212, year = {2023}, author = {Wang, H and Cheng, H and Huang, B and Hu, X and Chen, Y and Zheng, L and Yang, L and Deng, J and Wang, Q}, title = {Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1116172}, pmid = {37065212}, issn = {2235-2988}, mesh = {Humans ; Child ; Azithromycin/pharmacology ; *Salmonella enterica/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Salmonella Infections/microbiology ; Salmonella/genetics ; Plasmids/genetics ; Microbial Sensitivity Tests ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial ; }, abstract = {INTRODUCTION: Samonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied.<br><br>METHODS: This study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children's Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools.<br><br>RESULTS: In total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 &#xb5;g/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters.<br><br>CONCLUSION: mphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.}, }
@article {pmid37061654, year = {2023}, author = {Elbehery, AHA and Beason, E and Siam, R}, title = {Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {195}, pmid = {37061654}, issn = {1432-072X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Indian Ocean ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.}, }
@article {pmid37061183, year = {2023}, author = {Gilbert, C and Maumus, F}, title = {Sidestepping Darwin: horizontal gene transfer from plants to insects.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101035}, doi = {10.1016/j.cois.2023.101035}, pmid = {37061183}, issn = {2214-5753}, abstract = {Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (MEAM1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.}, }
@article {pmid37055994, year = {2023}, author = {Li, B and Jeon, MK and Li, X and Yan, T}, title = {Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130590}, doi = {10.1016/j.jhazmat.2022.130590}, pmid = {37055994}, issn = {1873-3336}, mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/analysis ; Genes, Bacterial ; Salinity ; Drug Resistance, Microbial/genetics ; }, abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, blaTEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and blaTEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and blaTEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.}, }
@article {pmid37054673, year = {2023}, author = {Moura de Sousa, J and Lourenço, M and Gordo, I}, title = {Horizontal gene transfer among host-associated microbes.}, journal = {Cell host &amp; microbe}, volume = {31}, number = {4}, pages = {513-527}, doi = {10.1016/j.chom.2023.03.017}, pmid = {37054673}, issn = {1934-6069}, mesh = {*Gene Transfer, Horizontal ; Bacteria/genetics ; Biological Evolution ; *Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.}, }
@article {pmid37052605, year = {2023}, author = {Calder, A and Snyder, LAS}, title = {Diversity of the type VI secretion systems in the Neisseria spp.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000986}, pmid = {37052605}, issn = {2057-5858}, mesh = {Humans ; *Type VI Secretion Systems/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.}, }
@article {pmid37052502, year = {2023}, author = {Tang, B and Yang, A and Liu, P and Wang, Z and Jian, Z and Chen, X and Yan, Q and Liang, X and Liu, W}, title = {Outer Membrane Vesicles Transmitting blaNDM-1 Mediate the Emergence of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0144422}, doi = {10.1128/aac.01444-22}, pmid = {37052502}, issn = {1098-6596}, abstract = {Dissemination of hypervirulent and carbapenem-resistant Klebsiella pneumoniae (CRKP) has been reported worldwide, posing a serious threat to antimicrobial therapy and public health. Outer membrane vesicles (OMVs) act as vectors for the horizontal transfer of virulence and resistance genes. However, K. pneumoniae OMVs that transfer carbapenem resistance genes into hypervirulent K. pneumoniae (hvKP) have been insufficiently investigated. Therefore, this study investigates the transmission of the blaNDM-1 gene encoding resistance via OMVs released from CRKP and the potential mechanism responsible for the carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) emergence. OMVs were isolated via ultracentrifugation from CRKP with or without meropenem selective pressure. OMVs were then used to transform classical K. pneumoniae (ckp) ATCC 10031, extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae ATCC 700603, and hvKP NTUH-K2044. Our results showed that meropenem treatment resulted in changes in the number and diameter of OMVs secreted by CRKP. OMVs derived from CRKP mediated the transfer of blaNDM-1 to ckp and hvKP, thereby increasing the carbapenem MIC of transformants. Further experiments confirmed that NTUH-K2044 transformants exhibited hypervirulence. Our study demonstrates, for the first time, that OMVs derived from CRKP can carry blaNDM-1 and deliver resistance genes to other K. pneumoniae strains, even hvKP. The transfer of carbapenem genes into hypervirulent strains may promote the emergence and dissemination of CR-hvKP. This study elucidates a new mechanism underlying the formation of CR-hvKP.}, }
@article {pmid37047476, year = {2023}, author = {Msaddak, A and Mars, M and Quiñones, MA and Lucas, MM and Pueyo, JJ}, title = {Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047476}, issn = {1422-0067}, mesh = {*Fabaceae/genetics/microbiology ; *Lupinus/genetics/microbiology ; Root Nodules, Plant/microbiology ; Phylogeny ; Gene Transfer, Horizontal ; Health Promotion ; DNA, Bacterial/genetics ; Vegetables/genetics ; *Rhizobium/genetics ; *Bradyrhizobium/genetics ; Symbiosis/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin's adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin's adaptability to marginal soils and climates.}, }
@article {pmid37043515, year = {2023}, author = {Novelo, M and Dutra, HL and Metz, HC and Jones, MJ and Sigle, LT and Frentiu, FD and Allen, SL and Chenoweth, SF and McGraw, EA}, title = {Dengue and chikungunya virus loads in the mosquito Aedes aegypti are determined by distinct genetic architectures.}, journal = {PLoS pathogens}, volume = {19}, number = {4}, pages = {e1011307}, doi = {10.1371/journal.ppat.1011307}, pmid = {37043515}, issn = {1553-7374}, abstract = {Aedes aegypti is the primary vector of the arboviruses dengue (DENV) and chikungunya (CHIKV). These viruses exhibit key differences in their vector interactions, the latter moving more quicky through the mosquito and triggering fewer standard antiviral pathways. As the global footprint of CHIKV continues to expand, we seek to better understand the mosquito's natural response to CHIKV-both to compare it to DENV:vector coevolutionary history and to identify potential targets in the mosquito for genetic modification. We used a modified full-sibling design to estimate the contribution of mosquito genetic variation to viral loads of both DENV and CHIKV. Heritabilities were significant, but higher for DENV (40%) than CHIKV (18%). Interestingly, there was no genetic correlation between DENV and CHIKV loads between siblings. These data suggest Ae. aegypti mosquitoes respond to the two viruses using distinct genetic mechanisms. We also examined genome-wide patterns of gene expression between High and Low CHIKV families representing the phenotypic extremes of viral load. Using RNAseq, we identified only two loci that consistently differentiated High and Low families: a long non-coding RNA that has been identified in mosquito screens post-infection and a distant member of a family of Salivary Gland Specific (SGS) genes. Interestingly, the latter gene is also associated with horizontal gene transfer between mosquitoes and the endosymbiotic bacterium Wolbachia. This work is the first to link the SGS gene to a mosquito phenotype. Understanding the molecular details of how this gene contributes to viral control in mosquitoes may, therefore, also shed light on its role in Wolbachia.}, }
@article {pmid37037946, year = {2023}, author = {Yang, P and Zhu, X and Ning, K}, title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {391}, pmid = {37037946}, issn = {2399-3642}, mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; }, abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.}, }
@article {pmid37037312, year = {2023}, author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M}, title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115866}, doi = {10.1016/j.envres.2023.115866}, pmid = {37037312}, issn = {1096-0953}, abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.}, }
@article {pmid37036996, year = {2023}, author = {Kalluraya, CA and Weitzel, AJ and Tsu, BV and Daugherty, MD}, title = {Bacterial origin of a key innovation in the evolution of the vertebrate eye.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2214815120}, doi = {10.1073/pnas.2214815120}, pmid = {37036996}, issn = {1091-6490}, support = {R35 GM133633/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Genes, Bacterial ; *Vertebrates/metabolism ; Eye Proteins/genetics ; Retinoids/metabolism ; Invertebrates/genetics ; Vision, Ocular/genetics ; }, abstract = {The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.}, }
@article {pmid37036995, year = {2023}, author = {Verster, KI and Cinege, G and Lipinszki, Z and Magyar, LB and Kurucz, &#xc9; and Tarnopol, RL and Ábrahám, E and Darula, Z and Karageorgi, M and Tamsil, JA and Akalu, SM and Andó, I and Whiteman, NK}, title = {Evolution of insect innate immunity through domestication of bacterial toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2218334120}, doi = {10.1073/pnas.2218334120}, pmid = {37036995}, issn = {1091-6490}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Domestication ; *Bacterial Toxins/metabolism ; Drosophila/genetics/metabolism ; Gene Transfer, Horizontal ; *Wasps/metabolism ; Immunity, Innate/genetics ; }, abstract = {Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.}, }
@article {pmid37036347, year = {2023}, author = {Lewis, AM and Willard, DJ and H Manesh, MJ and Sivabalasarma, S and Albers, SV and Kelly, RM}, title = {Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin.}, journal = {mBio}, volume = {}, number = {}, pages = {e0005323}, doi = {10.1128/mbio.00053-23}, pmid = {37036347}, issn = {2150-7511}, abstract = {A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.}, }
@article {pmid37036197, year = {2023}, author = {Mota-Bravo, L and Camps, M and Muñoz-Gutiérrez, I and Tatarenkov, A and Warner, C and Suarez, I and Cortés-Cortés, G}, title = {Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/64523}, pmid = {37036197}, issn = {1940-087X}, mesh = {*Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Plasmids/genetics ; Anti-Bacterial Agents ; }, abstract = {Conjugation represents one of the main mechanisms facilitating horizontal gene transfer in Gram-negative bacteria. This work describes methods for the study of the mobilization of naturally occurring conjugative plasmids, using two naturally-occurring plasmids as an example. These protocols rely on the differential presence of selectable markers in donor, recipient, and conjugative plasmid. Specifically, the methods described include 1) the identification of natural conjugative plasmids, 2) the quantification of conjugation rates in solid culture, and 3) the diagnostic detection of the antibiotic resistance genes and plasmid replicon types in transconjugant recipients by polymerase chain reaction (PCR). The protocols described here have been developed in the context of studying the evolutionary ecology of horizontal gene transfer, to screen for the presence of conjugative plasmids carrying antibiotic-resistance genes in bacteria found in the environment. The efficient transfer of conjugative plasmids observed in these experiments in culture highlights the biological relevance of conjugation as a mechanism promoting horizontal gene transfer in general and the spread of antibiotic resistance in particular.}, }
@article {pmid37033775, year = {2023}, author = {Alborzi, A and Hosseini, M and Bahrami, S and Ghorbanpoor, M and Tabandeh, M}, title = {Evaluation of hematological changes, oxidant/antioxidant status and immuno-logical responses in sheep and goats naturally infected with Linguatula serrata.}, journal = {Veterinary research forum : an international quarterly journal}, volume = {14}, number = {3}, pages = {161-167}, pmid = {37033775}, issn = {2008-8140}, abstract = {Linguatula serrata is a worldwide zoonotic food-borne parasite. The parasite is responsible for linguatulosis and poses a concern to human and animal health in endemic regions. This study investigated the hematological changes, oxidant/antioxidant status and immunological responses in goats and sheep naturally infected with L. serrata. Hematological changes, antioxidant enzymes and malondialdehyde (MDA) levels were measured. The level of inter-leukin-2 (IL-2), IL-4, IL-5, IL-10, and tumor necrosis factor alpha (TNF-α) mRNA expression was investigated in lymph nodes. According to the hemogram results, eosinophils were significantly increased in the infected goats and sheep, and Horizontal Gene Transfer (HGT), hematocrit (HCT), and mean corpuscular hemoglobin concentration (MCHC) were significantly decreased. The levels of MDA and the activity of glutathione peroxidase (GPx) were significantly higher in infected animals than in non-infected animals. However, the activity of superoxide dismutase (SOD) and catalase (CAT) was significantly lower in infected animals than in non-infected animals. A comparison of the cytokine mRNA expression in lymph nodes from infected and non-infected animals showed higher cytokine expression in the infected animals. Infection with L. serrata caused microcytic hypochromic and normocytic hypochromic anemia in goats and sheep. The inconsistent results of immunological changes were found in infected goats and sheep. In both animals, oxidative stress occurred and led to an increase in lipid peroxidation. L. serrata created a cytokine microenvironment biased towards the type 2 immune responses.}, }
@article {pmid37030228, year = {2023}, author = {Chen, J and Xia, H and Huang, K and Li, J and Xie, J}, title = {Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131315}, doi = {10.1016/j.jhazmat.2023.131315}, pmid = {37030228}, issn = {1873-3336}, abstract = {The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.}, }
@article {pmid37023995, year = {2023}, author = {Botts, RT and Page, DM and Bravo, JA and Brown, ML and Castilleja, CC and Guzman, VL and Hall, S and Henderson, JD and Kenney, SM and Lensink, ME and Paternoster, MV and Pyle, SL and Ustick, L and Walters-Laird, CJ and Top, EM and Cummings, DE}, title = {Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases.}, journal = {Plasmid}, volume = {126}, number = {}, pages = {102682}, doi = {10.1016/j.plasmid.2023.102682}, pmid = {37023995}, issn = {1095-9890}, abstract = {While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10[-3] transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.}, }
@article {pmid37023132, year = {2023}, author = {Urquhart, AS and Vogan, AA and Gardiner, DM and Idnurm, A}, title = {Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2214521120}, pmid = {37023132}, issn = {1091-6490}, mesh = {*DNA Transposable Elements/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Recombinases/genetics ; Tyrosine/genetics ; Evolution, Molecular ; }, abstract = {Transposable elements in eukaryotic organisms have historically been considered "selfish," at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are, in some cases, predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA "Captain" tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfers of Starships, implying that they jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defense, thereby having implications on the evolutionary stability of such elements.}, }
@article {pmid37023131, year = {2023}, author = {Benz, F and Hall, AR}, title = {Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2212147120}, pmid = {37023131}, issn = {1091-6490}, mesh = {Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Models, Theoretical ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance encoded on plasmids is a pressing global health problem. Predicting which plasmids spread in the long term remains very challenging, even though some key parameters influencing plasmid stability have been identified, such as plasmid growth costs and horizontal transfer rates. Here, we show these parameters evolve in a strain-specific way among clinical plasmids and bacteria, and this occurs rapidly enough to alter the relative likelihoods of different bacterium-plasmid combinations spreading. We used experiments with Escherichia coli and antibiotic-resistance plasmids isolated from patients, paired with a mathematical model, to track long-term plasmid stability (beyond antibiotic exposure). Explaining variable stability across six bacterium-plasmid combinations required accounting for evolutionary changes in plasmid stability traits, whereas initial variation of these parameters was a relatively poor predictor of long-term outcomes. Evolutionary trajectories were specific to particular bacterium-plasmid combinations, as evidenced by genome sequencing and genetic manipulation. This revealed epistatic (here, strain-dependent) effects of key genetic changes affecting horizontal plasmid transfer. Several genetic changes involved mobile elements and pathogenicity islands. Rapid strain-specific evolution can thus outweigh ancestral phenotypes as a predictor of plasmid stability. Accounting for strain-specific plasmid evolution in natural populations could improve our ability to anticipate and manage successful bacterium-plasmid combinations.}, }
@article {pmid37022443, year = {2023}, author = {Stentz, R and Cheema, J and Philo, M and Carding, SR}, title = {A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {37022443}, issn = {1432-1432}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.}, }
@article {pmid37022212, year = {2023}, author = {Tóth, AG and Judge, MF and Nagy, S&#xc1; and Papp, M and Solymosi, N}, title = {A survey on antimicrobial resistance genes of frequently used probiotic bacteria, 1901 to 2022.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {14}, pages = {}, doi = {10.2807/1560-7917.ES.2023.28.14.2200272}, pmid = {37022212}, issn = {1560-7917}, mesh = {*Gram-Positive Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Probiotics ; Bifidobacterium animalis/drug effects/genetics ; Lactobacillales/drug effects/genetics ; Genome, Bacterial ; *Genes, Bacterial ; }, abstract = {BackgroundAntimicrobial resistance (AMR) is caused by AMR determinants, mainly genes (ARGs) in the bacterial genome. Bacteriophages, integrative mobile genetic elements (iMGEs) or plasmids can allow ARGs to be exchanged among bacteria by horizontal gene transfer (HGT). Bacteria, including bacteria with ARGs, can be found in food. Thus, it is conceivable that in the gastrointestinal tract, bacteria from the gut flora could take up ARGs from food.AimThe study objective was to gain insight into the ARG set carried by commonly used probiotic bacteria that may enter the human body with non-fermented foods, fermented foods, or probiotic dietary supplements (FFPs) and to assess ARG mobility.MethodsNext generation sequencing whole genome data from 579 isolates of 12 commonly employed probiotic bacterial species were collected from a public repository. Using bioinformatical tools, ARGs were analysed and linkage with mobile genetic elements assessed.ResultsResistance genes were found in eight bacterial species. The ratios of ARG positive/negative samples per species were: Bifidobacterium animalis (65/0), Lactiplantibacillus plantarum (18/194), Lactobacillus delbrueckii (1/40), Lactobacillus helveticus (2/64), Lactococcus lactis (74/5), Leucoconstoc mesenteroides (4/8), Levilactobacillus brevis (1/46), Streptococcus thermophilus (4/19). In 66% (112/169) of the ARG-positive samples, at least one ARG could be linked to plasmids or iMGEs. No bacteriophage-linked ARGs were found.ConclusionThe finding of potentially mobile ARGs in probiotic strains for human consumption raises awareness of a possibility of ARG HGT in the gastrointestinal tract. In addition to existing recommendations, screening FFP bacterial strains for ARG content and mobility characteristics might be considered.}, }
@article {pmid37020720, year = {2023}, author = {Liu, Q and Yang, LL and Xin, YH}, title = {Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115168}, pmid = {37020720}, issn = {1664-302X}, abstract = {The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.}, }
@article {pmid37019751, year = {2023}, author = {Dart, E and Ahlgren, NA}, title = {New tRNA-targeting transposons that hijack phage and vesicles.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2023.03.004}, pmid = {37019751}, issn = {0168-9525}, abstract = {Genomic islands are hotspots for horizontal gene transfer (HGT) in bacteria, but, for Prochlorococcus, an abundant marine cyanobacterium, how these islands form has puzzled scientists. With the discovery of tycheposons, a new family of transposons, Hackl et al. provide evidence for elegant new mechanisms of gene rearrangement and transfer among Prochlorococcus and bacteria more broadly.}, }
@article {pmid37018030, year = {2023}, author = {Jerez, SA and Plaza, N and Bravo, V and Urrutia, IM and Blondel, CJ}, title = {Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000973}, pmid = {37018030}, issn = {2057-5858}, mesh = {Humans ; Type III Secretion Systems ; *Vibrionaceae ; Phylogeny ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.}, }
@article {pmid37017542, year = {2023}, author = {Joglekar, P and Ferrell, BD and Jarvis, T and Haramoto, K and Place, N and Dums, JT and Polson, SW and Wommack, KE and Fuhrmann, JJ}, title = {Spontaneously Produced Lysogenic Phages Are an Important Component of the Soybean Bradyrhizobium Mobilome.}, journal = {mBio}, volume = {}, number = {}, pages = {e0029523}, doi = {10.1128/mbio.00295-23}, pmid = {37017542}, issn = {2150-7511}, abstract = {The ability of Bradyrhizobium spp. to nodulate and fix atmospheric nitrogen in soybean root nodules is critical to meeting humanity's nutritional needs. The intricacies of soybean bradyrhizobia-plant interactions have been studied extensively; however, bradyrhizobial ecology as influenced by phages has received somewhat less attention, even though these interactions may significantly impact soybean yield. In batch culture, four soybean bradyrhizobia strains, Bradyrhizobium japonicum S06B (S06B-Bj), B. japonicum S10J (S10J-Bj), Bradyrhizobium diazoefficiens USDA 122 (USDA 122-Bd), and Bradyrhizobium elkanii USDA 76[T] (USDA 76-Be), spontaneously (without apparent exogenous chemical or physical induction) produced tailed phages throughout the growth cycle; for three strains, phage concentrations exceeded cell numbers by ~3-fold after 48 h of incubation. Phage terminase large-subunit protein phylogeny revealed possible differences in phage packaging and replication mechanisms. Bioinformatic analyses predicted multiple prophage regions within each soybean bradyrhizobia genome, preventing accurate identification of spontaneously produced prophage (SPP) genomes. A DNA sequencing and mapping approach accurately delineated the boundaries of four SPP genomes within three of the soybean bradyrhizobia chromosomes and suggested that the SPPs were capable of transduction. In addition to the phages, S06B-Bj and USDA 76-Be contained three to four times more insertion sequences (IS) and large, conjugable, broad host range plasmids, both of which are known drivers of horizontal gene transfer (HGT) in soybean bradyrhizobia. These factors indicate that SPP along with IS and plasmids participate in HGT, drive bradyrhizobia evolution, and play an outsized role in bradyrhizobia ecology. IMPORTANCE Previous studies have shown that IS and plasmids mediate HGT of symbiotic nodulation (nod) genes in soybean bradyrhizobia; however, these events require close cell-to-cell contact, which could be limited in soil environments. Bacteriophage-assisted gene transduction through spontaneously produced prophages provides a stable means of HGT not limited by the constraints of proximal cell-to-cell contact. These phage-mediated HGT events may shape soybean bradyrhizobia population ecology, with concomitant impacts on soybean agriculture.}, }
@article {pmid37017538, year = {2023}, author = {Jonsdottir, I and Given, C and Penttinen, R and Jalasvuori, M}, title = {Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0010723}, doi = {10.1128/msphere.00107-23}, pmid = {37017538}, issn = {2379-5042}, abstract = {Conjugative plasmids can confer antimicrobial resistance (AMR) to their host bacterium. The plasmids disperse even between distantly related host species, rescuing the host from otherwise detrimental effects of antibiotics. Little is known about the role of these plasmids in the spread of AMR during antibiotic treatment. One unstudied question is whether the past evolutionary history of a plasmid in a particular species creates host specificity in its rescue potential or if interspecific coevolution can improve interspecific rescues. To study this, we coevolved the plasmid RP4 under three different host settings; solely Escherichia coli or Klebsiella pneumoniae, or alternating between both of them. The ability of evolved plasmids in bacterial biofilm to rescue susceptible planktonic host bacteria of either the same or different species during beta-lactam treatment was tested. The interspecific coevolution seemed to decrease rescue potential for the RP4 plasmid, while the K. pneumoniae evolved plasmid became more host specific. Large deletion in the region encoding the mating pair formation (Tra2) apparatus was detected in the plasmids evolved with K. pneumoniae. This adaptation resulted in the exapted evolution of resistance against a plasmid-dependent bacteriophage PRD1. Further, previous studies have suggested that mutations in this region completely abolish the plasmid's ability to conjugate; however, our study shows it is not essential for conjugation but rather affects the host-specific conjugation efficiency. Overall, the results suggest that previous evolutionary history can result in the separation of host-specific plasmid lineages that may be further amplified by unselected exaptations such as phage resistance. IMPORTANCE Antimicrobial resistance (AMR) is a major global public health threat which can rapidly spread in microbial communities via conjugative plasmids. Here, we advance with evolutionary rescue via conjugation in a more natural setting, namely, biofilm, and incorporate a broad-host range plasmid RP4 to test whether intra- and interspecific host histories affect its transfer potential. Escherichia coli and Klebsiella pneumoniae hosts were seen to elicit different evolutionary influences on the RP4 plasmid, leading to clear differences in the rescue potential and underlining the significant role of the plasmid-host interactions in the spread of AMR. We also contradicted previous reports that established certain conjugal transfer genes of RP4 as essential. This work enhances the understanding of how plasmid host range evolve in different host settings and further, the potential effects it may have on the horizontal spread of AMR in complex environments such as biofilms.}, }
@article {pmid37014461, year = {2023}, author = {Talat, A and Miranda, C and Poeta, P and Khan, AU}, title = {Farm to table: colistin resistance hitchhiking through food.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {167}, pmid = {37014461}, issn = {1432-072X}, mesh = {Animals ; Humans ; *Colistin/pharmacology ; Farms ; Chickens/microbiology ; Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Poultry/microbiology ; *Escherichia coli Proteins/genetics ; Plasmids ; Microbial Sensitivity Tests ; }, abstract = {Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.}, }
@article {pmid37009500, year = {2023}, author = {Nodari, CS and Opazo-Capurro, A and Castillo-Ramirez, S and Mattioni Marchetti, V}, title = {Editorial: Mobile genetic elements as dissemination drivers of multidrug-resistant Gram-negative bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180510}, pmid = {37009500}, issn = {2235-2988}, mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Gram-Negative Bacteria/genetics ; Interspersed Repetitive Sequences ; }, }
@article {pmid37007505, year = {2023}, author = {Apari, P and Földvári, G}, title = {Domestication and microbiome succession may drive pathogen spillover.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1102337}, pmid = {37007505}, issn = {1664-302X}, abstract = {Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.}, }
@article {pmid37004306, year = {2023}, author = {Deng, X and Yuan, J and Chen, L and Chen, H and Wei, C and Nielsen, PH and Wuertz, S and Qiu, G}, title = {CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter.}, journal = {Water research}, volume = {235}, number = {}, pages = {119906}, doi = {10.1016/j.watres.2023.119906}, pmid = {37004306}, issn = {1879-2448}, mesh = {Prophages/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; Phylogeny ; Wastewater ; *Betaproteobacteria ; }, abstract = {Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.}, }
@article {pmid37002975, year = {2023}, author = {Stockdale, SR and Hill, C}, title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102307}, doi = {10.1016/j.mib.2023.102307}, pmid = {37002975}, issn = {1879-0364}, abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.}, }
@article {pmid37001724, year = {2023}, author = {Boiten, KE and Kuijper, EJ and Schuele, L and van Prehn, J and Bode, LGM and Maat, I and van Asten, SAV and Notermans, DW and Rossen, JWA and Veloo, ACM}, title = {Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands.}, journal = {Anaerobe}, volume = {81}, number = {}, pages = {102722}, doi = {10.1016/j.anaerobe.2023.102722}, pmid = {37001724}, issn = {1095-8274}, abstract = {OBJECTIVES: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization.<br><br>METHODS: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs).<br><br>RESULTS: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance.<br><br>CONCLUSIONS: Novel CTns, Tns, and plasmids were encountered in the five MDR B.&#xa0;fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.}, }
@article {pmid36996986, year = {2023}, author = {Cheng, Y and Wang, X and Zhao, L and Zhang, X and Kong, Q and Li, H and You, X and Li, Y}, title = {Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than pyrochar in an agricultural soil.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163088}, doi = {10.1016/j.scitotenv.2023.163088}, pmid = {36996986}, issn = {1879-1026}, abstract = {Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.}, }
@article {pmid36996977, year = {2023}, author = {Zhang, C and Wang, C and Zhao, X and Hakizimana, I}, title = {Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction.}, journal = {The Science of the total environment}, volume = {878}, number = {}, pages = {163142}, doi = {10.1016/j.scitotenv.2023.163142}, pmid = {36996977}, issn = {1879-1026}, abstract = {The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.}, }
@article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0466722}, doi = {10.1128/spectrum.04667-22}, pmid = {36995244}, issn = {2165-0497}, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, }
@article {pmid36995224, year = {2023}, author = {Piscon, B and Pia Esposito, E and Fichtman, B and Samburski, G and Efremushkin, L and Amselem, S and Harel, A and Rahav, G and Zarrilli, R and Gal-Mor, O}, title = {The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0368822}, doi = {10.1128/spectrum.03688-22}, pmid = {36995224}, issn = {2165-0497}, abstract = {Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.}, }
@article {pmid36993299, year = {2023}, author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M}, title = {Diverse and abundant viruses exploit conjugative plasmids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993299}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of bacterial viruses, phages, use chromosomally-encoded cell surface structures as receptors, plasmid dependent-phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages using a targeted discovery platform, and find that they are in fact common and abundant in nature, and vastly unexplored in terms of their genetic diversity. Plasmid-dependent tectiviruses have highly conserved genetic architecture but show profound differences in their host range which do not reflect bacterial phylogeny. Finally, we show that plasmid-dependent tectiviruses are missed by metaviromic analyses, showing the continued importance of culture-based phage discovery. Taken together, these results indicate plasmid-dependent phages play an unappreciated evolutionary role in constraining horizontal gene transfer.}, }
@article {pmid36990411, year = {2023}, author = {Sánchez-Arroyo, A and Plaza-Vinuesa, L and Rivas, BL and Mancheño, JM and Muñoz, R}, title = {The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986[T] is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity.}, journal = {International journal of biological macromolecules}, volume = {237}, number = {}, pages = {124230}, doi = {10.1016/j.ijbiomac.2023.124230}, pmid = {36990411}, issn = {1879-0003}, abstract = {The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986[T] (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.}, }
@article {pmid36989191, year = {2023}, author = {Rathnapala, JMSN and Ragab, W and Kawato, S and Furukawa, M and Nozaki, R and Kondo, H and Hirono, I}, title = {Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.13786}, pmid = {36989191}, issn = {1365-2761}, abstract = {Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.}, }
@article {pmid36989040, year = {2023}, author = {Sanow, S and Kuang, W and Schaaf, G and Huesgen, P and Schurr, U and Roessner, U and Watt, M and Arsova, B}, title = {Molecular mechanisms of Pseudomonas assisted plant nitrogen uptake - opportunities for modern agriculture.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-10-22-0223-CR}, pmid = {36989040}, issn = {0894-0282}, abstract = {Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT and Pseudomonas sp. K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which in turn have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N), and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signalling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions, and differs at sufficient and deficient N. The molecular controls behind different plant response are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas driven nitrogen fixation and to point to possible agricultural solutions.}, }
@article {pmid36988519, year = {2023}, author = {Low, WW and Seddon, C and Beis, K and Frankel, G}, title = {The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0006123}, doi = {10.1128/jb.00061-23}, pmid = {36988519}, issn = {1098-5530}, abstract = {Horizontal gene transfer via conjugation plays a major role in bacterial evolution. In F-like plasmids, efficient DNA transfer is mediated by close association between donor and recipient bacteria. This process, known as mating pair stabilization (MPS), is mediated by interactions between the plasmid-encoded outer membrane (OM) protein TraN in the donor and chromosomally-encoded OM proteins in the recipient. We have recently reported the existence of 7 TraN sequence types, which are grouped into 4 structural types, that we named TraNα, TraNβ, TraNγ, and TraNδ. Moreover, we have shown specific pairing between TraNα and OmpW, TraNβ and OmpK36 of Klebsiella pneumoniae, TraNγ and OmpA, and TraNδ and OmpF. In this study, we found that, although structurally similar, TraNα encoded by the Salmonella enterica pSLT plasmid (TraNα2) binds OmpW in both Escherichia coli and Citrobacter rodentium, while TraNα encoded by the R100-1 plasmid (TraNα1) only binds OmpW in E. coli. AlphaFold2 predictions suggested that this specificity is mediated by a single amino acid difference in loop 3 of OmpW, which we confirmed experimentally. Moreover, we show that single amino acids insertions into loop 3 of OmpK36 affect TraNβ-mediated conjugation efficiency of the K. pneumoniae resistance plasmid pKpQIL. Lastly, we report that TraNβ can also mediate MPS by binding OmpK35, making it the first TraN variant that can bind more than one OM protein in the recipient. Together, these data show that subtle sequence differences in the OM receptors can impact TraN-mediated conjugation efficiency. IMPORTANCE Conjugation plays a central role in the spread of antimicrobial resistance genes among bacterial pathogens. Efficient conjugation is mediated by formation of mating pairs via a pilus, followed by mating pair stabilization (MPS), mediated by tight interactions between the plasmid-encoded outer membrane protein (OMP) TraN in the donor (of which there are 7 sequence types grouped into the 4 structural isoforms α, β, γ, and δ), and an OMP receptor in the recipient (OmpW, OmpK36, OmpA, and OmpF, respectively). In this study, we found that subtle differences in OmpW and OmpK36 have significant consequences on conjugation efficiency and specificity, highlighting the existence of selective pressure affecting plasmid-host compatibility and the flow of horizontal gene transfer in bacteria.}, }
@article {pmid36985115, year = {2023}, author = {Gummalla, VS and Zhang, Y and Liao, YT and Wu, VCH}, title = {The Role of Temperate Phages in Bacterial Pathogenicity.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985115}, issn = {2076-2607}, abstract = {Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage-bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.}, }
@article {pmid36983453, year = {2023}, author = {Urquhart, AS and Idnurm, A}, title = {A Polyphasic Approach including Whole Genome Sequencing Reveals Paecilomyces paravariotii sp. nov. as a Cryptic Sister Species to P. variotii.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983453}, issn = {2309-608X}, abstract = {Whole genome sequencing is rapidly increasing phylogenetic resolution across many groups of fungi. To improve sequencing coverage in the genus Paecilomyces (Eurotiales), we report nine new Paecilomyces genomes representing five different species. Phylogenetic comparison between these genomes and those reported previously showed that Paecilomyces paravariotii is a distinct species from its close relative P. variotii. The independence of P. paravariotii is supported by analysis of overall gene identify (via BLAST), differences in secondary metabolism and an inability to form ascomata when paired with a fertile P. variotii strain of opposite mating type. Furthermore, whole genome sequencing resolves the P. formosus clade into three separate species, one of which lacked a valid name that is now provided.}, }
@article {pmid36982992, year = {2023}, author = {Liu, W and Huang, Y and Zhang, H and Liu, Z and Huan, Q and Xiao, X and Wang, Z}, title = {Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982992}, issn = {1422-0067}, mesh = {Drug Resistance, Microbial ; *Intestines ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.}, }
@article {pmid36980919, year = {2023}, author = {Weltzer, ML and Wall, D}, title = {Social Diversification Driven by Mobile Genetic Elements.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980919}, issn = {2073-4425}, mesh = {*Bacteria/genetics ; *Myxococcales/genetics ; Biological Evolution ; Genome ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.}, }
@article {pmid36975806, year = {2023}, author = {Desingu, PA and Nagarajan, K and Sundaresan, NR}, title = {Unique Tandem Repeats in the Inverted Terminal Repeat Regions of Monkeypox Viruses.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0319922}, pmid = {36975806}, issn = {2165-0497}, abstract = {The genetic diversity, especially in noncoding regions between clade I, clade IIa, and clade IIb monkeypox viruses (MPXVs), is still not fully understood. Here, we report that unique 16-nucleotide-length tandem repeats in MPXVs viruses are located in the noncoding regions of inverted terminal repeats (ITR), and the copy number of this repeat is different among clade I, clade IIa, and clade IIb viruses. It is noteworthy that tandem repeats containing these specific sequences (AACTAACTTATGACTT) are only present in MPXVs and are not found in other poxviruses. Also, the tandem repeats containing these specific sequences (AACTAACTTATGACTT) do not correspond to the tandem repeats present in the human and rodent (mice and rat) genomes. On the other hand, some of the reported tandem repeats in the human and rodent (mice and rat) genomes are present in the clade IIb-B.1 lineage of MPXV. In addition, it is noteworthy that the genes flanking these tandem repeats are lost and gained compared between clade I, clade IIa, and clade IIb MPXV. IMPORTANCE The different groups of MPXVs contain unique tandem repeats with different copy numbers in the ITR regions, and these repeats may be likely to play a role in the genetic diversity of the virus. Clade IIb (B) MPXV contains 38 and 32 repeats similar to the Tandem repeats reported in the human and rodent genome, respectively. However, none of these 38 (human) and 32 (rodent) tandem repeats matched the tandem repeats (AACTAACTTATGACTT) found in the present study. Finally, when developing attenuated or modified MPXV vaccine strains, these repeats in noncoding genomic regions can be exploited to incorporate foreign proteins (adjuvants/other virus proteins/racking fluorescent proteins such as green fluorescent protein) to carry out studies such as vaccine production and virus pathogenesis.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36964199}, issn = {1751-7370}, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36961781, year = {2023}, author = {Belal, NA and Heath, LS}, title = {A complete theoretical framework for inferring horizontal gene transfers using partial order sets.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0281824}, pmid = {36961781}, issn = {1932-6203}, mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; }, abstract = {We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.}, }
@article {pmid36958858, year = {2023}, author = {Bird, SM and Ford, S and Thompson, CMA and Little, R and Hall, JPJ and Jackson, RW and Malone, J and Harrison, E and Brockhurst, MA}, title = {Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {4}, pages = {}, pmid = {36958858}, issn = {1574-6941}, support = {BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Rhizosphere ; Plasmids/genetics ; Mutation ; *Pseudomonas fluorescens/genetics ; }, abstract = {Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here, we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens SBW25 in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their environmental niche.}, }
@article {pmid36958158, year = {2023}, author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH}, title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131200}, doi = {10.1016/j.jhazmat.2023.131200}, pmid = {36958158}, issn = {1873-3336}, abstract = {The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.}, }
@article {pmid36951100, year = {2023}, author = {Lin, H and Moody, ERR and Williams, TA and Moreau, JW}, title = {On the Origin and Evolution of Microbial Mercury Methylation.}, journal = {Genome biology and evolution}, volume = {15}, number = {4}, pages = {}, pmid = {36951100}, issn = {1759-6653}, mesh = {*Mercury ; *Methylmercury Compounds ; Methylation ; Phylogeny ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The origin of microbial mercury methylation has long been a mystery. Here, we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury-methylating gene, hgcAB, constrain the ancestral origin of the hgc operon, and explain the distribution of hgc in Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded by merB) reduced a selective advantage for mercury methylators and resulted in widespread loss of hgc in Bacteria and Archaea.}, }
@article {pmid36950985, year = {2023}, author = {Ding, D and Wang, B and Zhang, X and Zhang, J and Zhang, H and Liu, X and Gao, Z and Yu, Z}, title = {The spread of antibiotic resistance to humans and potential protection strategies.}, journal = {Ecotoxicology and environmental safety}, volume = {254}, number = {}, pages = {114734}, doi = {10.1016/j.ecoenv.2023.114734}, pmid = {36950985}, issn = {1090-2414}, mesh = {Animals ; Humans ; *Bacteria/genetics ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.}, }
@article {pmid36949816, year = {2023}, author = {Guzmán-Herrador, DL and Fernández-Gómez, A and Llosa, M}, title = {Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1146000}, pmid = {36949816}, issn = {2235-2988}, mesh = {Humans ; *Bacterial Secretion Systems/genetics ; *Bacteria/metabolism ; Virulence ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/metabolism ; }, abstract = {Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.}, }
@article {pmid36949153, year = {2023}, author = {Wang, Q and Wei, S and Silva, AF and Madsen, JS}, title = {Cooperative antibiotic resistance facilitates horizontal gene transfer.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36949153}, issn = {1751-7370}, abstract = {The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.}, }
@article {pmid36949027, year = {2023}, author = {Tanaka, E and Wajima, T and Nakaminami, H and Uchiya, KI}, title = {Contribution of amino acid substitutions in ParE to quinolone resistance in Haemophilus haemolyticus revealed through a horizontal transfer assay using Haemophilus influenzae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkad074}, pmid = {36949027}, issn = {1460-2091}, abstract = {BACKGROUND: In 2019, a high-level quinolone-resistant Haemophilus haemolyticus strain (levofloxacin MIC = 16 mg/L) was isolated from a paediatric patient. In this study, we aimed to determine whether the quinolone resistance of H. haemolyticus could be transferred to Haemophilus influenzae and to identify the mechanism underlying the high-level quinolone resistance of H. haemolyticus.<br><br>METHODS: A horizontal gene transfer assay to H. influenzae was performed using genomic DNA or PCR-amplified quinolone-targeting genes from the high-level quinolone-resistant H. haemolyticus 2019-19 strain. The amino acids responsible for conferring quinolone resistance were identified through site-directed mutagenesis.<br><br>RESULTS: By adding the genomic DNA of H. haemolyticus 2019-19, resistant colonies were obtained on agar plates containing quinolones. Notably, H. influenzae grown on levofloxacin agar showed the same level of resistance as H. haemolyticus. Sequencing analysis showed that gyrA, parC and parE of H. influenzae were replaced by those of H. haemolyticus, suggesting that horizontal transfer occurred between the two strains. When the quinolone-targeting gene fragments were added sequentially, the addition of parE, as well as gyrA and parC, contributed to high-level resistance. In particular, amino acid substitutions at both the 439th and 502nd residues of ParE were associated with high-level resistance.<br><br>CONCLUSIONS: These findings indicate that quinolone resistance can be transferred between species and that amino acid substitutions at the 439th and 502nd residues of ParE, in addition to amino acid substitutions in both GyrA and ParC, contribute to high-level quinolone resistance.}, }
@article {pmid36948313, year = {2023}, author = {Fenibo, EO and Selvarajan, R and Abia, ALK and Matambo, T}, title = {Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162951}, doi = {10.1016/j.scitotenv.2023.162951}, pmid = {36948313}, issn = {1879-1026}, abstract = {Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.}, }
@article {pmid36946779, year = {2023}, author = {Johnston, EL and Zavan, L and Bitto, NJ and Petrovski, S and Hill, AF and Kaparakis-Liaskos, M}, title = {Planktonic and Biofilm-Derived Pseudomonas aeruginosa Outer Membrane Vesicles Facilitate Horizontal Gene Transfer of Plasmid DNA.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0517922}, pmid = {36946779}, issn = {2165-0497}, abstract = {Outer membrane vesicles (OMVs) produced by Gram-negative bacteria package various cargo, including DNA that can be transferred to other bacteria or to host cells. OMV-associated DNA has been implicated in mediating horizontal gene transfer (HGT) between bacteria, which includes the dissemination of antibiotic resistance genes within and between bacterial species. Despite the known ability of OMVs to mediate HGT, the mechanisms of DNA packaging into OMVs remain poorly characterized, as does the effect of bacterial growth conditions on the DNA cargo composition of OMVs and their subsequent abilities to mediate HGT. In this study, we examined the DNA content of OMVs produced by the opportunistic pathogen Pseudomonas aeruginosa grown in either planktonic or biofilm conditions. Analysis of planktonic growth-derived OMVs revealed their ability to package and protect plasmid DNA from DNase degradation and to transfer plasmid-encoded antibiotic resistance genes to recipient, antibiotic-sensitive P. aeruginosa bacteria at a greater efficiency than transformation with plasmid alone. Comparisons of planktonic and biofilm-derived P. aeruginosa OMVs demonstrated that biofilm-derived OMVs were smaller but were associated with more plasmid DNA than planktonic-derived OMVs. Additionally, biofilm-derived P. aeruginosa OMVs were more efficient in the transformation of competent P. aeruginosa bacteria, compared to transformations with an equivalent number of planktonic-derived OMVs. The findings of this study highlight the importance of bacterial growth conditions for the packaging of DNA within P. aeruginosa OMVs and their ability to facilitate HGT, thus contributing to the spread of antibiotic resistance genes between P. aeruginosa bacteria. IMPORTANCE Bacterial membrane vesicles (BMVs) mediate interbacterial communication, and their ability to package DNA specifically contributes to biofilm formation, antibiotic resistance, and HGT between bacteria. However, the ability of P. aeruginosa OMVs to mediate HGT has not yet been demonstrated. Here, we reveal that P. aeruginosa planktonic and biofilm-derived OMVs can deliver plasmid-encoded antibiotic resistance to recipient P. aeruginosa. Additionally, we demonstrated that P. aeruginosa biofilm-derived OMVs were associated with more plasmid DNA compared to planktonic-derived OMVs and were more efficient in the transfer of plasmid DNA to recipient bacteria. Overall, this demonstrated the ability of P. aeruginosa OMVs to facilitate the dissemination of antibiotic resistance genes, thereby enabling the survival of susceptible bacteria during antibiotic treatment. Investigating the roles of biofilm-derived BMVs may contribute to furthering our understanding of the role of BMVs in HGT and the spread of antibiotic resistance in the environment.}, }
@article {pmid36945052, year = {2023}, author = {Wang, Y and Zhang, Y and Hu, Y and Liu, L and Liu, SJ and Zhang, T}, title = {Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {56}, pmid = {36945052}, issn = {2049-2618}, mesh = {Humans ; *Sewage/microbiology ; *Bacteria/genetics/metabolism ; Metagenomics ; Metagenome/genetics ; Metabolic Networks and Pathways ; Phylogeny ; }, abstract = {BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.<br><br>RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.<br><br>CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.}, }
@article {pmid36943061, year = {2023}, author = {Nielsen, FD and Skov, MN and Sydenham, TV and Justesen, US}, title = {Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0511122}, pmid = {36943061}, issn = {2165-0497}, abstract = {Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.}, }
@article {pmid36943058, year = {2023}, author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Qi, YL and Jiao, JY and Shu, WS and Hua, ZS and Li, WJ}, title = {Metagenomic Discovery of "Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0125222}, doi = {10.1128/msystems.01252-22}, pmid = {36943058}, issn = {2379-5077}, abstract = {"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.}, }
@article {pmid36941487, year = {2023}, author = {Bhakta, S and Bhattacharya, A}, title = {In silico evolutionary and structural analysis of cAMP response proteins (CARPs) from Leishmania major.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {125}, pmid = {36941487}, issn = {1432-072X}, mesh = {Animals ; *Leishmania major/genetics/metabolism ; Cyclic AMP/metabolism ; Phylogeny ; Signal Transduction/physiology ; *Carps ; }, abstract = {With unidentified chemical triggers and novel-effectors, cAMP signaling is broadly noncanonical in kinetoplastida parasites. Though novel protein kinase A regulatory subunits (PKAR) have been identified earlier, cAMP Response Proteins (CARPs) have been identified as a unique and definite cAMP effector of trypanosomatids. CARP1-CARP4 emerged as critical regulatory components of cAMP signaling pathway in Trypanosoma with evidences that CARP3 can directly interact with a flagellar adenylate cyclase (AC). CARP-mediated regulations, identified so far, reflects the mechanistic diversity of cAMP signaling. Albeit the function of the orthologous is not yet delineated, in kinetoplastids like Leishmania, presence of CARP1, 2 and 4 orthologues suggests existence of conserved effector mechanisms. Targeting CARP orthologues in Leishmania, a comprehensive evolutionary analysis of CARPs have been aimed in this study which revealed phylogenetic relationship, codon adaptation and structural heterogeneity among the orthologues, warranting functional analysis in future to explore their involvement in infectivity.}, }
@article {pmid36941328, year = {2023}, author = {Zumkeller, S and Polsakiewicz, M and Knoop, V}, title = {Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {296}, pmid = {36941328}, issn = {2399-3642}, mesh = {Introns/genetics ; *Ferns/genetics ; *Genome, Mitochondrial ; Trans-Splicing ; Plants/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.}, }
@article {pmid36940043, year = {2023}, author = {Chaudhary, S and Kishen, S and Singh, M and Jassal, S and Pathania, R and Bisht, K and Sareen, D}, title = {Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin.}, journal = {AMB Express}, volume = {13}, number = {1}, pages = {34}, pmid = {36940043}, issn = {2191-0855}, abstract = {Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.}, }
@article {pmid36937147, year = {2023}, author = {Cao, H and Liang, S and Zhang, C and Liu, B and Fei, Y}, title = {Molecular Profiling of a Multi-Strain Hypervirulent Klebsiella pneumoniae Infection Within a Single Patient.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1367-1380}, pmid = {36937147}, issn = {1178-6973}, abstract = {BACKGROUND: The rising prevalence of infections caused by carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKP) has outpaced our understanding of their evolutionary diversity. By straining the antimicrobial options and constant horizontal gene transfer of various pathogenic elements, CR-hvKP poses a global health threat.<br><br>METHODS: Six KP isolates (KP1~KP6) from urine, sputum and groin infection secretion of a single patient were characterized phenotypically and genotypically. The antimicrobial susceptibility, carbapenemase production, hypermucoviscosity, serum resistance, virulence factors, MLST and serotypes were profiled. Genomic variations were identified by whole-genome sequencing and the phylogenetic differentiation was analyzed by Enterobacterial repetitive intergenic consensus (ERIC)-PCR.<br><br>RESULTS: All KP strains were multi-drug resistant. Four of them (KP1, KP3, KP5 and KP6) belonged to ST11-K64, with high genetic closeness (relatedness coefficient above 0.96), sharing most resistance and virulence genes. Compared with KP1, the later isolates KP3, KP5 and KP6 acquired bla KPC-1 and lost bla SHV-182 genes. KP2 and KP4 had the same clonal origin of ST35-K16 (relatedness coefficient 0.98), containing almost identical genes for resistance and virulence. They were non-mucoid and carried bla NDM-5 gene.<br><br>CONCLUSION: A co-infection with two types of CR-hvKP affiliated with different clades within a single patient amplified the treatment difficulties. In addition to source control and epidemiological surveillance, investigation of the in-host interactions between CR-hvKP variants may provide valuable treatment solutions.}, }
@article {pmid36932546, year = {2023}, author = {Weaver, BP and Haselwandter, CA and Boedicker, JQ}, title = {Stochastic effects in bacterial communication mediated by extracellular vesicles.}, journal = {Physical review. E}, volume = {107}, number = {2-1}, pages = {024409}, doi = {10.1103/PhysRevE.107.024409}, pmid = {36932546}, issn = {2470-0053}, mesh = {*Bacteria ; Quorum Sensing/physiology ; Communication ; *Extracellular Vesicles ; }, abstract = {Quorum sensing (QS) allows bacterial cells to sense changes in local cell density and, hence, to regulate multicellular processes, including biofilm formation, regulation of virulence, and horizontal gene transfer. While, traditionally, QS was thought to involve the exchange of extracellular signal molecules free in solution, recent experiments have shown that for some bacterial systems a substantial fraction of signal molecules are packaged and delivered in extracellular vesicles. How the packaging of signal molecules in extracellular vesicles influences the ability of cells to communicate and coordinate multicellular behaviors remains largely unknown. We present here a stochastic reaction-diffusion model of QS that accounts for the exchange of both freely diffusing and vesicle-associated signal molecules. We find that the delivery of signal molecules via extracellular vesicles amplifies local fluctuations in the signal concentration, which can strongly affect the dynamics and spatial range of bacterial communication. For systems with multiple bacterial colonies, extracellular vesicles provide an alternate pathway for signal transport between colonies, and may be crucial for long-distance signal exchange in environments with strong degradation of free signal molecules.}, }
@article {pmid36931217, year = {2023}, author = {Zhao, Q and Hu, Z and Zhang, J and Wang, Y}, title = {Determination of the fate of antibiotic resistance genes and the response mechanism of plants during enhanced antibiotic degradation in a bioelectrochemical-constructed wetland system.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131207}, doi = {10.1016/j.jhazmat.2023.131207}, pmid = {36931217}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Wastewater ; Waste Disposal, Fluid ; Wetlands ; Genes, Bacterial ; Chloramphenicol/analysis ; Drug Resistance, Microbial/genetics ; }, abstract = {Chloramphenicol (CAP) has a high concentration and detection frequency in aquatic environments due to its insufficient degradation in traditional biological wastewater treatment processes. In this study, bioelectrochemical assistant-constructed wetland systems (BES-CWs) were developed as advanced processes for efficient CAP removal, in which the degradation and transfer of CAP and the fate of antibiotic resistance genes (ARGs) were evaluated. The CAP removal efficiency could reach as high as 90.2%, while the removed CAP can be partially adsorbed and bioaccumulated in plants, significantly affecting plant growth. The vertical gene transfer and horizontal gene transfer increased the abundance of ARGs under high voltage and CAP concentrations. Microbial community analysis showed that CAP pressure and electrical stimulation selected the functional bacteria to increase CAP removal and antibiotic resistance. CAP degradation species carrying ARGs could increase their opposition to the biotoxicity of CAP and maintain system performance. In addition, ARGs are transferred into the plant and upward, which can potentially enter the food chain. This study provides an essential reference for enhancing antibiotic degradation and offers fundamental support for the underlying mechanism and ARG proliferation during antibiotic biodegradation.}, }
@article {pmid36931215, year = {2023}, author = {Lin, D and Zhu, L and Yao, Y and Zhu, L and Wang, M}, title = {The ecological and molecular mechanism underlying effective reduction of antibiotic resistance genes pollution in soil by fermentation broth from fruit and vegetable waste.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131201}, doi = {10.1016/j.jhazmat.2023.131201}, pmid = {36931215}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Vegetables ; Soil ; Fermentation ; Fruit ; Genes, Bacterial ; Tetracycline/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {The strategies to relieve antibiotic resistance genes (ARGs) pollution are urgently needed. Fermentation broth from fruit and vegetable waste (FFVW), an agricultural amendment, exhibits a remarkable capacity to reduce ARG pollution; however, the underlying mechanism of this effect remains unclear. We performed microcosm experiments to reappear the phenomenon of FFVW-driven reduction in ARGs. Moderate-level FFVW reduced gene resistance to sulfonamide (41.2 %), macrolide-lincosamide-streptogramin (MLS) (47.2 %), chloramphenicol (63.2 %), and tetracycline (61.4 %). Binning and network analyses revealed that Actinobacteria comprise the primary hosts of ARGs in arable soil, and FFVW substantially inhibited the growth and metabolic activity of these organisms. Moreover, tetracycline and MLS production was partially/completely inhibited by FFVW, further reducing the transfer frequency by 52.9-86.1 % and 46.6-66.6 % in the intragenic and intergenic mating systems, respectively. Furthermore, the expression of genes related to conjugation pairing and plasmid transfer was downregulated. Thus, FFVW effectively reduces ARG pollution by inhibiting Actinobacteria proliferation, thereby reducing selective pressure and restricting horizontal gene transfer. Our findings highlight the important underlying mechanisms of FFVW involved in ARG reduction, supporting its use in arable soil.}, }
@article {pmid36928121, year = {2023}, author = {Gandini, CL and Garcia, LE and Abbona, CC and Ceriotti, LF and Kushnir, S and Geelen, D and Sanchez-Puerta, MV}, title = {Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mt-HGT.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erad104}, pmid = {36928121}, issn = {1460-2431}, abstract = {Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, our lab described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid between N. tabacum and Physochlaina orientalis and re-analyzed the somatic hybrids previously generated in our lab. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (~80%) were asymmetrical, consistent with the break-induced replication (BIR) pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. BIR is the main pathway of interparental recombination in somatic hybrid mitochondria. Findings of this study are relevant to mitogenome editing assays and to mechanistic aspects of DNA integration following mitochondrial DNA horizontal transfer events.}, }
@article {pmid36927397, year = {2023}, author = {Teklemariam, AD and Al Hindi, R and Qadri, I and Alharbi, MG and Hashem, AM and Alrefaei, AA and Basamad, NA and Haque, S and Alamri, T and Harakeh, S}, title = {Phage cocktails - an emerging approach for the control of bacterial infection with major emphasis on foodborne pathogens.}, journal = {Biotechnology &amp; genetic engineering reviews}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/02648725.2023.2178870}, pmid = {36927397}, issn = {2046-5556}, abstract = {Phage therapy has recently attracted a great deal of attention to counteract the rapid emergence of antibiotic-resistant bacteria. In comparison to monophage therapy, phage cocktails are typically used to treat individual and/or multi-bacterial infections since the bacterial agents are unlikely to become resistant as a result of exposure to multiple phages simultaneously. The bacteriolytic effect of phage cocktails may produce efficient killing effect in comparison to individual phage. However, multiple use of phages (complex cocktails) may lead to undesirable side effects such as dysbiosis, horizontal gene transfer, phage resistance, cross resistance, and/or higher cost of production. Cocktail formulation, therefore, representa compromise between limiting the complexity of the cocktail and achieving substantial bacterial load reduction towards the targeted host organisms. Despite some constraints, the applications of monophage therapy have been well documented in the literature. However, phage cocktails-based approaches and their role for the control of pathogens have not been well investigated. In this review, we discuss the principle of phage cocktail formulations, their optimization strategies, major phage cocktail preparations, and their efficacy in inactivating various food borne bacterial pathogens.}, }
@article {pmid36927158, year = {2023}, author = {Karnkowska, A and Yubuki, N and Maruyama, M and Yamaguchi, A and Kashiyama, Y and Suzaki, T and Keeling, PJ and Hampl, V and Leander, BS}, title = {Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {12}, pages = {e2220100120}, pmid = {36927158}, issn = {1091-6490}, mesh = {*Photosynthesis/genetics ; Plastids/genetics/metabolism ; Eukaryota/genetics ; *Chlorophyta/genetics/metabolism ; Transcriptome ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Kleptoplasts (kP) are distinct among photosynthetic organelles in eukaryotes (i.e., plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light-dark cycles, and [13]C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 276 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis. These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early evolutionary stages in the green alga-derived secondary plastids of euglenophytes also involved kleptoplasty.}, }
@article {pmid36925471, year = {2023}, author = {Cerbino, GN and Traglia, GM and Ayala Nuñez, T and Parmeciano Di Noto, G and Ramírez, MS and Centrón, D and Iriarte, A and Quiroga, C}, title = {Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1124225}, pmid = {36925471}, issn = {1664-302X}, abstract = {Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.}, }
@article {pmid36922599, year = {2023}, author = {Nyerges, A and Vinke, S and Flynn, R and Owen, SV and Rand, EA and Budnik, B and Keen, E and Narasimhan, K and Marchand, JA and Baas-Thomas, M and Liu, M and Chen, K and Chiappino-Pepe, A and Hu, F and Baym, M and Church, GM}, title = {A swapped genetic code prevents viral infections and gene transfer.}, journal = {Nature}, volume = {615}, number = {7953}, pages = {720-727}, pmid = {36922599}, issn = {1476-4687}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, mesh = {*Amino Acids/genetics/metabolism ; Codon/genetics ; Ecosystem ; *Escherichia coli/genetics/virology ; *Genetic Code/genetics ; Leucine/genetics/metabolism ; *Protein Biosynthesis/genetics ; RNA, Transfer/genetics/metabolism ; Serine/genetics ; *Virus Diseases/genetics/prevention &amp; control ; *Host Microbial Interactions/genetics ; Organisms, Genetically Modified/genetics ; Genome, Bacterial/genetics ; *Gene Transfer, Horizontal/genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer[1-6]. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus[7-9], potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature[10]. Our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.}, }
@article {pmid36915058, year = {2023}, author = {Zumkeller, S and Knoop, V}, title = {Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {5}, pmid = {36915058}, issn = {2730-7182}, mesh = {Introns/genetics ; *Evolution, Molecular ; *Mitochondria/genetics ; Plants/genetics ; Cell Nucleus ; }, abstract = {Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.}, }
@article {pmid36914349, year = {2023}, author = {Wang, D and Fletcher, GC and Gagic, D and On, SLW and Palmer, JS and Flint, SH}, title = {Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.}, journal = {Food research international (Ottawa, Ont.)}, volume = {166}, number = {}, pages = {112605}, doi = {10.1016/j.foodres.2023.112605}, pmid = {36914349}, issn = {1873-7145}, mesh = {*Vibrio parahaemolyticus/genetics ; Biofilms ; Genomics ; Operon ; Cellulose ; }, abstract = {Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.}, }
@article {pmid36913905, year = {2023}, author = {Despotovic, M and de Nies, L and Busi, SB and Wilmes, P}, title = {Reservoirs of antimicrobial resistance in the context of One Health.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102291}, doi = {10.1016/j.mib.2023.102291}, pmid = {36913905}, issn = {1879-0364}, abstract = {The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.}, }
@article {pmid36912846, year = {2023}, author = {Qi, Q and Ghaly, TM and Penesyan, A and Rajabal, V and Stacey, JA and Tetu, SG and Gillings, MR}, title = {Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology.}, journal = {Environmental science &amp; technology}, volume = {57}, number = {12}, pages = {4870-4879}, doi = {10.1021/acs.est.2c09739}, pmid = {36912846}, issn = {1520-5851}, mesh = {Humans ; *Integrons/genetics ; *Drug Resistance, Bacterial/genetics ; Cell Fusion ; Bacteria/genetics ; Polymerase Chain Reaction ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.}, }
@article {pmid36912090, year = {2023}, author = {Deng, L and Wang, C and Zhang, X and Yang, W and Tang, H and Chen, X and Du, S and Chen, X}, title = {Cell-to-cell natural transformation in Bacillus subtilis facilitates large scale of genomic exchanges and the transfer of long continuous DNA regions.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad138}, pmid = {36912090}, issn = {1362-4962}, abstract = {Natural transformation is one of the major mechanisms of horizontal gene transfer. Although it is usually studied using purified DNA in the laboratory, recent studies showed that many naturally competent bacteria acquired exogenous DNA from neighboring donor cells. Our previous work indicates that cell-to-cell natural transformation (CTCNT) using two different Bacillus subtilis strains is a highly efficient process; however, the mechanism is unclear. In this study, we further characterized CTCNT and mapped the transferred DNA in the recombinants using whole genome sequencing. We found that a recombinant strain generated by CTCNT received up to 66 transferred DNA segments; the average length of acquired continuous DNA stretches was approximately 27 kb with a maximum length of 347 kb. Moreover, up to 1.54 Mb genomic DNA (37% of the chromosome) was transferred from the donors into one recipient cell. These results suggest that B. subtilis CTCNT facilitates horizontal gene transfer by increasing the transfer of DNA segments and fostering the exchange of large continuous genomic regions. This indicates that the potency of bacterial natural transformation is underestimated using traditional approaches and reveals that DNA donor cells may play an important role in the transformation process in natural environments.}, }
@article {pmid36909625, year = {2023}, author = {Verhoeve, VI and Lehman, SS and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates origins of pathogen effectors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36909625}, support = {R21 AI126108/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, abstract = {Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.}, }
@article {pmid36909515, year = {2023}, author = {Boys, IN and Johnson, AG and Quinlan, M and Kranzusch, PJ and Elde, NC}, title = {Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36909515}, abstract = {Viruses acquire host genes via horizontal gene transfer and can express them to manipulate host biology during infections. Some viral and host homologs retain sequence identity, but evolutionary divergence can obscure host origins. We used structural modeling to compare vaccinia virus proteins with metazoan proteomes. We identified vaccinia A47L as a homolog of gasdermins, the executioners of pyroptosis. An X-ray crystal structure of A47 confirmed this homology and cell-based assays revealed that A47 inhibits pyroptosis. We also identified vaccinia C1L as the product of a cryptic gene fusion event coupling a Bcl-2 related fold with a pyrin domain. C1 associates with components of the inflammasome, a cytosolic innate immune sensor involved in pyroptosis, yet paradoxically enhances inflammasome activity, suggesting a benefit to poxvirus replication in some circumstances. Our findings demonstrate the potential of structural homology screens to reveal genes that viruses capture from hosts and repurpose to benefit viral fitness.}, }
@article {pmid36901726, year = {2023}, author = {Sonnenberg, CB and Haugen, P}, title = {Bipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36901726}, issn = {1422-0067}, mesh = {*Genome, Bacterial ; Plasmids ; Bacteria/genetics ; *Gammaproteobacteria ; Codon Usage ; Gene Transfer, Horizontal ; }, abstract = {Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.}, }
@article {pmid36897935, year = {2023}, author = {Carr, VR and Pissis, SP and Mullany, P and Shoaie, S and Gomez-Cabrero, D and Moyes, DL}, title = {Palidis: fast discovery of novel insertion sequences.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, doi = {10.1099/mgen.0.000917}, pmid = {36897935}, issn = {2057-5858}, support = {BB/M009513/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016899/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *DNA Transposable Elements ; *Bacteria/genetics ; Computational Biology ; Genome, Microbial ; Metagenomics ; }, abstract = {The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.}, }
@article {pmid36897181, year = {2023}, author = {Wackett, LP}, title = {Horizontal gene transfer (HGT) and microbial evolution: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {772-773}, doi = {10.1111/1462-2920.16053}, pmid = {36897181}, issn = {1462-2920}, mesh = {*Gene Transfer, Horizontal ; *Environmental Microbiology ; }, }
@article {pmid36896589, year = {2023}, author = {Yu, R and Chen, X and Long, L and Jost, M and Zhao, R and Liu, L and Mower, JP and dePamphilis, CW and Wanke, S and Jiao, Y}, title = {De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36896589}, issn = {1759-6653}, mesh = {*Genome, Mitochondrial ; Biological Evolution ; *Magnoliopsida/genetics ; Introns ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {The mitochondrial genome of Liriodendron tulipifera exhibits many ancestral angiosperm features and a remarkably slow evolutionary rate, while mitochondrial genomes of other magnoliids remain yet to be characterized. We assembled nine new mitochondrial genomes, representing all genera of perianth-bearing Piperales, as well as for a member of the sister clade: three complete or nearly complete mitochondrial genomes from Aristolochiaceae and six additional draft assemblies including Thottea, Asaraceae, Lactoridaceae, and Hydnoraceae. For comparative purpose, a complete mitochondrial genome was assembled for Saururus, a member of the perianth-less Piperales. The average number of short repeats (50-99 bp) was much larger in genus Aristolochia than in other angiosperm mitochondrial genomes, and approximately 30% of repeats (<350 bp) were found to have the capacity to mediate recombination. We found mitochondrial genomes in perianth-bearing Piperales comprising conserved repertories of protein-coding genes and rRNAs but variable copy numbers of tRNA genes. We identified several shifts from cis- to trans-splicing of the Group II introns of nad1i728, cox2i373, and nad7i209. Two short regions of the cox1 and atp8 genes were likely derived from independent horizontal gene transfer events in perianth-bearing Piperales. We found biased enrichment of specific substitution types in different lineages of magnoliids and the Aristolochiaceae family showed the highest ratio of A:T > T:A substitutions of all other investigated angiosperm groups. Our study reports the first mitochondrial genomes for Piperales and uses this new information for a better understanding of the evolutionary patterns of magnoliids and angiosperms in general.}, }
@article {pmid36893903, year = {2023}, author = {Khan, AA and Nema, V and Ashraf, MT}, title = {Host-microbiota interactions and oncogenesis: Crosstalk and its implications in etiology.}, journal = {Microbial pathogenesis}, volume = {178}, number = {}, pages = {106063}, doi = {10.1016/j.micpath.2023.106063}, pmid = {36893903}, issn = {1096-1208}, mesh = {Humans ; Carcinogenesis ; *Microbiota/genetics ; *Neoplasms ; Host Microbial Interactions ; }, abstract = {A number of articles have discussed the potential of microbiota in oncogenesis. Several of these have evaluated the modulation of microbiota and its influence on cancer development. Even in recent past, a plethora of studies have gathered in order to understand the difference in microbiota population among different cancer and normal individuals. Although in majority of studies, microbiota mediated oncogenesis has been primarily attributed to the inflammatory mechanisms, there are several other ways through which microbiota can influence oncogenesis. These relatively less discussed aspects including the hormonal modulation through estrobolome and endobolome, production of cyclomodulins, and lateral gene transfer need more attention of scientific community. We prepared this article to discuss the role of microbiota in oncogenesis in order to provide concise information on these relatively less discussed microbiota mediated oncogenesis mechanisms.}, }
@article {pmid36892288, year = {2023}, author = {Große, C and Scherer, J and Schleuder, G and Nies, DH}, title = {Interplay between Two-Component Regulatory Systems Is Involved in Control of Cupriavidus metallidurans Metal Resistance Genes.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0034322}, doi = {10.1128/jb.00343-22}, pmid = {36892288}, issn = {1098-5530}, abstract = {Metal resistance of Cupriavidus metallidurans is based on determinants that were acquired in the past by horizontal gene transfer during evolution. Some of these determinants encode transmembrane metal efflux systems. Expression of most of the respective genes is controlled by two-component regulatory systems composed of a membrane-bound sensor/sensory histidine kinase (HK) and a cytoplasmic, DNA-binding response regulator (RR). Here, we investigated the interplay between the three closely related two-component regulatory systems CzcRS, CzcR2S2, and AgrRS. All three systems regulate the response regulator CzcR, while the RRs AgrR and CzcR2 were not involved in czc regulation. Target promoters were czcNp and czcPp for genes upstream and downstream of the central czc gene region. The two systems together repressed CzcRS-dependent upregulation of czcP-lacZ at low zinc concentrations in the presence of CzcS but activated this signal transmission at higher zinc concentrations. AgrRS and CzcR2S2 interacted to quench CzcRS-mediated expression of czcNp-lacZ and czcPp-lacZ. Together, cross talk between the three two-component regulatory systems enhanced the capabilities of the Czc systems by controlling expression of the additional genes czcN and czcP. IMPORTANCE Bacteria are able to acquire genes encoding resistance to metals and antibiotics by horizontal gene transfer. To bestow an evolutionary advantage on their host cell, new genes must be expressed, and their expression should be regulated so that resistance-mediating proteins are produced only when needed. Newly acquired regulators may interfere with those already present in a host cell. Such an event was studied here in the metal-resistant bacterium Cupriavidus metallidurans. The results demonstrate how regulation by the acquired genes interacts with the host's extant regulatory network. This leads to emergence of a new system level of complexity that optimizes the response of the cell to periplasmic signals.}, }
@article {pmid36892285, year = {2023}, author = {Brown, PJB and Chang, JH and Fuqua, C}, title = {Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0000523}, doi = {10.1128/jb.00005-23}, pmid = {36892285}, issn = {1098-5530}, abstract = {Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.}, }
@article {pmid36892101, year = {2023}, author = {Sun, H and Li, H and Zhang, X and Liu, Y and Chen, H and Zheng, L and Zhai, Y and Zheng, H}, title = {The honeybee gut resistome and its role in antibiotic resistance dissemination.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12714}, pmid = {36892101}, issn = {1749-4877}, abstract = {There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.}, }
@article {pmid36889142, year = {2023}, author = {Hussain, M and Etebari, K and Asgari, S}, title = {Analysing inhibition of dengue virus in Wolbachia-infected mosquito cells following the removal of Wolbachia.}, journal = {Virology}, volume = {581}, number = {}, pages = {48-55}, doi = {10.1016/j.virol.2023.02.017}, pmid = {36889142}, issn = {1096-0341}, mesh = {Animals ; *Dengue Virus/physiology ; *Wolbachia/physiology ; Virus Replication ; *RNA Viruses/genetics ; *Aedes ; *Dengue ; }, abstract = {Wolbachia pipientis is known to block replication of positive sense RNA viruses. Previously, we created an Aedes aegypti Aag2 cell line (Aag2.wAlbB) transinfected with the wAlbB strain of Wolbachia and a matching tetracycline-cured Aag2.tet cell line. While dengue virus (DENV) was blocked in Aag2.wAlbB cells, we found significant inhibition of DENV in Aag2.tet cells. RNA-Seq analysis of the cells confirmed removal of Wolbachia and lack of expression of Wolbachia genes that could have been due to lateral gene transfer in Aag2.tet cells. However, we noticed a substantial increase in the abundance of phasi charoen-like virus (PCLV) in Aag2.tet cells. When RNAi was used to reduce the PCLV levels, DENV replication was significantly increased. Further, we found significant changes in the expression of antiviral and proviral genes in Aag2.tet cells. Overall, the results reveal an antagonistic interaction between DENV and PCLV and how PCLV-induced changes could contribute to DENV inhibition.}, }
@article {pmid36889077, year = {2023}, author = {Yang, X and Niu, Y and Yang, Y and Zhou, H and Li, J and Fu, X and Shen, Z and Wang, J and Qiu, Z}, title = {Pheromone effect of estradiol regulates the conjugative transfer of pCF10 carrying antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131087}, doi = {10.1016/j.jhazmat.2023.131087}, pmid = {36889077}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/metabolism ; *Pheromones/pharmacology/genetics/metabolism ; Estradiol/pharmacology/metabolism ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; Enterococcus faecalis/genetics/metabolism ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) mediated by conjugative plasmids greatly contributes to bacteria evolution and the transmission of antibiotic resistance genes (ARGs). In addition to the selective pressure imposed by extensive antibiotic use, environmental chemical pollutants facilitate the dissemination of antibiotic resistance, consequently posing a serious threat to the ecological environment. Presently, the majority of studies focus on the effects of environmental compounds on R plasmid-mediated conjugation transfer, and pheromone-inducible conjugation has largely been neglected. In this study, we explored the pheromone effect and potential molecular mechanisms of estradiol in promoting the conjugative transfer of pCF10 plasmid in Enterococcus faecalis. Environmentally relevant concentrations of estradiol significantly increased the conjugative transfer of pCF10 with a maximum frequency of 3.2 × 10[-2], up to 3.5-fold change compared to that of control. Exposure to estradiol induced the activation of pheromone signaling cascade by increasing the expression of ccfA. Furthermore, estradiol might directly bind to the pheromone receptor PrgZ and promote pCF10 induction and finally enhance the conjugative transfer of pCF10. These findings cast valuable insights on the roles of estradiol and its homolog in increasing antibiotic resistance and the potential ecological risk.}, }
@article {pmid36881118, year = {2023}, author = {Veremeichik, GN and Bulgakov, DV and Solomatina, TO and Makhazen, DS}, title = {In the interkingdom horizontal gene transfer, the small rolA gene is a big mystery.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {7-8}, pages = {2097-2109}, pmid = {36881118}, issn = {1432-0614}, mesh = {Plants, Genetically Modified ; *Gene Transfer, Horizontal ; DNA ; Genetic Engineering ; Oncogenes ; *Rhizobium/genetics ; }, abstract = {The biological function of the agrobacterial oncogene rolA is very poorly understood compared to other components of the mechanism of horizontal gene transfer during agrobacterial colonization of plants. Research groups around the world have worked on this problem, and available information is reviewed in this review, but other rol oncogenes have been studied much more thoroughly. Having one unexplored element makes it impossible to form a complete picture. However, the limited data suggest that the rolA oncogene and its regulatory apparatus have great potential in plant biotechnology and genetic engineering. Here, we collect and discuss available experimental data about the function and structure of rolA. There is still no clear understanding of the mechanism of RolA and its structure and localization. We believe this is because of the nucleotide structure of a frameshift in the most well-studied rolA gene of the agropine type pRi. In fact, interest in the genes of agrobacteria as natural tools for the phenotypic or biochemical engineering of plants increased. We believe that a detailed understanding of the molecular mechanisms will be forthcoming. KEY POINTS: • Among pRi T-DNA oncogenes, rolA is the least understood in spite of many studies. • Frameshift may be the reason for the failure to elucidate the role of agropine rolA. • Understanding of rolA is promising for the phenotypic and biochemical engineering of plants.}, }
@article {pmid36880348, year = {2023}, author = {Tholl, D and Rebholz, Z and Morozov, AV and O'Maille, PE}, title = {Terpene synthases and pathways in animals: enzymology and structural evolution in the biosynthesis of volatile infochemicals.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d2np00076h}, pmid = {36880348}, issn = {1460-4752}, abstract = {Covering: up to the beginning of 2023Many animals release volatile or semi-volatile terpenes as semiochemicals in intra- and inter-specific interactions. Terpenes are important constituents of pheromones and serve as chemical defenses to ward off predators. Despite the occurrence of terpene specialized metabolites from soft corals to mammals, the biosynthetic origin of these compounds has largely remained obscure. An increasing number of animal genome and transcriptome resources is facilitating the identification of enzymes and pathways that allow animals to produce terpenes independent of their food sources or microbial endosymbionts. Substantial evidence has emerged for the presence of terpene biosynthetic pathways such as in the formation of the iridoid sex pheromone nepetalactone in aphids. In addition, terpene synthase (TPS) enzymes have been discovered that are evolutionary unrelated to canonical plant and microbial TPSs and instead resemble precursor enzymes called isoprenyl diphosphate synthases (IDSs) in central terpene metabolism. Structural modifications of substrate binding motifs in canonical IDS proteins presumably facilitated the transition to TPS function at an early state in insect evolution. Other arthropods such as mites appear to have adopted their TPS genes from microbial sources via horizontal gene transfer. A similar scenario likely occurred in soft corals, where TPS families with closer resemblance to microbial TPSs have been discovered recently. Together, these findings will spur the identification of similar or still unknown enzymes in terpene biosynthesis in other lineages of animals. They will also help develop biotechnological applications for animal derived terpenes of pharmaceutical value or advance sustainable agricultural practices in pest management.}, }
@article {pmid36878032, year = {2023}, author = {Yu, X and Zhou, ZC and Shuai, XY and Lin, ZJ and Liu, Z and Zhou, JY and Lin, YH and Zeng, GS and Ge, ZY and Chen, H}, title = {Microplastics exacerbate co-occurrence and horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131130}, doi = {10.1016/j.jhazmat.2023.131130}, pmid = {36878032}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Genes, Bacterial ; Plastics/analysis ; Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×10[8] copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4-1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.}, }
@article {pmid36874978, year = {2023}, author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA}, title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14924}, pmid = {36874978}, issn = {2167-8359}, mesh = {*Ecotype ; Phylogeny ; *Genes, Viral ; Genome, Viral ; Cycadopsida ; }, abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.<br><br>METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.<br><br>RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.<br><br>CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.}, }
@article {pmid36871940, year = {2023}, author = {Yan, K and Wei, M and Li, F and Wu, C and Yi, S and Tian, J and Liu, Y and Lu, H}, title = {Diffusion and enrichment of high-risk antibiotic resistance genes (ARGs) via the transmission chain (mulberry leave, guts and feces of silkworm, and soil) in an ecological restoration area of manganese mining, China: Role of heavy metals.}, journal = {Environmental research}, volume = {225}, number = {}, pages = {115616}, doi = {10.1016/j.envres.2023.115616}, pmid = {36871940}, issn = {1096-0953}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bombyx/genetics ; Manganese ; Genes, Bacterial ; *Morus/genetics ; Soil ; Escherichia coli ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/toxicity ; Feces ; Mining ; }, abstract = {This study investigated the diffusion and enrichment of antibiotic resistance genes (ARGs) and pathogens via the transmission chain (mulberry leaves - silkworm guts - silkworm feces - soil) near a manganese mine restoration area (RA) and control area (CA, away from RA). Horizontal gene transfer (HGT) of ARGs was testified by an IncP a-type broad host range plasmid RP4 harboring ARGs (tetA) and conjugative genes (e.g., korB, trbA, and trbB) as an indicator. Compared to leaves, the abundances of ARGs and pathogens in feces after silkworms ingested leaves from RA increased by 10.8% and 52.3%, respectively, whereas their abundance in feces from CA dropped by 17.1% and 97.7%, respectively. The predominant ARG types in feces involved the resistances to β-lactam, quinolone, multidrug, peptide, and rifamycin. Therein, several high-risk ARGs (e.g., qnrB, oqxA, and rpoB) carried by pathogens were more enriched in feces. However, HGT mediated by plasmid RP4 in this transmission chain was not a main factor to promote the enrichment of ARGs due to the harsh survival environment of silkworm guts for the plasmid RP4 host E. coli. Notably, Zn, Mn, and As in feces and guts promoted the enrichment of qnrB and oqxA. Worriedly, the abundance of qnrB and oqxA in soil increased by over 4-fold after feces from RA were added into soil for 30 days regardless of feces with or without E. coli RP4. Overall, ARGs and pathogens could diffuse and enrich in environment via the sericulture transmission chain developed at RA, especially some high-risk ARGs carried by pathogens. Thus, greater attentions should be paid to dispel such high-risk ARGs to support benign development of sericulture industry in the safe utilization of some RAs.}, }
@article {pmid36871872, year = {2023}, author = {Henoun Loukili, N and Loquet, A and Perrin, A and Gaillot, O and Bruandet, A and Sendid, B and Zahar, JR and Nseir, S}, title = {Time to intestinal clearance of carbapenemase-producing Enterobacterales in hospital patients: a longitudinal retrospective observational cohort study.}, journal = {The Journal of hospital infection}, volume = {135}, number = {}, pages = {4-10}, doi = {10.1016/j.jhin.2023.01.022}, pmid = {36871872}, issn = {1532-2939}, abstract = {BACKGROUND: Intestinal clearance of carbapenemase-producing Enterobacterales (CPE-IC) is a cornerstone to discontinue isolation precautions for CPE patients in hospitals. This study aimed to evaluate the time to spontaneous CPE-IC and identify its potential associated risk factors.<br><br>METHODS: This retrospective cohort study was carried out between January 2018 and September 2020 on all patients in a 3200-bed teaching referral hospital with confirmed CPE intestinal carriage. CPE-IC was defined as at least three consecutive CPE-negative rectal swab cultures without a subsequent positive result. A survival analysis was performed to determine the median time to CPE-IC. A multivariate Cox model was implemented to explore the factors associated with CPE-IC.<br><br>RESULTS: A total of 110 patients were positives for CPE, of whom 27 (24.5%) achieved CPE-IC. Median time to CPE-IC was 698 days. Univariate analysis showed that female sex (P=0.046), multiple CPE-species in index cultures (P=0.005), Escherichia coli or Klebsiella spp. (P=0.001 and P=0.028, respectively) were significantly associated with the time to CPE-IC. Multivariate analysis highlighted that identification of E. coli carbapenemase-producing or CPEs harbouring ESBL genes in index culture extended the median time to CPE-IC, respectively (adjusted hazard ratio (aHR)&#xa0;= 0.13 (95% confidence interval: 0.04-0.45]; P=0.001 and aHR&#xa0;= 0.34 (95% confidence interval: 0.12-0.90); P=0.031).<br><br>CONCLUSION: Intestinal decolonization of CPE can take several months to years to occur. Carbapenemase-producing E.&#xa0;coli are likely to play a key role in delaying intestinal decolonization, probably through horizontal gene transfer between species. Therefore, discontinuation of isolation precautions in CPE-patients should be considered with caution.}, }
@article {pmid36867924, year = {2023}, author = {Mirtaleb, MS and Falak, R and Heshmatnia, J and Bakhshandeh, B and Taheri, RA and Soleimanjahi, H and Zolfaghari Emameh, R}, title = {An insight overview on COVID-19 mRNA vaccines: Advantageous, pharmacology, mechanism of action, and prospective considerations.}, journal = {International immunopharmacology}, volume = {117}, number = {}, pages = {109934}, pmid = {36867924}, issn = {1878-1705}, mesh = {Humans ; COVID-19 Vaccines ; *COVID-19/prevention &amp; control ; Pandemics/prevention &amp; control ; Prospective Studies ; SARS-CoV-2 ; RNA, Messenger ; mRNA Vaccines ; *Viral Vaccines ; }, abstract = {The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has urged scientists to present some novel vaccine platforms during this pandemic to provide a rather prolonged immunity against this respiratory viral infection. In spite of many campaigns formed against the administration of mRNA-based vaccines, those platforms were the most novel types, which helped us meet the global demand by developing protection against COVID-19 and reducing the development of severe forms of this respiratory viral infection. Some societies are worry about the COVID-19 mRNA vaccine administration and the potential risk of genetic integration of inoculated mRNA into the human genome. Although the efficacy and long-term safety of mRNA vaccines have not yet been fully clarified, obviously their application has switched the mortality and morbidity of the COVID-19 pandemic. This study describes the structural features and technologies used in producing of COVID-19 mRNA-based vaccines as the most influential factor in controlling this pandemic and a successful pattern for planning to produce other kind of genetic vaccines against infections or cancers.}, }
@article {pmid36864029, year = {2023}, author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C}, title = {Population-level impacts of antibiotic usage on the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1191}, pmid = {36864029}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Metagenome/genetics ; Genome, Human ; }, abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.}, }
@article {pmid36863279, year = {2023}, author = {Zhang, H and Song, J and Zheng, Z and Li, T and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H}, title = {Fungicide exposure accelerated horizontal transfer of antibiotic resistance genes via plasmid-mediated conjugation.}, journal = {Water research}, volume = {233}, number = {}, pages = {119789}, doi = {10.1016/j.watres.2023.119789}, pmid = {36863279}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; *Fungicides, Industrial ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {Co-pollution of soil with pesticide residues and antibiotic resistance genes (ARGs) is increasing due to the substantial usage of pesticides and organic fertilizers in greenhouse-based agricultural production. Non-antibiotic stresses, including those from agricultural fungicides, are potential co-selectors for the horizontal transfer of ARGs, but the underlying mechanism remains unclear. Intragenus and intergenus conjugative transfer systems of the antibiotic resistant plasmid RP4 were established to examine conjugative transfer frequency under stress from four widely used fungicides: triadimefon, chlorothalonil, azoxystrobin, and carbendazim. The mechanisms were elucidated at the cellular and molecular levels using transmission electron microscopy, flow cytometry, RT-qPCR, and RNA-seq techniques. The conjugative transfer frequency of plasmid RP4 between Escherichia coli strains increased with the rising exposure concentrations of chlorothalonil, azoxystrobin, and carbendazim, but was suppressed between E. coli and Pseudomonas putida by a high fungicide concentration (10 µg/mL). Triadimefon did not significantly affect conjugative transfer frequency. Exploration of the underlying mechanisms revealed that: (i) chlorothalonil exposure mainly promoted generation of intracellular reactive oxygen species, stimulated the SOS response, and increased cell membrane permeability, while (ii) azoxystrobin and carbendazim primarily enhanced expression of conjugation-related genes on the plasmid. These findings reveal the fungicide-triggered mechanisms associated with plasmid conjugation and highlight the potential role of non-bactericidal pesticides on the dissemination of ARGs.}, }
@article {pmid36863168, year = {2023}, author = {Horne, T and Orr, VT and Hall, JP}, title = {How do interactions between mobile genetic elements affect horizontal gene transfer?.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102282}, doi = {10.1016/j.mib.2023.102282}, pmid = {36863168}, issn = {1879-0364}, abstract = {Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.}, }
@article {pmid36863149, year = {2023}, author = {Zhang, Y and Xiang, Y and Xu, R and Huang, J and Deng, J and Zhang, X and Wu, Z and Huang, Z and Yang, Z and Xu, J and Xiong, W and Li, H}, title = {Magnetic biochar promotes the risk of mobile genetic elements propagation in sludge anaerobic digestion.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117492}, doi = {10.1016/j.jenvman.2023.117492}, pmid = {36863149}, issn = {1095-8630}, mesh = {*Sewage ; *Genes, Bacterial ; Anaerobiosis ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences ; Magnetic Phenomena ; Manure/microbiology ; }, abstract = {Mobile genetic elements (MGEs) mediated horizontal gene transfer is the primary reason for the propagation of antibiotic resistance genes in environment. The behavior of MGEs under magnetic biochar pressure in sludge anaerobic digestion (AD) is still unknown. This study evaluated the effects of different dosage magnetic biochar on the MGEs in AD reactors. The results showed that the biogas yield was highest (106.68 ± 1.16 mL g[-1] VSadded) with adding optimal dosage of magnetic biochar (25 mg g[-1] TSadded), due to it increased the microorganism's abundance involved in hydrolysis and methanogenesis. While, the total absolute abundance of MGEs in the reactors with magnetic biochar addition increased by 11.58%-77.37% compared with the blank reactor. When the dosage of magnetic biochar was 12.5 mg g[-1] TSadded, the relative abundance of most MGEs was the highest. The enrichment effect on ISCR1 was the most significant, and the enrichment rate reached 158.90-214.16%. Only the intI1 abundance was reduced and the removal rates yield 14.38-40.00%, which was inversely proportional to the dosage of magnetic biochar. Co-occurrence network explored that Proteobacteria (35.64%), Firmicutes (19.80%) and Actinobacteriota (15.84%) were the main potential host of MGEs. Magnetic biochar changed MGEs abundance by affecting the potential MGEs-host community structure and abundance. Redundancy analysis and variation partitioning analysis showed that the combined effect of polysaccharides, protein and sCOD exhibited the greatest contribution (accounted for 34.08%) on MGEs variation. These findings demonstrated that magnetic biochar increases the risk of MGEs proliferation in AD system.}, }
@article {pmid36858028, year = {2023}, author = {Martins, SJ and Pasche, JM and Silva, HA and Selten, GG and Savastano, N and Abreu, L and Bais, H and Garrett, KA and Kraisitudomsook, N and Pieterse, CMJ and Cernava, T}, title = {The Use of Synthetic Microbial Communities (SynComs) to Improve Plant Health.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-01-23-0016-IA}, pmid = {36858028}, issn = {0031-949X}, abstract = {Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites and ability to induce plant resistance are some of the microbial traits to take into consideration when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors, as compared to the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability are still some of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.}, }
@article {pmid36853054, year = {2023}, author = {Du, Y and Zou, J and Yin, Z and Chen, T}, title = {Pan-Chromosome and Comparative Analysis of Agrobacterium fabrum Reveal Important Traits Concerning the Genetic Diversity, Evolutionary Dynamics, and Niche Adaptation of the Species.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0292422}, pmid = {36853054}, issn = {2165-0497}, abstract = {Agrobacterium fabrum has been critical for the development of plant genetic engineering and agricultural biotechnology due to its ability to transform eukaryotic cells. However, the gene composition, evolutionary dynamics, and niche adaptation of this species is still unknown. Therefore, we established a comparative genomic analysis based on a pan-chromosome data set to evaluate the genetic diversity of A. fabrum. Here, 25 A. fabrum genomes were selected for analysis by core genome phylogeny combined with the average nucleotide identity (ANI), amino acid identity (AAI), and in silico DNA-DNA hybridization (DDH) values. An open pan-genome of A. fabrum exhibits genetic diversity with variable accessorial genes as evidenced by a consensus pan-genome of 12 representative genomes. The genomic plasticity of A. fabrum is apparent in its putative sequences for mobile genetic elements (MGEs), limited horizontal gene transfer barriers, and potentially horizontally transferred genes. The evolutionary constraints and functional enrichment in the pan-chromosome were measured by the Clusters of Orthologous Groups (COG) categories using eggNOG-mapper software, and the nonsynonymous/synonymous rate ratio (dN/dS) was determined using HYPHY software. Comparative analysis revealed significant differences in the functional enrichment and the degree of purifying selection between the core genome and non-core genome. We demonstrate that the core gene families undergo stronger purifying selection but have a significant bias to contain one or more positively selected sites. Furthermore, although they shared similar genetic diversity, we observed significant differences between chromosome 1 (Chr I) and the chromid in their functional features and evolutionary constraints. We demonstrate that putative genetic elements responsible for plant infection, ecological adaptation, and speciation represent the core genome, highlighting their importance in the adaptation of A. fabrum to plant-related niches. Our pan-chromosome analysis of A. fabrum provides comprehensive insights into the genetic properties, evolutionary patterns, and niche adaptation of the species. IMPORTANCE Agrobacterium spp. live in diverse plant-associated niches such as soil, the rhizosphere, and vegetation, which are challenged by multiple stressors such as diverse energy sources, plant defenses, and microbial competition. They have evolved the ability to utilize diverse resources, escape plant defenses, and defeat competitors. However, the underlying genetic diversity and evolutionary dynamics of Agrobacterium spp. remain unexplored. We examined the phylogeny and pan-genome of A. fabrum to define intraspecies evolutionary relationships. Our results indicate an open pan-genome and numerous MGEs and horizontally transferred genes among A. fabrum genomes, reflecting the flexibility of the chromosomes and the potential for genetic exchange. Furthermore, we observed significant differences in the functional features and evolutionary constraints between the core and accessory genomes and between Chr I and the chromid, respectively.}, }
@article {pmid36851563, year = {2023}, author = {Elois, MA and Silva, RD and Pilati, GVT and Rodríguez-Lázaro, D and Fongaro, G}, title = {Bacteriophages as Biotechnological Tools.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851563}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics ; Prophages ; Lysogeny ; Biofilms ; Biotechnology ; }, abstract = {Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.}, }
@article {pmid36847532, year = {2023}, author = {Cooke, MB and Herman, C}, title = {Conjugation's Toolkit: the Roles of Nonstructural Proteins in Bacterial Sex.}, journal = {Journal of bacteriology}, volume = {205}, number = {3}, pages = {e0043822}, pmid = {36847532}, issn = {1098-5530}, support = {DP1 AI152073/AI/NIAID NIH HHS/United States ; }, mesh = {Plasmids ; *Type IV Secretion Systems/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial conjugation, a form of horizontal gene transfer, relies on a type 4 secretion system (T4SS) and a set of nonstructural genes that are closely linked. These nonstructural genes aid in the mobile lifestyle of conjugative elements but are not part of the T4SS apparatus for conjugative transfer, such as the membrane pore and relaxosome, or the plasmid maintenance and replication machineries. While these nonstructural genes are not essential for conjugation, they assist in core conjugative functions and mitigate the cellular burden on the host. This review compiles and categorizes known functions of nonstructural genes by the stage of conjugation they modulate: dormancy, transfer, and new host establishment. Themes include establishing a commensalistic relationship with the host, manipulating the host for efficient T4SS assembly and function and assisting in conjugative evasion of recipient cell immune functions. These genes, taken in a broad ecological context, play important roles in ensuring proper propagation of the conjugation system in a natural environment.}, }
@article {pmid36844929, year = {2023}, author = {Nielsen, FD and Møller-Jensen, J and Jørgensen, MG}, title = {Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1074212}, pmid = {36844929}, issn = {2673-7647}, abstract = {Introduction: Whole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. Methods/Results: In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Discussion: Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.}, }
@article {pmid36841913, year = {2023}, author = {Stockdale, SR and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O' Regan, O and Nolan, JA and Sutton, TDS and Clooney, AG and Ryan, FJ and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C}, title = {Interpersonal variability of the human gut virome confounds disease signal detection in IBD.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {221}, pmid = {36841913}, issn = {2399-3642}, mesh = {Humans ; Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Viruses/genetics ; *Colitis, Ulcerative/genetics/microbiology ; *Inflammatory Bowel Diseases/genetics ; }, abstract = {Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and β-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.}, }
@article {pmid36840598, year = {2023}, author = {Densi, A and Iyer, RS and Bhat, PJ}, title = {Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0384722}, pmid = {36840598}, issn = {2165-0497}, abstract = {Ammonium transporters are present in all three domains of life. They have undergone extensive horizontal gene transfer (HGT), gene duplication, and functional diversification and therefore offer an excellent paradigm to study protein evolution. We attempted to complement a mep1Δmep2Δmep3Δ strain of Saccharomyces cerevisiae (triple-deletion strain), which otherwise cannot grow on ammonium as a sole nitrogen source at concentrations of <3 mM, with amtA of Dictyostelium discoideum, an orthologue of S. cerevisiae MEP2. We observed that amtA did not complement the triple-deletion strain of S. cerevisiae for growth on low-ammonium medium. We isolated two mutant derivatives of amtA (amtA M1 and amtA M2) from a PCR-generated mutant plasmid library that complemented the triple-deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions, which are necessary for its functionality. amtA M2 bears two nonsynonymous substitutions and one synonymous substitution, all of which are necessary for functionality. Interestingly, AmtA M1 transports ammonium but does not confer methylamine toxicity, while AmtA M2 transports ammonium and confers methylamine toxicity, demonstrating functional diversification. Preliminary biochemical analyses indicated that the mutants differ in their conformations as well as their mechanisms of ammonium transport. These intriguing results clearly point out that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions in isolation. The above-described observations have significant implications for various facets of biological processes and are discussed in detail. IMPORTANCE Functional diversification following gene duplication is one of the major driving forces of protein evolution. While the role of nonsynonymous substitutions in the functional diversification of proteins is well recognized, knowledge of the role of synonymous substitutions in protein evolution is in its infancy. Using functional complementation, we isolated two functional alleles of the D. discoideum ammonium transporter gene (amtA), which otherwise does not function in S. cerevisiae as an ammonium transporters. One of them is an ammonium transporter, while the other is an ammonium transporter that also confers methylammonium (ammonium analogue) toxicity, suggesting functional diversification. Surprisingly, both alleles require a combination of synonymous and nonsynonymous substitutions for their functionality. These results bring out a hitherto-unknown pathway of protein evolution and pave the way for not only understanding protein evolution but also interpreting single nucleotide polymorphisms (SNPs).}, }
@article {pmid36840559, year = {2023}, author = {Winter, M and Harms, K and Johnsen, P and Vos, M}, title = {Collection of Annotated Acinetobacter Genome Sequences.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0109422}, pmid = {36840559}, issn = {2576-098X}, abstract = {The genus Acinetobacter contains environmental species as well as opportunistic pathogens of humans. Several species are competent for natural transformation, an important mechanism of horizontal gene transfer. Here, we present the genome sequences of 19 Acinetobacter strains used in past and upcoming studies of natural transformation.}, }
@article {pmid36838481, year = {2023}, author = {Tsilipounidaki, K and Florou, Z and Skoulakis, A and Fthenakis, GC and Miriagou, V and Petinaki, E}, title = {Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838481}, issn = {2076-2607}, abstract = {The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.}, }
@article {pmid36838414, year = {2023}, author = {Zayed, AR and Bitar, DM and Steinert, M and Lück, C and Spröer, C and Brettar, I and Höfle, MG and Bunk, B}, title = {Comparative Genomics of Legionella pneumophila Isolates from the West Bank and Germany Support Molecular Epidemiology of Legionnaires' Disease.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838414}, issn = {2076-2607}, abstract = {Legionella pneumophila is an environmental bacterium and clinical pathogen that causes many life-threating outbreaks of an atypical pneumonia called Legionnaires' disease (LD). Studies of this pathogen have focused mainly on Europe and the United States. A shortage in L. pneumophila data is clearly observed for developing countries. To reduce this knowledge gap, L. pneumophila isolates were studied in two widely different geographical areas, i.e., the West Bank and Germany. For this study, we sequenced and compared the whole genome of 38 clinical and environmental isolates of L. pneumophila covering different MLVA-8(12) genotypes in the two areas. Sequencing was conducted using the Illumina HiSeq 2500 platform. In addition, two isolates (A194 and H3) were sequenced using a Pacific Biosciences (PacBio) RSII platform to generate complete reference genomes from each of the geographical areas. Genome sequences from 55 L. pneumophila strains, including 17 reference strains, were aligned with the genome sequence of the closest strain (L. pneumophila strain Alcoy). A whole genome phylogeny based on single nucleotide polymorphisms (SNPs) was created using the ParSNP software v 1.0. The reference genomes obtained for isolates A194 and H3 consisted of circular chromosomes of 3,467,904 bp and 3,691,263 bp, respectively. An average of 36,418 SNPs (min. 8569, max. 70,708 SNPs) against our reference strain L. pneumophila str. Alcoy, and 2367 core-genes were identified among the fifty-five strains. An analysis of the genomic population structure by SNP comparison divided the fifty-five L. pneumophila strains into six branches. Individual isolates in sub-lineages in these branches differed by less than 120 SNPs if they had the same MLVA genotype and were isolated from the same location. A bioinformatics analysis identified the genomic islands (GIs) for horizontal gene transfer and mobile genetic elements, demonstrating that L. pneumophila showed high genome plasticity. Four L. pneumophila isolates (H3, A29, A129 and L10-091) contained well-defined plasmids. On average, only about half of the plasmid genes could be matched to proteins in databases. In silico phage findings suggested that 43 strains contained at least one phage. However, none of them were found to be complete. BLASTp analysis of proteins from the type IV secretion Dot/Icm system showed those proteins highly conserved, with less than 25% structural differences in the new L. pneumophila isolates. Overall, we demonstrated that whole genome sequencing provides a molecular surveillance tool for L. pneumophila at the highest conceivable discriminatory level, i.e., two to eight SNPs were observed for isolates from the same location but several years apart.}, }
@article {pmid36838403, year = {2023}, author = {Hirose, J}, title = {Diversity and Evolution of Integrative and Conjugative Elements Involved in Bacterial Aromatic Compound Degradation and Their Utility in Environmental Remediation.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838403}, issn = {2076-2607}, abstract = {Integrative and conjugative elements (ICEs) are mobile DNA molecules that can be transferred through excision, conjugation, and integration into chromosomes. They contribute to the horizontal transfer of genomic islands across bacterial species. ICEs carrying genes encoding aromatic compound degradation pathways are of interest because of their contribution to environmental remediation. Recent advances in DNA sequencing technology have increased the number of newly discovered ICEs in bacterial genomes and have enabled comparative analysis of their evolution. The two different families of ICEs carry various aromatic compound degradation pathway genes. ICEclc and its related ICEs contain a number of members with diverse catabolic capabilities. In addition, the Tn4371 family, which includes ICEs that carry the chlorinated biphenyl catabolic pathway, has been identified. It is apparent that they underwent evolution through the acquisition, deletion, or exchange of modules to adapt to an environmental niche. ICEs have the property of both stability and mobility in the chromosome. Perspectives on the use of ICEs in environmental remediation are also discussed.}, }
@article {pmid36838273, year = {2023}, author = {Werner, KA and Feyen, L and Hübner, T and Brüggemann, N and Prost, K and Grohmann, E}, title = {Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838273}, issn = {2076-2607}, abstract = {Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes blaCTX-M, blaIMP, and blaTEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in blaCTX-M and blaTEM copy numbers and a mean increase in blaIMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.}, }
@article {pmid36835573, year = {2023}, author = {Ngcobo, PE and Nkosi, BVZ and Chen, W and Nelson, DR and Syed, K}, title = {Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835573}, issn = {1422-0067}, mesh = {Humans ; *Ferredoxins/metabolism ; *Archaea/metabolism ; Phylogeny ; Oxidation-Reduction ; Cytochrome P-450 Enzyme System/metabolism ; Bacteria/metabolism ; }, abstract = {Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study's results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.}, }
@article {pmid36833369, year = {2023}, author = {Wittich, RM and Haïdour, A and Aguilar-Romero, I and de la Torre-Zúñiga, J and van Dillewijn, P}, title = {Biodegradation of Microtoxic Phenylpropanoids (Phenylpropanoic Acid and Ibuprofen) by Bacteria and the Relevance for Their Removal from Wastewater Treatment Plants.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833369}, issn = {2073-4425}, mesh = {*Ibuprofen/chemistry/metabolism ; Anti-Inflammatory Agents, Non-Steroidal ; Bacteria/metabolism ; Biodegradation, Environmental ; *Water Purification ; }, abstract = {The NSAID ibuprofen (2-(4-isobutylphenyl)propanoic acid) and the structurally related 3-phenylpropanoic acid (3PPA), are widely used pharmaceutical and personal care products (PPCPs) which enter municipal waste streams but whose relatively low rates of elimination by wastewater treatment plants (WWTPs) are leading to the contamination of aquatic resources. Here, we report the isolation of three bacterial strains from a municipal WWTP, which as a consortium are capable of mineralizing ibuprofen. These were identified as the Pseudomonas citronellolis species, termed RW422, RW423 and RW424, in which the first two of these isolates were shown to contain the catabolic ipf operon responsible for the first steps of ibuprofen mineralization. These ipf genes which are associated with plasmids could, experimentally, only be transferred between other Sphingomonadaceae species, such as from the ibuprofen degrading Sphingopyxis granuli RW412 to the dioxins degrading Rhizorhabdus wittichii RW1, generating RW421, whilst a transfer from the P. citronellolis isolates to R. wittichii RW1 was not observed. RW412 and its derivative, RW421, as well as the two-species consortium RW422/RW424, can also mineralize 3PPA. We show that IpfF can convert 3PPA to 3PPA-CoA; however, the growth of RW412 with 3PPA produces a major intermediate that was identified by NMR to be cinnamic acid. This and the identification of other minor products from 3PPA allows us to propose the major pathway used by RW412 to mineralize 3PPA. Altogether, the findings in this study highlight the importance of ipf genes, horizontal gene transfer, and alternative catabolic pathways in the bacterial populations of WWTPs to eliminate ibuprofen and 3PPA.}, }
@article {pmid36833214, year = {2023}, author = {Gosselin, SP and Arsenault, DR and Jennings, CA and Gogarten, JP}, title = {The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833214}, issn = {2073-4425}, mesh = {*Evolution, Molecular ; *Inteins/genetics ; Gene Transfer, Horizontal ; Endonucleases/genetics ; DNA ; }, abstract = {Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction-modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.}, }
@article {pmid36833201, year = {2023}, author = {Liu, S and Jiao, J and Tian, CF}, title = {Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833201}, issn = {2073-4425}, mesh = {*Rhizobium/genetics ; Symbiosis/genetics ; Gene Transfer, Horizontal ; Ecosystem ; Nitrogen Fixation/genetics ; *Fabaceae/microbiology ; }, abstract = {There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.}, }
@article {pmid36830600, year = {2023}, author = {Zhao, B and van Bodegom, PM and Trimbos, KB}, title = {Antibiotic Resistance Genes in Interconnected Surface Waters as Affected by Agricultural Activities.}, journal = {Biomolecules}, volume = {13}, number = {2}, pages = {}, pmid = {36830600}, issn = {2218-273X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial ; Sulfonamides/pharmacology ; }, abstract = {Pastures have become one of the most important sources of antibiotic resistance genes (ARGs) pollution, bringing risks to human health through the environment and the food that is grown there. Another significant source of food production is greenhouse horticulture, which is typically located near pastures. Through waterways, pasture-originated ARGs may transfer to the food in greenhouses. However, how these pasture-originated ARGs spread to nearby waterways and greenhouses has been much less investigated, while this may pose risks to humans through agricultural products. We analyzed 29 ARGs related to the most used antibiotics in livestock in the Netherlands at 16 locations in an agricultural area, representing pastures, greenhouses and lakes. We found that ARGs were prevalent in all surface waters surrounding pastures and greenhouses and showed a similar composition, with sulfonamide ARGs being dominant. This indicates that both pastures and greenhouses cause antibiotic resistance pressures on neighboring waters. However, lower pressures were found in relatively larger and isolated lakes, suggesting that a larger water body or a non-agricultural green buffer zone could help reducing ARG impacts from agricultural areas. We also observed a positive relationship between the concentrations of the class 1 integron (intl1 gene)-used as a proxy for horizontal gene transfer-and ARG concentration and composition. This supports that horizontal gene transfer might play a role in dispersing ARGs through landscapes. In contrast, none of the measured four abiotic factors (phosphate, nitrate, pH and dissolved oxygen) showed any impact on ARG concentrations. ARGs from different classes co-occurred, suggesting simultaneous use of different antibiotics. Our findings help to understand the spatial patterns of ARGs, specifically the impacts of ARGs from pastures and greenhouses on each other and on nearby waterways. In this way, this study guides management aiming at reducing ARGs' risk to human health from agricultural products.}, }
@article {pmid36830312, year = {2023}, author = {Bunduruș, IA and Balta, I and Ștef, L and Ahmadi, M and Peț, I and McCleery, D and Corcionivoschi, N}, title = {Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830312}, issn = {2079-6382}, abstract = {Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.}, }
@article {pmid36830244, year = {2023}, author = {Shi, H and Hu, X and Li, W and Zhang, J and Hu, B and Lou, L}, title = {Soil Component: A Potential Factor Affecting the Occurrence and Spread of Antibiotic Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830244}, issn = {2079-6382}, abstract = {In recent years, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil have become research hotspots in the fields of public health and environmental ecosystems, but the effects of soil types and soil components on the occurrence and spread of ARGs still lack systematic sorting and in-depth research. Firstly, investigational information about ARB and ARGs contamination of soil was described. Then, existing laboratory studies about the influence of the soil component on ARGs were summarized in the following aspects: the influence of soil types on the occurrence of ARGs during natural or human activities and the control of exogenously added soil components on ARGs from the macro perspectives, the effects of soil components on the HGT of ARGs in a pure bacterial system from the micro perspectives. Following that, the similarities in pathways by which soil components affect HGT were identified, and the potential mechanisms were discussed from the perspectives of intracellular responses, plasmid activity, quorum sensing, etc. In the future, related research on multi-component systems, multi-omics methods, and microbial communities should be carried out in order to further our understanding of the occurrence and spread of ARGs in soil.}, }
@article {pmid36830238, year = {2023}, author = {Michaelis, C and Grohmann, E}, title = {Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830238}, issn = {2079-6382}, abstract = {Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.}, }
@article {pmid36830192, year = {2023}, author = {Sánchez-Osuna, M and Barbé, J and Erill, I}, title = {Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830192}, issn = {2079-6382}, abstract = {The emergence of pathogenic strains resistant to multiple antimicrobials is a pressing problem in modern healthcare. Antimicrobial resistance is mediated primarily by dissemination of resistance determinants via horizontal gene transfer. The dissemination of some resistance genes has been well documented, but few studies have analyzed the patterns underpinning the dissemination of antimicrobial resistance genes. Analyzing the %GC content of plasmid-borne antimicrobial resistance genes relative to their host genome %GC content provides a means to efficiently detect and quantify dissemination of antimicrobial resistance genes. In this work we automate %GC content analysis to perform a comprehensive analysis of known antimicrobial resistance genes in publicly available plasmid sequences. We find that the degree to which antimicrobial resistance genes are disseminated depends primarily on the resistance mechanism. Our analysis identifies conjugative plasmids as primary dissemination vectors and indicates that most broadly disseminated genes have spread from single genomic backgrounds. We show that resistance dissemination profiles vary greatly among antimicrobials, oftentimes reflecting stewardship measures. Our findings establish %GC content analysis as a powerful, intuitive and scalable method to monitor the dissemination of resistance determinants using publicly available sequence data.}, }
@article {pmid36829548, year = {2023}, author = {Tang, J and Yao, D and Zhou, H and Wang, M and Daroch, M}, title = {Distinct Molecular Patterns of Two-Component Signal Transduction Systems in Thermophilic Cyanobacteria as Revealed by Genomic Identification.}, journal = {Biology}, volume = {12}, number = {2}, pages = {}, pmid = {36829548}, issn = {2079-7737}, abstract = {Two-component systems (TCSs) play crucial roles in sensing and responding to environmental signals, facilitating the acclimation of cyanobacteria to hostile niches. To date, there is limited information on the TCSs of thermophilic cyanobacteria. Here, genome-based approaches were used to gain insights into the structure and architecture of the TCS in 17 well-described thermophilic cyanobacteria, namely strains from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. The results revealed a fascinating complexity and diversity of the TCSs. A distinct composition of TCS genes existed among these thermophilic cyanobacteria. A majority of TCS genes were classified as orphan, followed by the paired and complex cluster. A high proportion of histidine kinases (HKs) were predicted to be cytosolic subcellular localizations. Further analyses suggested diversified domain architectures of HK and response regulators (RRs), putatively in association with various functions. Comparative and evolutionary genomic analyses indicated that the horizontal gene transfer, as well as duplications events, might be involved in the evolutionary history of TCS genes in Thermostichus and Thermosynechococcus strains. A comparative analysis between thermophilic and mesophilic cyanobacteria indicated that one HK cluster and one RR cluster were uniquely shared by all the thermophilic cyanobacteria studied, while two HK clusters and one RR cluster were common to all the filamentous thermophilic cyanobacteria. These results suggested that these thermophile-unique clusters may be related to thermal characters and morphology. Collectively, this study shed light on the TCSs of thermophilic cyanobacteria, which may confer the necessary regulatory flexibility; these findings highlight that the genomes of thermophilic cyanobacteria have a broad potential for acclimations to environmental fluctuations.}, }
@article {pmid36827095, year = {2023}, author = {Pardo-De la Hoz, CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno, M and Carbone, I and Miadlikowska, J and Lutzoni, F}, title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syad008}, pmid = {36827095}, issn = {1076-836X}, abstract = {Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic datasets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic datasets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated datasets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic datasets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.}, }
@article {pmid36824529, year = {2022}, author = {Shippy, TD and Miller, S and Tamayo, B and Hosmani, PS and Flores-Gonzalez, M and Mueller, LA and Hunter, WB and Brown, SJ and D'Elia, T and Saha, S}, title = {Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri.}, journal = {GigaByte (Hong Kong, China)}, volume = {2022}, number = {}, pages = {gigabyte46}, pmid = {36824529}, issn = {2709-4715}, abstract = {Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium causing Huanglongbing, or citrus greening disease, a devastating citrus disease. We identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high-quality gene models to aid the design of interdictory molecules for pest control. We categorized the D. citri chitinases according to an established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases from known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.}, }
@article {pmid36823453, year = {2023}, author = {Webb, EA and Held, NA and Zhao, Y and Graham, ED and Conover, AE and Semones, J and Lee, MD and Feng, Y and Fu, FX and Saito, MA and Hutchins, DA}, title = {Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {15}, pmid = {36823453}, issn = {2730-6151}, abstract = {The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.}, }
@article {pmid36823299, year = {2023}, author = {Baek, MG and Kim, KW and Yi, H}, title = {Subspecies-level genome comparison of Lactobacillus delbrueckii.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3171}, pmid = {36823299}, issn = {2045-2322}, mesh = {*Lactobacillus delbrueckii/classification/genetics ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Biological Evolution ; }, abstract = {Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.}, }
@article {pmid36822312, year = {2023}, author = {Sun, L and Tang, D and Tai, X and Wang, J and Long, M and Xian, T and Jia, H and Wu, R and Ma, Y and Jiang, Y}, title = {Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121323}, doi = {10.1016/j.envpol.2023.121323}, pmid = {36822312}, issn = {1873-6424}, mesh = {*Composting ; *Manure ; *Drug Resistance, Bacterial ; Brassica/microbiology ; Interspersed Repetitive Sequences ; Soil Microbiology ; *Agriculture/methods ; *Swine ; Animals ; Soil/chemistry ; }, abstract = {The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.}, }
@article {pmid36821031, year = {2023}, author = {Milligan, EG and Calarco, J and Davis, BC and Keenum, IM and Liguori, K and Pruden, A and Harwood, VJ}, title = {A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water.}, journal = {Current environmental health reports}, volume = {}, number = {}, pages = {}, pmid = {36821031}, issn = {2196-5412}, abstract = {PURPOSE OF REVIEW: Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.<br><br>RECENT FINDINGS: Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20&#xa0;years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.}, }
@article {pmid36818863, year = {2023}, author = {Matveeva, T and Аndronov, E and Chen, K}, title = {Editorial: Rhizobiaceae mediated HGT: Facts, mechanisms, and evolutionary consequences.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1149426}, doi = {10.3389/fpls.2023.1149426}, pmid = {36818863}, issn = {1664-462X}, }
@article {pmid36813198, year = {2023}, author = {Huang, Q and Liu, Z and Guo, Y and Li, B and Yang, Z and Liu, X and Ni, J and Li, X and Zhang, X and Zhou, N and Yin, H and Jiang, C and Hao, L}, title = {Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162330}, doi = {10.1016/j.scitotenv.2023.162330}, pmid = {36813198}, issn = {1879-1026}, mesh = {*Soil ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; Coal ; }, abstract = {A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.}, }
@article {pmid36809063, year = {2023}, author = {Li, Y and Li, D and Liang, Y and Cui, J and He, K and He, D and Liu, J and Hu, G and Yuan, L}, title = {Characterization of a Tigecycline-Resistant and blaCTX-M-Bearing Klebsiella pneumoniae Strain from a Peacock in a Chinese Zoo.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0176422}, pmid = {36809063}, issn = {1098-5336}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Colistin ; Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella Infections/veterinary/microbiology ; *Klebsiella pneumoniae/drug effects/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics ; Tigecycline/pharmacology ; Animals ; Birds/microbiology ; }, abstract = {In Chinese zoos, there are usually specially designed bird parks, similar to petting zoos, that allow children and adults to interact with diverse birds. However, such behaviors present a risk for the transmission of zoonotic pathogens. Recently, we isolated eight strains of Klebsiella pneumoniae and identified two blaCTX-M-positive strains from 110 birds, including parrots, peacocks, and ostriches, using anal or nasal swabs in a bird park of a zoo in China. There, K. pneumoniae LYS105A was obtained from a diseased peacock with chronic respiratory diseases by a nasal swab, which harbored the blaCTX-M-3 gene and exhibited resistance to amoxicillin, cefotaxime, gentamicin, oxytetracycline, doxycycline, tigecycline, florfenicol, and enrofloxacin. According to an analysis by whole-genome sequencing, K. pneumoniae LYS105A belongs to serotype ST859 (sequence type 859)-K19 (capsular serotype 19) and contains two plasmids, of which pLYS105A-2 can be transferred by electrotransformation and harbors numerous resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91. The above-mentioned genes are located in a novel mobile composite transposon, Tn7131, which makes horizontal transfer more flexible. Although no known genes were identified in the chromosome, a significant increase in SoxS upregulated the expression levels of phoPQ, acrEF-tolC, and oqxAB, which contributed to strain LYS105A acquiring resistance to tigecycline (MIC = 4 mg/L) and intermediate resistance to colistin (MIC = 2 mg/L). Altogether, our findings show that bird parks in zoos may act as important vehicles for the spread of multidrug-resistant bacteria from birds to humans and vice versa. IMPORTANCE A multidrug-resistant ST859-K19 K. pneumoniae strain, LYS105A, was obtained from a diseased peacock in a Chinese zoo. In addition, multiple resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91 were located in a novel composite transposon, Tn7131, of a mobile plasmid, implying that most of the resistance genes in strain LYS105A can be moved easily via horizontal gene transfer. Meanwhile, an increase in SoxS can further positively regulate the expression of phoPQ, acrEF-tolC, and oqxAB, which is the key factor for strain LYS105A to develop resistance to tigecycline and colistin. Taken together, these findings enrich our understanding of the horizontal cross-species spread of drug resistance genes, which will help us curb the development of bacterial resistance.}, }
@article {pmid36808308, year = {2023}, author = {Zhu, Y and Wang, T and Zhu, W and Wei, Q}, title = {Influence of class 2 integron integrase concentration on gene cassette insertion and excision in vivo.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {36808308}, issn = {1678-4405}, abstract = {Integron can capture and express antimicrobial resistance gene cassettes and plays important roles in horizontal gene transfer. The establishment of a complete in vitro reaction system will help to reveal integron integrase mediated site-specific recombination process and regulation mechanism. As an enzymatic reaction, the concentration of integrase is assumed to have a great influence on the reaction rate. To determine the influence of different concentrations of integrase on the reaction rate and to find the best range of enzyme concentration were essential to optimizing the in vitro reaction system. In this study, plasmids with gradient transcription levels of class 2 integron integrase gene intI2 under different promoters were constructed. Among plasmids pI2W16, pINTI2N, pI2W, and pI2NW, intI2 transcription levels ranged from about 0.61-fold to 49.65-fold of that in pINTI2N. And the frequencies of gene cassette sat2 integration and excision catalyzed by IntI2 were positively correlated with the transcription levels of intI2 within this range. Western blotting results indicated high expression of IntI2 partly existed in the form of an inclusion body. When compared with Pc of class 1 integron, the spacer sequence of PintI2 can increase the strength of PcW but decrease the strength of PcS. In conclusion, the frequencies of gene cassette integration and excision were positively correlated with the concentration of IntI2. intI2 driving by PcW with PintI2 spacer sequence can obtain the optimum IntI2 concentration required to achieve the maximum recombination efficiency in vivo in this study.}, }
@article {pmid36805559, year = {2023}, author = {Huang, Y and Sheth, RU and Zhao, S and Cohen, LA and Dabaghi, K and Moody, T and Sun, Y and Ricaurte, D and Richardson, M and Velez-Cortes, F and Blazejewski, T and Kaufman, A and Ronda, C and Wang, HH}, title = {High-throughput microbial culturomics using automation and machine learning.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36805559}, issn = {1546-1696}, abstract = {Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform for the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology and genomic data to maximize the diversity of microbes isolated and enable targeted picking of specific genera. Application of this platform on fecal samples from 20 humans yields personalized gut microbiome biobanks totaling 26,997 isolates that represented >80% of all abundant taxa. Spatial analysis on >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae, Bacteroidaceae, Coriobacteriaceae and Bifidobacteriaceae families that suggest important microbial interactions. Comparative analysis of 1,197 high-quality genomes from these biobanks shows interesting intra- and interpersonal strain evolution, selection and horizontal gene transfer. This culturomics framework should empower new research efforts to systematize the collection and quantitative analysis of imaging-based phenotypes with high-resolution genomics data for many emerging microbiome studies.}, }
@article {pmid36805463, year = {2023}, author = {Engin, AB and Engin, ED and Engin, A}, title = {Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors.}, journal = {Environmental toxicology and pharmacology}, volume = {98}, number = {}, pages = {104081}, doi = {10.1016/j.etap.2023.104081}, pmid = {36805463}, issn = {1872-7077}, mesh = {*Genes, Bacterial ; Bacteria ; Drug Resistance, Microbial/genetics ; *Metals, Heavy ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.}, }
@article {pmid36805209, year = {2023}, author = {Rius, M and Rest, JS and Filloramo, GV and Novák Vanclová, AMG and Archibald, JM and Collier, JL}, title = {Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36805209}, issn = {1759-6653}, mesh = {*Carotenoids ; beta Carotene/genetics ; Gene Transfer, Horizontal ; *Stramenopiles ; Bacteria/genetics ; }, abstract = {Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding a protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid biosynthesis in the thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore the evolutionary origins of CrtIBY and discover that the closest related protein domains are present in a small but diverse group of other heterotrophic protists, including the apusomonad Thecamonas trahens and the dinoflagellates Oxyrrhis marina and Noctiluca scintillans. Each organism within this cluster also contains one or more β-carotene 15-15' oxygenase genes (blh and rpe65), suggesting that the acquisition of β-carotene biosynthesis genes may have been related to the production of retinal. Our findings support a novel origin of eukaryotic (apo)carotenoid biosynthesis by horizontal gene transfer from Actinobacteria, Bacteroidetes, and/or Archaea. This reveals a remarkable case of parallel evolution of eukaryotic (apo)carotenogenesis in divergent protistan lineages by repeated gene transfers.}, }
@article {pmid36798152, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.06.527410}, pmid = {36798152}, abstract = {UNLABELLED: Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbionts Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of the Knuthellervirus genus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system.<br><br>IMPORTANCE: Phages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as "pink berries" found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.}, }
@article {pmid36795748, year = {2023}, author = {Johnston, CHG and Hope, R and Soulet, AL and Dewailly, M and De Lemos, D and Polard, P}, title = {The RecA-directed recombination pathway of natural transformation initiates at chromosomal replication forks in the pneumococcus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {8}, pages = {e2213867120}, pmid = {36795748}, issn = {1091-6490}, mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Rec A Recombinases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Chromosomes/metabolism ; DNA/metabolism ; DNA, Single-Stranded/genetics/metabolism ; }, abstract = {Homologous recombination (HR) is a crucial mechanism of DNA strand exchange that promotes genetic repair and diversity in all kingdoms of life. Bacterial HR is driven by the universal recombinase RecA, assisted in the early steps by dedicated mediators that promote its polymerization on single-stranded DNA (ssDNA). In bacteria, natural transformation is a prominent HR-driven mechanism of horizontal gene transfer specifically dependent on the conserved DprA recombination mediator. Transformation involves internalization of exogenous DNA as ssDNA, followed by its integration into the chromosome by RecA-directed HR. How DprA-mediated RecA filamentation on transforming ssDNA is spatiotemporally coordinated with other cellular processes remains unknown. Here, we tracked the localization of fluorescent fusions to DprA and RecA in Streptococcus pneumoniae and revealed that both accumulate in an interdependent manner with internalized ssDNA at replication forks. In addition, dynamic RecA filaments were observed emanating from replication forks, even with heterologous transforming DNA, which probably represent chromosomal homology search. In conclusion, this unveiled interaction between HR transformation and replication machineries highlights an unprecedented role for replisomes as landing pads for chromosomal access of tDNA, which would define a pivotal early HR step for its chromosomal integration.}, }
@article {pmid36792883, year = {2023}, author = {Lau, DYL and Aguirre Sánchez, JR and Baker-Austin, C and Martinez-Urtaza, J}, title = {What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios.}, journal = {Advances in experimental medicine and biology}, volume = {1404}, number = {}, pages = {337-352}, pmid = {36792883}, issn = {0065-2598}, mesh = {Humans ; Phylogeny ; *Vibrio cholerae/genetics ; *Vibrio parahaemolyticus/genetics ; *Vibrio vulnificus/genetics ; Whole Genome Sequencing ; }, abstract = {When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.}, }
@article {pmid36792876, year = {2023}, author = {Amaro, C and Carmona-Salido, H}, title = {Vibrio vulnificus, an Underestimated Zoonotic Pathogen.}, journal = {Advances in experimental medicine and biology}, volume = {1404}, number = {}, pages = {175-194}, pmid = {36792876}, issn = {0065-2598}, mesh = {Humans ; Animals ; *Vibrio vulnificus/genetics ; *Vibrio Infections/veterinary/epidemiology ; Aquaculture ; Gene Transfer, Horizontal ; Virulence/genetics ; }, abstract = {V. vulnificus, continues being an underestimated yet lethal zoonotic pathogen. In this chapter, we provide a comprehensive review of numerous aspects of the biology, epidemiology, and virulence mechanisms of this poorly understood pathogen. We will emphasize the widespread role of horizontal gene transfer in V. vulnificus specifically virulence plasmids and draw parallels from aquaculture farms to human health. By placing current findings in the context of climate change, we will also contend that fish farms act as evolutionary drivers that accelerate species evolution and the emergence of new virulent groups. Overall, we suggest that on-farm control measures should be adopted both to protect animals from Vibriosis, and also as a public health measure to prevent the emergence of new zoonotic groups.}, }
@article {pmid36792581, year = {2023}, author = {Filée, J and Becker, HF and Mellottee, L and Eddine, RZ and Li, Z and Yin, W and Lambry, JC and Liebl, U and Myllykallio, H}, title = {Bacterial origins of thymidylate metabolism in Asgard archaea and Eukarya.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {838}, pmid = {36792581}, issn = {2041-1723}, mesh = {*Archaea/metabolism ; *Eukaryota/genetics/metabolism ; Phylogeny ; Thymidylate Synthase/genetics/metabolism ; Bacteria/genetics/metabolism ; Amino Acids/metabolism ; Folic Acid/metabolism ; DNA/metabolism ; }, abstract = {Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, we investigate the evolution and function of Asgard thymidylate synthases and other folate-dependent enzymes required for the biosynthesis of DNA, RNA, amino acids and vitamins, as well as syntrophic amino acid utilization. Phylogenies of Asgard folate-dependent enzymes are consistent with their horizontal transmission from various bacterial groups. We experimentally validate the functionality of thymidylate synthase ThyX of the cultured 'Candidatus Prometheoarchaeum syntrophicum'. The enzyme efficiently uses bacterial-like folates and is inhibited by mycobacterial ThyX inhibitors, even though the majority of experimentally tested archaea are known to use carbon carriers distinct from bacterial folates. Our phylogenetic analyses suggest that the eukaryotic thymidylate synthase, required for de novo DNA synthesis, is not closely related to archaeal enzymes and might have been transferred from bacteria to protoeukaryotes during eukaryogenesis. Altogether, our study suggests that the capacity of eukaryotic cells to duplicate their genetic material is a sum of archaeal (replisome) and bacterial (thymidylate synthase) characteristics. We also propose that recent prevalent lateral gene transfer from bacteria has markedly shaped the metabolism of Asgard archaea.}, }
@article {pmid36792019, year = {2023}, author = {Lekired, A and Cherif-Silini, H and Silini, A and Ben Yahia, H and Ouzari, HI}, title = {Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments.}, journal = {Genomics}, volume = {115}, number = {2}, pages = {110579}, doi = {10.1016/j.ygeno.2023.110579}, pmid = {36792019}, issn = {1089-8646}, mesh = {*Metals, Heavy ; *Pantoea/genetics ; Biodegradation, Environmental ; Interspersed Repetitive Sequences ; Genomics ; }, abstract = {Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.}, }
@article {pmid36791498, year = {2023}, author = {Sharma, A and Gupta, S and Paul, K}, title = {Evolution of codon and amino acid usage in bacterial protein toxins.}, journal = {Biochemical and biophysical research communications}, volume = {651}, number = {}, pages = {47-55}, doi = {10.1016/j.bbrc.2023.02.001}, pmid = {36791498}, issn = {1090-2104}, mesh = {*Bacterial Proteins/genetics/metabolism ; Amino Acids/metabolism ; *Bacterial Toxins/chemistry ; Bacteria/genetics/metabolism ; Codon/genetics ; }, abstract = {Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s).}, }
@article {pmid36790109, year = {2023}, author = {van Rooijen, LE and Tromer, EC and van Hooff, JJE and Kops, GJPL and Snel, B}, title = {Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36790109}, issn = {1759-6653}, mesh = {Humans ; *Kinetochores ; Microtubule-Associated Proteins/genetics ; Phylogeny ; Microtubules ; Cell Division ; Cell Cycle Proteins/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; Chromosomal Proteins, Non-Histone/genetics ; }, abstract = {Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.}, }
@article {pmid36788632, year = {2023}, author = {Sezmis, AL and Woods, LC and Peleg, AY and McDonald, MJ}, title = {Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36788632}, issn = {1537-1719}, mesh = {*Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Plasmids ; Drug Resistance, Microbial ; *Acinetobacter baumannii/genetics ; }, abstract = {Horizontal gene transfer (HGT) is important for microbial evolution, but how evolutionary forces shape the frequencies of horizontally transferred genetic variants in the absence of strong selection remains an open question. In this study, we evolve laboratory populations of Acinetobacter baylyi (ADP1) with HGT from two clinically relevant strains of multidrug-resistant Acinetobacter baumannii (AB5075 and A9844). We find that DNA can cross the species barrier, even without strong selection, and despite substantial DNA sequence divergence between the two species. Our results confirm previous findings that HGT can drive the spread of antibiotic resistance genes (ARGs) without selection for that antibiotic, but not for all of the resistance genes present in the donor genome. We quantify the costs and benefits of horizontally transferred variants and use whole population sequencing to track the spread of ARGs from HGT donors into antibiotic-sensitive recipients. We find that even though most ARGs are taken up by populations of A. baylyi, the long-term fate of an individual gene depends both on its fitness cost and on the type of genetic element that carries the gene. Interestingly, we also found that an integron, but not its host plasmid, is able to spread in A. baylyi populations despite its strong deleterious effect. Altogether, our results show how HGT provides an evolutionary advantage to evolving populations by facilitating the spread of non-selected genetic variation including costly ARGs.}, }
@article {pmid36787297, year = {2023}, author = {Thompson, CMA and Hall, JPJ and Chandra, G and Martins, C and Saalbach, G and Panturat, S and Bird, SM and Ford, S and Little, RH and Piazza, A and Harrison, E and Jackson, RW and Brockhurst, MA and Malone, JG}, title = {Plasmids manipulate bacterial behaviour through translational regulatory crosstalk.}, journal = {PLoS biology}, volume = {21}, number = {2}, pages = {e3001988}, pmid = {36787297}, issn = {1545-7885}, support = {BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T004363/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010568/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Proteomics ; Plasmids/genetics ; *Bacteria/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.}, }
@article {pmid36786613, year = {2023}, author = {Yang, D and Yang, Y and Qiao, P and Jiang, F and Zhang, X and Zhao, Z and Cai, T and Li, G and Cai, W}, title = {Genomic Island-Encoded Histidine Kinase and Response Regulator Coordinate Mannose Utilization with Virulence in Enterohemorrhagic Escherichia coli.}, journal = {mBio}, volume = {}, number = {}, pages = {e0315222}, doi = {10.1128/mbio.03152-22}, pmid = {36786613}, issn = {2150-7511}, abstract = {Enterohemorrhagic Escherichia coli (EHEC) is a highly adaptive pathogen and has acquired diverse genetic elements, such as genomic islands and prophages, via horizontal gene transfer to promote fitness in vivo. Two-component signaling systems (TCSs) allow bacteria to sense, respond to, and adapt to various environments. This study identified a putative two-component signaling system composed of the histidine kinase EDL5436 (renamed LmvK) and the response regulator EDL5428 (renamed LmvR) in EHEC. lmvK and lmvR along with EDL5429 to EDL5434 (EDL5429-5434) between them constitute the OI167 genomic island and are highly associated with the EHEC pathotype. EDL5429-5434 encode transporters and metabolic enzymes that contribute to growth on mannose and are directly upregulated by LmvK/LmvR in the presence of mannose, as revealed by quantitative PCR (qPCR) and DNase I footprint assays. Moreover, LmvR directly activates the expression of the type III secretion system in response to mannose and promotes the formation of attaching and effacing lesions on HeLa cells. Using human colonoid and mouse infection models, we show that lmvK and lmvR contributed greatly to adherence and microcolony (MC) formation ex vivo and colonization in vivo. Finally, RNA sequencing and chromatin immunoprecipitation coupled with sequencing analyses identified additional direct targets of LmvR, most of which are involved in metabolism. Given that mannose is a mucus-derived sugar that induces virulence and is preferentially used by EHEC during infection, our data revealed a previously unknown mechanism by which EHEC recognizes the host metabolic landscape and regulates virulence expression accordingly. Our findings provide insights into how pathogenic bacteria evolve by acquiring genetic elements horizontally to adapt to host environments. IMPORTANCE The gastrointestinal tract represents a complex and challenging environment for enterohemorrhagic Escherichia coli (EHEC). However, EHEC is a highly adaptable pathogen, requiring only 10 to 100 CFUs to cause infection. This ability was achieved partially by acquiring mobile genetic elements, such as genomic islands, that promote overall fitness. Mannose is an intestinal mucus-derived sugar that stimulates virulence and is preferentially used by EHEC during infection. Here, we characterize the OI167 genomic island of EHEC, which encodes a novel two-component signaling system (TCS) and transporters and metabolic enzymes (EDL5429-5434) involved in mannose utilization. The TCS directly upregulates EDL5429-5434 and genes encoding the type III secretion system in the presence of mannose. Moreover, the TCS contributes greatly to EHEC virulence ex vivo and in vivo. Our data demonstrate an elegant example in which EHEC strains evolve by acquiring genetic elements horizontally to recognize the host metabolic landscape and regulate virulence expression accordingly, leading to successful infections.}, }
@article {pmid36781732, year = {2023}, author = {Suzuki, M and Hashimoto, Y and Hirabayashi, A and Yahara, K and Yoshida, M and Fukano, H and Hoshino, Y and Shibayama, K and Tomita, H}, title = {Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2632}, number = {}, pages = {227-246}, pmid = {36781732}, issn = {1940-6029}, mesh = {*Nanopore Sequencing ; Bacteria/genetics ; Plasmids/genetics ; Genomics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.}, }
@article {pmid36780569, year = {2023}, author = {McKeithen-Mead, SA and Grossman, AD}, title = {Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host.}, journal = {PLoS genetics}, volume = {19}, number = {2}, pages = {e1010524}, pmid = {36780569}, issn = {1553-7404}, support = {R01 GM050895/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial/genetics ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; Chromosomes/metabolism ; Bacteria/genetics ; DNA Transposable Elements ; }, abstract = {Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.}, }
@article {pmid36779718, year = {2023}, author = {Kuntová, L and Mašlaňová, I and Obořilová, R and Šimečková, H and Finstrlová, A and Bárdy, P and Šiborová, M and Troianovska, L and Botka, T and Gintar, P and Šedo, O and Farka, Z and Doškař, J and Pantůček, R}, title = {Staphylococcus aureus Prophage-Encoded Protein Causes Abortive Infection and Provides Population Immunity against Kayviruses.}, journal = {mBio}, volume = {}, number = {}, pages = {e0249022}, doi = {10.1128/mbio.02490-22}, pmid = {36779718}, issn = {2150-7511}, abstract = {Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.}, }
@article {pmid36778052, year = {2022}, author = {Seshadri, R and Roux, S and Huber, KJ and Wu, D and Yu, S and Udwary, D and Call, L and Nayfach, S and Hahnke, RL and Pukall, R and White, JR and Varghese, NJ and Webb, C and Palaniappan, K and Reimer, LC and Sardà, J and Bertsch, J and Mukherjee, S and Reddy, TBK and Hajek, PP and Huntemann, M and Chen, IA and Spunde, A and Clum, A and Shapiro, N and Wu, ZY and Zhao, Z and Zhou, Y and Evtushenko, L and Thijs, S and Stevens, V and Eloe-Fadrosh, EA and Mouncey, NJ and Yoshikuni, Y and Whitman, WB and Klenk, HP and Woyke, T and Göker, M and Kyrpides, NC and Ivanova, NN}, title = {Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.}, journal = {Cell genomics}, volume = {2}, number = {12}, pages = {100213}, pmid = {36778052}, issn = {2666-979X}, abstract = {The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.}, }
@article {pmid36772873, year = {2023}, author = {Molina-Santiago, C and Bernal, P}, title = {Nanotube-mediated plasmid transfer as a natural alternative for the improvement of industrially relevant bacteria.}, journal = {Microbial biotechnology}, volume = {16}, number = {4}, pages = {706-708}, pmid = {36772873}, issn = {1751-7915}, mesh = {Plasmids ; DNA, Bacterial ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; }, }
@article {pmid36772829, year = {2023}, author = {Shen, M and Goldlust, K and Daniel, S and Lesterlin, C and Yamaichi, Y}, title = {Recipient UvrD helicase is involved in single- to double-stranded DNA conversion during conjugative plasmid transfer.}, journal = {Nucleic acids research}, volume = {51}, number = {6}, pages = {2790-2799}, pmid = {36772829}, issn = {1362-4962}, mesh = {Conjugation, Genetic/genetics ; DNA ; *DNA Helicases/genetics/metabolism ; DNA, Bacterial/genetics/metabolism ; *DNA, Single-Stranded/genetics ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics ; Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; }, abstract = {Dissemination of antibiotic resistance, a current societal challenge, is often driven by horizontal gene transfer through bacterial conjugation. During conjugative plasmid transfer, single-stranded (ss) DNA is transferred from the donor to the recipient cell. Subsequently, a complete double-stranded (ds) plasmid molecule is generated and plasmid-encoded genes are expressed, allowing successful establishment of the transconjugant cell. Such dynamics of transmission can be modulated by host- or plasmid-encoded factors, either in the donor or in the recipient cell. We applied transposon insertion sequencing to identify host-encoded factors that affect conjugative transfer frequency in Escherichia coli. Disruption of the recipient uvrD gene decreased the acquisition frequency of conjugative plasmids belonging to different incompatibility groups. Results from various UvrD mutants suggested that dsDNA binding activity and interaction with RNA polymerase are dispensable, but ATPase activity is required for successful plasmid establishment of transconjugant cells. Live-cell microscopic imaging showed that the newly transferred ssDNA within a uvrD- recipient often failed to be converted to dsDNA. Our work suggested that in addition to its role in maintaining genome integrity, UvrD is also key for the establishment of horizontally acquired plasmid DNA that drives genome diversity and evolution.}, }
@article {pmid36768888, year = {2023}, author = {Zhang, C and Jiao, C and Sun, X and Li, X}, title = {A MYB Transcription Factor Atlas Provides Insights into the Evolution of Environmental Adaptations in Plants.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768888}, issn = {1422-0067}, mesh = {*Transcription Factors/genetics/metabolism ; Phylogeny ; DNA Copy Number Variations ; Plants/genetics/metabolism ; Genome, Plant ; *Magnoliopsida/genetics ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Evolution, Molecular ; }, abstract = {The MYB transcription factor superfamily includes key regulators of plant development and responses to environmental changes. The diversity of lifestyles and morphological characteristics exhibited by plants are potentially associated with the genomic dynamics of the MYB superfamily. With the release of the plant genomes, a comprehensive phylogenomic analysis of the MYB superfamily across Viridiplantae is allowed. The present study performed phylogenetic, phylogenomic, syntenic, horizontal gene transfer, and neo/sub-functionalization analysis of the MYB superfamily to explore the evolutionary contributions of MYB members to species diversification, trait formation, and environmental adaptation in 437 different plant species. We identified major changes in copy number variation and genomic context within subclades across lineages. Multiple MYB subclades showed highly conserved copy number patterns and synteny across flowering plants, whereas others were more dynamic and showed lineage-specific patterns. As examples of lineage-specific morphological divergence, we hypothesize that the gain of a MYB orthogroup associated with flower development and environmental responses and an orthogroup associated with auxin and wax biosynthesis in angiosperms were correlated with the emergence of flowering plants, unbiased neo-/sub-functionalization of gene duplicates contributed to environmental adaptation, and species-specific neo-/sub-functionalization contributed to phenotype divergence between species. Transposable element insertion in promoter regions may have facilitated the sub-/neo-functionalization of MYB genes and likely played a tissue-specific role contributing to sub-/neo-functionalization in plant root tissues. This study provides new insights into the evolutionary divergence of the MYB superfamily across major flowering and non-flowering lineages and emphasizes the need for lineage-/tissue-specific characterization to further understand trait variability and environmental adaptation.}, }
@article {pmid36764681, year = {2023}, author = {Van Etten, J and Benites, LF and Stephens, TG and Yoon, HS and Bhattacharya, D}, title = {Algae obscura: The potential of rare species as model systems.}, journal = {Journal of phycology}, volume = {59}, number = {2}, pages = {293-300}, doi = {10.1111/jpy.13321}, pmid = {36764681}, issn = {1529-8817}, support = {80NSSC19K0462/NASA/NASA/United States ; }, mesh = {Phylogeny ; *Biological Evolution ; Plants ; Eukaryota/genetics ; *Rhodophyta/genetics ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems.}, }
@article {pmid36764395, year = {2023}, author = {Van Dijck, C and Laumen, JGE and de Block, T and Abdellati, S and De Baetselier, I and Tsoumanis, A and Malhotra-Kumar, S and Manoharan-Basil, SS and Kenyon, C and Xavier, BB}, title = {The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study.}, journal = {The Journal of infection}, volume = {86}, number = {4}, pages = {329-337}, doi = {10.1016/j.jinf.2023.02.006}, pmid = {36764395}, issn = {1532-2742}, mesh = {Male ; Humans ; Homosexuality, Male ; Sexual Behavior ; *Pre-Exposure Prophylaxis ; *HIV Infections/prevention &amp; control/epidemiology ; Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Sexual and Gender Minorities ; Oropharynx ; Drug Resistance, Microbial ; Fluoroquinolones ; Macrolides ; }, abstract = {BACKGROUND: Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.<br><br>METHODS: We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.<br><br>FINDINGS: ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.<br><br>INTERPRETATION: The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.}, }
@article {pmid36762480, year = {2023}, author = {Arbel-Goren, R and McKeithen-Mead, SA and Voglmaier, D and Afremov, I and Teza, G and Grossman, AD and Stavans, J}, title = {Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad068}, pmid = {36762480}, issn = {1362-4962}, support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; }, abstract = {Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.}, }
@article {pmid36762093, year = {2022}, author = {Li, Z and Shen, J and Wang, F and Wang, M and Shen, J and Li, Y and Zhu, Q and Wu, J}, title = {Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1075234}, pmid = {36762093}, issn = {1664-302X}, abstract = {The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.}, }
@article {pmid36758922, year = {2023}, author = {Wang, M and Lian, Y and Wang, Y and Zhu, L}, title = {The role and mechanism of quorum sensing on environmental antimicrobial resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {322}, number = {}, pages = {121238}, doi = {10.1016/j.envpol.2023.121238}, pmid = {36758922}, issn = {1873-6424}, mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/toxicity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {As more environmental contaminants emerging, antibiotics and antibiotic resistance genes (ARGs) have caused a substantial increase of antimicrobial resistance (AMR) in environment. Quorum sensing (QS) is a bacterial cell-to-cell communication process that regulates many traits and gene expression, including ARGs and the related genes that contribute to AMR development. Herein, we summarize the role, physiology, and genetic mechanisms of bacterial QS in AMR development in the environment. First, the effect of QS on AMR is introduced. Next, the role of QS in bacterial physiological behaviors that promote AMR development, including membrane permeability, tactic movement, biofilm formation, persister formation, and small colony variants (SCVs), is systematically analyzed. Furthermore, the regulation of QS on the expression of ARGs, generation of reactive oxygen species (ROS), which affects ARGs formation, and horizontal gene transfer (HGT), which accelerates the transmission of ARGs, are discussed to reveal the molecular mechanism for AMR development. This review provides a reference for a better understanding of AMR evolution and novel insights into AMR prevention.}, }
@article {pmid36758429, year = {2023}, author = {Li, X and Lu, H and Yang, K and Zhu, L}, title = {Attenuation of tetracyclines and related resistance genes in soil when exposed to nanoscale zero-valent iron.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130867}, doi = {10.1016/j.jhazmat.2023.130867}, pmid = {36758429}, issn = {1873-3336}, mesh = {Humans ; *Tetracyclines/pharmacology ; Soil ; Iron ; Anti-Bacterial Agents/pharmacology ; Biodegradation, Environmental ; *Environmental Restoration and Remediation ; }, abstract = {Antibiotics pollution in soil poses increasing threats to human health due to stimulated proliferation and transmission of antibiotic resistance genes (ARGs). Nanoscale zero-valent iron (NZVI) is a promising material for the remediation of antibiotics, but how NZVI affects the diversity, abundance, and horizontal gene transfer potentials of ARGs remains unclear. Herein, the biotic and abiotic effects of NZVI at different concentrations on tetracyclines (TCs) and the associated ARGs were investigated. Results showed NZVI could effectively accelerate the degradation of TCs, which increased from 51.38% (without NZVI) to 57.96%- 71.66% (1-10 g NZVI/kg) in 20 days. Biotic degradation contributed to 66.10%- 76.30% of the total TCs removal. NZVI induced TCs biodegradation was probably due to alleviated toxicity of TCs on cells and increased microbial biomass and enzyme activities. Additionally, TCs-related ARGs were attenuated with decreased horizontal gene transfer potentials of intI1 and ISCR1, but opposite effects were observed for non TC-related ARGs, especially during excess exposure to NZVI. This study illustrated the possibility of remediating of antibiotic contaminated soil by NZVI and meanwhile reducing the potential risks of ARGs.}, }
@article {pmid36756971, year = {2023}, author = {Chen, Y and Jia, B and Li, JY and Li, D and He, W}, title = {Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/09593330.2023.2176261}, pmid = {36756971}, issn = {1479-487X}, abstract = {Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10[-7] to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.}, }
@article {pmid36753420, year = {2023}, author = {Beamud, B and García-González, N and Gómez-Ortega, M and González-Candelas, F and Domingo-Calap, P and Sanjuan, R}, title = {Genetic determinants of host tropism in Klebsiella phages.}, journal = {Cell reports}, volume = {42}, number = {2}, pages = {112048}, pmid = {36753420}, issn = {2211-1247}, abstract = {Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.}, }
@article {pmid36752380, year = {2023}, author = {Yuan, L and Lu, H and Li, F and Nielsen, J and Kerkhoven, EJ}, title = {HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, pmid = {36752380}, issn = {1477-4054}, mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Genomics ; Genome ; Evolution, Molecular ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species.<br><br>RESULTS: In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species.<br><br>CONCLUSIONS: The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.}, }
@article {pmid36750723, year = {2023}, author = {Beltran, LC and Cvirkaite-Krupovic, V and Miller, J and Wang, F and Kreutzberger, MAB and Patkowski, JB and Costa, TRD and Schouten, S and Levental, I and Conticello, VP and Egelman, EH and Krupovic, M}, title = {Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {666}, pmid = {36750723}, issn = {2041-1723}, support = {R35 GM122510/GM/NIGMS NIH HHS/United States ; S10 RR025067/RR/NCRR NIH HHS/United States ; G20 RR031199/RR/NCRR NIH HHS/United States ; U24 GM116790/GM/NIGMS NIH HHS/United States ; K99 GM138756/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Agrobacterium tumefaciens/genetics ; Bacterial Proteins/genetics ; *Conjugation, Genetic ; Cryoelectron Microscopy ; *DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Plasmids ; *Aeropyrum/genetics ; *Pyrobaculum/genetics ; }, abstract = {Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.}, }
@article {pmid36748704, year = {2023}, author = {Anbo, M and Jelsbak, L}, title = {A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748704}, issn = {2057-5858}, mesh = {Serogroup ; *Pseudomonas aeruginosa ; Drug Resistance, Microbial ; *Gene Transfer, Horizontal ; }, abstract = {High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.}, }
@article {pmid36748580, year = {2022}, author = {Wietz, M and López-Pérez, M and Sher, D and Biller, SJ and Rodriguez-Valera, F}, title = {Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {11}, pages = {}, doi = {10.1099/mic.0.001236}, pmid = {36748580}, issn = {1465-2080}, mesh = {*Genome, Bacterial/genetics ; *Alteromonas/genetics/metabolism ; Phenotype ; Adaptation, Physiological ; Phylogeny ; Seawater/microbiology ; }, abstract = {Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.}, }
@article {pmid36748576, year = {2022}, author = {Kupczok, A and Bailey, ZM and Refardt, D and Wendling, CC}, title = {Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748576}, issn = {2057-5858}, mesh = {*Bacteriophages/genetics ; Mosaicism ; Operon ; }, abstract = {Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.}, }
@article {pmid36748570, year = {2023}, author = {Sengupta, S and Azad, RK}, title = {Leveraging comparative genomics to uncover alien genes in bacterial genomes.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748570}, issn = {2057-5858}, mesh = {*Genome, Bacterial ; *Genomics/methods ; Algorithms ; Biological Evolution ; }, abstract = {A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.}, }
@article {pmid36748564, year = {2023}, author = {Colombi, E and Hill, Y and Lines, R and Sullivan, JT and Kohlmeier, MG and Christophersen, CT and Ronson, CW and Terpolilli, JJ and Ramsay, JP}, title = {Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748564}, issn = {2057-5858}, mesh = {Gene Transfer, Horizontal ; *Mesorhizobium/genetics ; Symbiosis/genetics ; Metagenomics ; Nitrogen ; Australia ; *Lotus/microbiology ; Soil ; }, abstract = {Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.}, }
@article {pmid36748528, year = {2022}, author = {Tamminga, SM and Völpel, SL and Schipper, K and Stehle, T and Pannekoek, Y and van Sorge, NM}, title = {Genetic diversity of Staphylococcus aureus wall teichoic acid glycosyltransferases affects immune recognition.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, pmid = {36748528}, issn = {2057-5858}, mesh = {Humans ; *Staphylococcus aureus/genetics/metabolism ; Glycosyltransferases/genetics/chemistry/metabolism ; Teichoic Acids/chemistry/metabolism ; Bacterial Proteins/metabolism ; *Staphylococcal Infections ; Codon, Nonsense/metabolism ; }, abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections and systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for S. aureus nasal colonization, phage-mediated horizontal gene transfer, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with N-acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP. TarS and TarP modify WTA with β-linked GlcNAc at the C-4 (β1,4-GlcNAc) and the C-3 position (β1,3-GlcNAc) of the RboP subunit, respectively, whereas TarM modifies WTA with α-linked GlcNAc at the C-4 position (α1,4-GlcNAc). Importantly, these WTA glycosylation patterns impact immune recognition and clearance of S. aureus. Previous studies suggest that tarS is near-universally present within the S. aureus population, whereas a smaller proportion co-contain either tarM or tarP. To gain more insight into the presence and genetic variation of tarS, tarM and tarP in the S. aureus population, we analysed a collection of 25 652 S. aureus genomes within the PubMLST database. Over 99 % of isolates contained tarS. Co-presence of tarS/tarM or tarS/tarP occurred in 37 and 7 % of isolates, respectively, and was associated with specific S. aureus clonal complexes. We also identified 26 isolates (0.1 %) that contained all three glycosyltransferase genes. At sequence level, we identified tar alleles with amino acid substitutions in critical enzymatic residues or with premature stop codons. Several tar variants were expressed in a S. aureus tar-negative strain. Analysis using specific monoclonal antibodies and human langerin showed that WTA glycosylation was severely attenuated or absent. Overall, our data provide a broad overview of the genetic diversity of the three WTA glycosyltransferases in the S. aureus population and the functional consequences for immune recognition.}, }
@article {pmid36748517, year = {2022}, author = {Greig, DR and Bird, MT and Chattaway, MA and Langridge, GC and Waters, EV and Ribeca, P and Jenkins, C and Nair, S}, title = {Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, pmid = {36748517}, issn = {2057-5858}, support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Salmonella typhi/genetics ; *Bacteriophages/genetics ; Bacteriophage P1/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.}, }
@article {pmid36744899, year = {2023}, author = {Prasad, A and Ene, A and Jablonska, S and Du, J and Wolfe, AJ and Putonti, C}, title = {Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068722}, doi = {10.1128/msphere.00687-22}, pmid = {36744899}, issn = {2379-5042}, abstract = {Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.}, }
@article {pmid36744093, year = {2023}, author = {Qi, Q and Rajabal, V and Ghaly, TM and Tetu, SG and Gillings, MR}, title = {Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091391}, pmid = {36744093}, issn = {1664-302X}, abstract = {Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.}, }
@article {pmid36741554, year = {2022}, author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW}, title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.}, journal = {Fungal systematics and evolution}, volume = {10}, number = {}, pages = {177-215}, pmid = {36741554}, issn = {2589-3831}, abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.}, }
@article {pmid36740055, year = {2023}, author = {Markowicz, A}, title = {The significance of metallic nanoparticles in the emerging, development and spread of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162029}, doi = {10.1016/j.scitotenv.2023.162029}, pmid = {36740055}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Metal Nanoparticles/toxicity ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; }, abstract = {An ever-increasing number of newly synthesised nanoparticles have a constantly expanding range of applications. The large-scale implementation of nanoparticles will inevitably lead to intentional or accidental contamination of various environments. Since the major benefit of using several metallic nanoparticles is antimicrobial activity, these emerging contaminants may have a potentially hazardous impact on the development and spread of antibiotic resistance - a challenge that threats infection therapy worldwide. Few studies underline that metallic nanoparticles may affect the emergence and evolution of resistance via mutations and horizontal transfer between different bacterial species. Due to the complexity of factors and mechanisms involved in disseminating antibiotic resistance, it is crucial to investigate if metallic nanoparticles play a significant role in this process through co-selection ability and pressure exerted on bacteria. The aim of this review is to summarise the current research on mutations and three main horizontal gene transfer modes facilitated by nanoparticles. Here, the current results in the field are presented, major knowledge gaps and the necessity for more environmentally relevant studies are discussed.}, }
@article {pmid36739179, year = {2023}, author = {Islam, T and Azad, RB and Kasfy, SH and Rahman, AA and Khan, TZ}, title = {Horizontal gene transfer from plant to whitefly.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2023.01.007}, pmid = {36739179}, issn = {1879-3096}, abstract = {The recent discovery of the horizontal transfer of a toxin-neutralizing gene from plant to whitefly (Bemisia tabaci), a polyphagous insect, sparked a new area of study. In this forum, we discuss some potential biotechnological applications of this newly discovered knowledge in the coevolutionary arms race between plants and whitefly.}, }
@article {pmid36738814, year = {2023}, author = {Bhowmik, P and Bharatham, N and Murakami, S and Ramachandran, V and Datta, S}, title = {Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis.}, journal = {Research in microbiology}, volume = {174}, number = {4}, pages = {104039}, doi = {10.1016/j.resmic.2023.104039}, pmid = {36738814}, issn = {1769-7123}, abstract = {OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.}, }
@article {pmid36738611, year = {2023}, author = {Zhang, Y and Zhao, Z and Xu, H and Wang, L and Liu, R and Jia, X}, title = {Fate of antibiotic resistance genes and bacteria in a coupled water-processing system with wastewater treatment plants and constructed wetlands in coastal eco-industrial parks.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114606}, doi = {10.1016/j.ecoenv.2023.114606}, pmid = {36738611}, issn = {1090-2414}, mesh = {*Anti-Bacterial Agents/pharmacology/analysis ; *Waste Disposal, Fluid ; Genes, Bacterial ; Wetlands ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Tetracycline/pharmacology ; Sulfanilamide ; Aminoglycosides/pharmacology ; }, abstract = {In coastal eco-industrial zones, wastewater treatment plants (WWTPs) and constructed wetlands (CWs) can alleviate the challenge of water shortage and the negative effect of sewage discharge, while the problems of antibiotic resistance genes (ARGs) have not attracted enough attention. In this research, the Wafergen SmartChip system was adopted to investigate the ARG profiles in a coupled system combined WWTPs and CWs in a coastal industrial park. Potential risks of antibiotic resistance in chemical industrial wastewater were confirmed due to the higher abundance of target ARGs (> 10[7] copies/mL). General decline with partial enrichment in absolute and relative abundance of ARGs from the WWTPs to CWs revealed the effective removal of ARGs in the coupled system, while the fate of different ARG types varied greatly. Aminoglycoside and sulfonamide ARGs were detected with higher abundance (up to 5.34 ×10[7] and 3.61 ×10[7] copies/mL), especially aac(6')-Ib and sul1. Denitrification, secondary sedimentation, and acid hydrolysis contributed to the removal of aminoglycoside, sulfonamide, β-lactamase, chloramphenicol, and multidrug ARGs. Catalytic ozonation contributed to the removal of tetracycline and MLSB ARGs. Subsurface CWs worked effectively for the removal of sulfonamide, tetracycline, and multidrug ARGs, especially tetX, cphA, tetG, and strB. Close correlations between ARGs and MGEs emphasized the vital roles of anthropogenic pollutants and horizontal gene transfer on the diffusion of ARGs. Actinobacteria, Bacteroidota, and Cyanobacteria were dominant in the CWs, while Proteobacteria, Firmicutes, and Planctomycetota were prevalent in the WWTPs. Redundancy analysis and variance partitioning analysis indicated that transposase and water quality posed greater influences on the distribution of ARGs. Co-occurrence network revealed that potential multiple antibiotic resistant pathogenic bacteria decreased in the CWs. The coupled system has a limited effect on the reduction of ARGs and potential ARG hosts, providing a comprehensive insight into the fate of ARGs in conventional water-processing systems.}, }
@article {pmid36732595, year = {2023}, author = {Bhattacharjee, AS and Schulz, F and Woyke, T and Orcutt, BN and Martínez Martínez, J}, title = {Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {10}, pmid = {36732595}, issn = {2730-6151}, abstract = {The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNA[Tyr] gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.}, }
@article {pmid36727472, year = {2023}, author = {Daveri, A and Benigno, V and van der Meer, JR}, title = {Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida.}, journal = {Nucleic acids research}, volume = {51}, number = {5}, pages = {2345-2362}, pmid = {36727472}, issn = {1362-4962}, mesh = {*Pseudomonas putida/genetics ; Type IV Secretion Systems/genetics ; Bacterial Proteins/genetics ; Plasmids/genetics ; Conjugation, Genetic/genetics ; Gene Transfer, Horizontal ; }, abstract = {Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.}, }
@article {pmid36726572, year = {2022}, author = {Calero-Cáceres, W and Rodríguez, K and Medina, A and Medina, J and Ortuño-Gutiérrez, N and Sunyoto, T and Dias, CAG and Bastidas-Caldes, C and Ramírez, MS and Harries, AD}, title = {Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032753}, pmid = {36726572}, issn = {1664-302X}, abstract = {The importance of the One Health concept in attempting to deal with the increasing levels of multidrug-resistant bacteria in both human and animal health is a challenge for the scientific community, policymakers, and the industry. The discovery of the plasmid-borne mobile colistin resistance (mcr) in 2015 poses a significant threat because of the ability of these plasmids to move between different bacterial species through horizontal gene transfer. In light of these findings, the World Health Organization (WHO) recommends that countries implement surveillance strategies to detect the presence of plasmid-mediated colistin-resistant microorganisms and take suitable measures to control and prevent their dissemination. Seven years later, ten different variants of the mcr gene (mcr-1 to mcr-10) have been detected worldwide in bacteria isolated from humans, animals, foods, the environment, and farms. However, the possible transmission mechanisms of the mcr gene among isolates from different geographical origins and sources are largely unknown. This article presents an analysis of whole-genome sequences of Escherichia coli that harbor mcr-1 gene from different origins (human, animal, food, or environment) and geographical location, to identify specific patterns related to virulence genes, plasmid content and antibiotic resistance genes, as well as their phylogeny and their distribution with their origin. In general, E. coli isolates that harbor mcr-1 showed a wide plethora of ARGs. Regarding the plasmid content, the highest concentration of plasmids was found in animal samples. In turn, Asia was the continent that led with the largest diversity and occurrence of these plasmids. Finally, about virulence genes, terC, gad, and traT represent the most frequent virulence genes detected. These findings highlight the relevance of analyzing the environmental settings as an integrative part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance.}, }
@article {pmid36726175, year = {2023}, author = {Petersen, C and Sørensen, T and Nielsen, MR and Sondergaard, TE and Sørensen, JL and Fitzpatrick, DA and Frisvad, JC and Nielsen, KL}, title = {Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {3}, pmid = {36726175}, issn = {2210-6340}, abstract = {The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.}, }
@article {pmid36724669, year = {2023}, author = {Adenaya, A and Berger, M and Brinkhoff, T and Ribas-Ribas, M and Wurl, O}, title = {Usage of antibiotics in aquaculture and the impact on coastal waters.}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114645}, doi = {10.1016/j.marpolbul.2023.114645}, pmid = {36724669}, issn = {1879-3363}, mesh = {Humans ; *Anti-Bacterial Agents/analysis ; Ecosystem ; Aquaculture ; *Environmental Pollutants ; Water ; }, abstract = {For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.}, }
@article {pmid36724283, year = {2023}, author = {Sarma, S and Bhattacharjee, A and Devi, MV and Panyang, PP and Singh, AK}, title = {Long-term adaptation of ParA, RelE/ParE partition system, replication protein and phage proteins encoding low-cost plasmids of Escherichia species isolated from diarrheic children of North East India.}, journal = {Journal of applied microbiology}, volume = {134}, number = {2}, pages = {}, doi = {10.1093/jambio/lxac065}, pmid = {36724283}, issn = {1365-2672}, mesh = {Humans ; Child ; beta-Lactamases/genetics/metabolism ; Escherichia coli/genetics ; Klebsiella pneumoniae/genetics/metabolism ; Plasmids/genetics ; Klebsiella/metabolism ; India ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Bacterial Toxins ; *Escherichia coli Proteins/genetics ; }, abstract = {AIMS: The prevalent distribution of plasmid-mediated β-lactam resistance is the most pressing global problem in enteric diseases. The current work aims to characterize plasmid-carrying β-lactam resistant Enterobacteriaceae isolates from North East India for horizontal gene transfer (HGT) and plasmid adaptation study.<br><br>METHODS AND RESULTS: In vitro transconjugation and transformation showed overall high conjugation frequency (4.11&#xa0;&#xd7;&#xa0;10-1-9.2&#xa0;&#xd7;&#xa0;10-1) and moderate transformation efficiency/&#xb5;g DNA (1.02&#xa0;&#xd7;&#xa0;102 -1&#xa0;&#xd7;&#xa0;103), and the highest conjugation frequency (9.2&#xa0;&#xd7;&#xa0;10-1) and transformation efficiency (1&#xa0;&#xd7;&#xa0;103) for Escherichia species S-10. Intra/intergenus plasmid transformation efficiency was highest for the transformation of Klebsiella pneumoniae S-2 to Shigellaflexneri S-42 (1.3&#xa0;&#xd7;&#xa0;103) and lowest for Escherichia species S-10 to Escherichia fergusonii S-30 (2&#xa0;&#xd7;&#xa0;102). In the plasmid stability test, S-10 was detected with the highest plasmid carrying frequency (83.44%) and insignificant segregational loss rate (0.0004) until the 60th day with low plasmid cost on the host. The above findings were also validated by whole-plasmid sequencing of Escherichia species S-10. The genome was identified with two plasmids constituting multiple phage proteins, relaxosomal protein NikA, replication protein RepA, and the plasmid maintenance proteins (ParA, RelE/ParE), thus assisting stable plasmid maintenance.<br><br>CONCLUSIONS: The results thus indicate that the high conjugation ability and low plasmid fitness cost might lead to horizontal gene transfer of the plasmid to the environment due to their prolonged adaptation in nonselective conditions, intensifying the infection's severity.}, }
@article {pmid36722946, year = {2023}, author = {Carrilero, L and Dunn, SJ and Moran, RA and McNally, A and Brockhurst, MA}, title = {Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0071322}, pmid = {36722946}, issn = {2379-5077}, support = {BB/R006253/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R006261/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {*Escherichia coli/genetics ; Plasmids/genetics ; *Genome, Bacterial/genetics ; Drug Resistance, Multiple ; Genomics ; }, abstract = {Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ~700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions. IMPORTANCE Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. Using experimental evolution with diverse E. coli lineages and a clinical multidrug resistance plasmid, we show that although plasmids drove unique evolutionary paths per lineage, there was a surprising degree of convergence in the functions targeted by mutations across lineages, dominated by metabolic functions. Remarkably, these same metabolic functions show higher evolutionary rates in MDR-lineages in nature and in some cases, like anaerobic metabolism, their expression is directly manipulated by the plasmid. Interactions with other mobile elements resident in the genomes accelerated adaptation by disrupting genes and regulatory sequences that they inserted into. Beyond their role in horizontal gene transfer, plasmids are an important selective force driving the evolution of bacterial genomes and core cellular functions.}, }
@article {pmid36720410, year = {2023}, author = {Zhao, H and Liu, X and Sun, Y and Liu, J and Waigi, MG}, title = {Effects and mechanisms of plant growth regulators on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation.}, journal = {Chemosphere}, volume = {318}, number = {}, pages = {137997}, doi = {10.1016/j.chemosphere.2023.137997}, pmid = {36720410}, issn = {1879-1298}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Escherichia coli/genetics ; Plant Growth Regulators/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria ; Genes, Bacterial ; Plasmids/genetics ; Gene Transfer, Horizontal ; }, abstract = {A vast number of bacteria occur in both soil and plants, with some of them harboring antibiotic resistance genes (ARGs). When bacteria congregate on the interface of soil particles or on plant root surfaces, these ARGs can be transferred between bacteria via conjugation, leading to the formation of antibiotic-resistant pathogens that threaten human health. Plant growth regulators (PGRs) are widely used in agricultural production, promoting plant growth and increasing crop yields. However, until now, little information has been known about the effects of PGRs on the horizontal gene transfer (HGT) of ARGs. In this study, with Escherichia coli DH5α (carrying RP4 plasmid with Tet[R], Amp[R], Kan[R]) as the donor and E. coli HB101 as the recipient, a series of diparental conjugation experiments were conducted to investigate the effects of indoleacetic acid (IAA), ethel (ETH) and gibberellin (GA3) on HGT of ARGs via plasmid-mediated conjugation. Furthermore, the mechanisms involved were also clarified. The results showed that all three PGRs affected the ARG transfer frequency by inducing the intracellular reactive oxygen species (ROS) formation, changing the cell membrane permeability, and regulating the gene transcription of traA, traL, trfAp, trbBp, kilA, and korA in plasmid RP4. In detail, 50-100 mg⋅L[-1] IAA, 20-50 mg⋅L[-1] ETH and 1500-2500 mg⋅L[-1] GA3 all significantly promoted the ARG conjugation. This study indicated that widespread use of PGRs in agricultural production could affect the HGT of ARGs via plasmid-mediated conjugation, and the application of reasonable concentrations of PGRs could reduce the ARG transmission in both soil environments and plants.}, }
@article {pmid36719227, year = {2023}, author = {Cesa-Luna, C and Geudens, N and Girard, L and De Roo, V and Maklad, HR and Martins, JC and Höfte, M and De Mot, R}, title = {Charting the Lipopeptidome of Nonpathogenic Pseudomonas.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0098822}, pmid = {36719227}, issn = {2379-5077}, mesh = {*Pseudomonas/genetics ; *Pseudomonas fluorescens/genetics ; Lipopeptides ; Phylogeny ; }, abstract = {A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.}, }
@article {pmid36717488, year = {2023}, author = {Ishibashi, K and Tanaka, Y and Morishita, Y}, title = {Evolutionary Overview of Aquaporin Superfamily.}, journal = {Advances in experimental medicine and biology}, volume = {1398}, number = {}, pages = {81-98}, doi = {10.1007/978-981-19-7415-1_6}, pmid = {36717488}, issn = {0065-2598}, mesh = {Phylogeny ; *Genome ; *Aquaporins/genetics/chemistry/metabolism ; }, abstract = {Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.}, }
@article {pmid36715351, year = {2023}, author = {Liu, H and Huang, W and Yu, Y and Chen, D}, title = {Lightning-Rod Effect on Nanowire Tips Reinforces Electroporation and Electrochemical Oxidation: An Efficient Strategy for Eliminating Intracellular Antibiotic Resistance Genes.}, journal = {ACS nano}, volume = {17}, number = {3}, pages = {3037-3046}, doi = {10.1021/acsnano.2c11811}, pmid = {36715351}, issn = {1936-086X}, mesh = {Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Disinfection ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Electroporation ; Genes, Bacterial ; *Lightning ; *Nanowires ; *Water Purification/methods ; Oxidation-Reduction ; Intracellular Space/metabolism ; }, abstract = {Conventional oxidative disinfection methods are usually inefficient to eliminate intracellular antibiotic resistance genes (i-ARGs) due to competitive oxidation of cellular components of antibiotic-resistant bacteria (ARB), resulting in the ubiquitous occurrence of ARGs in drinking water systems. Herein, we developed the strategy of coupling electroporation and electrochemical oxidation on a Co3O4-nanowires-modified electrode to destroy the multiresistant Escherichia coli cells and promote subsequent i-ARG (blaTEM-1 and aac(3)-II) degradation. The lightning-rod effect over nanowire tips can form finite regions with a locally enhanced electric field and highly concentrated charge density, in turn facilitating the electroporation for ARB cell damage and electrochemical reactivity for reactive chlorine/oxygen species generation. Characterization of the ARB membrane integrity and morphology revealed that electroporation-induced cell pores were further enlarged by the oxidation of reactive species, resulting in i-ARG removal at lower applied voltages and with 6-9 times lower energy consumption than the conventional electrochemical oxidation approach with a Co3O4-film-modified electrode. The satisfactory application and effective inhibition of horizontal gene transfer in tap water further demonstrated the great potential of our strategy in the control of the ARG dissemination risk in drinking water systems.}, }
@article {pmid36714980, year = {2023}, author = {Cheng, YY and Zhou, Z and Papadopoulos, JM and Zuke, JD and Falbel, TG and Anantharaman, K and Burton, BM and Venturelli, OS}, title = {Efficient plasmid transfer via natural competence in a microbial co-culture.}, journal = {Molecular systems biology}, volume = {19}, number = {3}, pages = {e11406}, pmid = {36714980}, issn = {1744-4292}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Coculture Techniques ; Plasmids/genetics ; *DNA ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; }, abstract = {The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.}, }
@article {pmid36714722, year = {2022}, author = {Zhu, X and Chen, WJ and Bhatt, K and Zhou, Z and Huang, Y and Zhang, LH and Chen, S and Wang, J}, title = {Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1063393}, pmid = {36714722}, issn = {1664-462X}, abstract = {With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.}, }
@article {pmid36712336, year = {2022}, author = {Kuroyanagi, T and Bulasag, AS and Fukushima, K and Ashida, A and Suzuki, T and Tanaka, A and Camagna, M and Sato, I and Chiba, S and Ojika, M and Takemoto, D}, title = {Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac274}, pmid = {36712336}, issn = {2752-6542}, abstract = {The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in >400 plant species, but it is not known how this pathogen evolved this polyxenous nature. Botrytis cinerea can metabolize a wide range of phytoalexins, including the stilbenoid resveratrol in grape, and the sesquiterpenoids capsidiol in tobacco and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone, which was then further oxidized, while rishitin was directly oxidized to epoxy- or hydroxyrishitins, indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNA-seq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are found in taxonomically distant Ascomycota fungi but not in related Leotiomycetes species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.}, }
@article {pmid36708845, year = {2023}, author = {Xiao, R and Huang, D and Du, L and Song, B and Yin, L and Chen, Y and Gao, L and Li, R and Huang, H and Zeng, G}, title = {Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161855}, doi = {10.1016/j.scitotenv.2023.161855}, pmid = {36708845}, issn = {1879-1026}, mesh = {Humans ; *Soil/chemistry ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.}, }
@article {pmid36706177, year = {2023}, author = {Melamed, JR and Yerneni, SS and Arral, ML and LoPresti, ST and Chaudhary, N and Sehrawat, A and Muramatsu, H and Alameh, MG and Pardi, N and Weissman, D and Gittes, GK and Whitehead, KA}, title = {Ionizable lipid nanoparticles deliver mRNA to pancreatic β cells via macrophage-mediated gene transfer.}, journal = {Science advances}, volume = {9}, number = {4}, pages = {eade1444}, pmid = {36706177}, issn = {2375-2548}, mesh = {RNA, Messenger/genetics ; *Insulin-Secreting Cells ; Lipids ; *Nanoparticles ; Macrophages ; }, abstract = {Systemic messenger RNA (mRNA) delivery to organs outside the liver, spleen, and lungs remains challenging. To overcome this issue, we hypothesized that altering nanoparticle chemistry and administration routes may enable mRNA-induced protein expression outside of the reticuloendothelial system. Here, we describe a strategy for delivering mRNA potently and specifically to the pancreas using lipid nanoparticles. Our results show that delivering lipid nanoparticles containing cationic helper lipids by intraperitoneal administration produces robust and specific protein expression in the pancreas. Most resultant protein expression occurred within insulin-producing β cells. Last, we found that pancreatic mRNA delivery was dependent on horizontal gene transfer by peritoneal macrophage exosome secretion, an underappreciated mechanism that influences the delivery of mRNA lipid nanoparticles. We anticipate that this strategy will enable gene therapies for intractable pancreatic diseases such as diabetes and cancer.}, }
@article {pmid36695602, year = {2023}, author = {Anderson, REV and Chalmers, G and Murray, R and Mataseje, L and Pearl, DL and Mulvey, M and Topp, E and Boerlin, P}, title = {Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0186922}, pmid = {36695602}, issn = {1098-5336}, mesh = {Animals ; Cattle ; Humans ; *Cephalosporins/pharmacology ; Escherichia coli/genetics ; Manure ; Anti-Bacterial Agents/pharmacology ; Ontario ; Multilocus Sequence Typing ; Phylogeny ; beta-Lactamases/genetics ; *Escherichia coli Infections/microbiology ; Plasmids/genetics ; }, abstract = {Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.}, }
@article {pmid36692711, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X}, title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {44430-44438}, pmid = {36692711}, issn = {1614-7499}, mesh = {*Wetlands ; Phylogeny ; Oxidation-Reduction ; *Microbiota ; Sulfur/metabolism ; }, abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.}, }
@article {pmid36692352, year = {2023}, author = {Chen, M and Shao, Y and Luo, J and Yuan, L and Wang, M and Chen, M and Guo, Q}, title = {Penicillin and Cefotaxime Resistance of Quinolone-Resistant Neisseria meningitidis Clonal Complex 4821, Shanghai, China, 1965-2020.}, journal = {Emerging infectious diseases}, volume = {29}, number = {2}, pages = {341-350}, pmid = {36692352}, issn = {1080-6059}, mesh = {*Neisseria meningitidis/genetics ; Penicillins ; *Quinolones/pharmacology ; Cefotaxime/pharmacology ; China/epidemiology ; Neisseria/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Penicillin Resistance/genetics ; }, abstract = {Clonal complex 4821 (CC4821) Neisseria meningitidis, usually resistant to quinolones but susceptible to penicillin and third-generation cephalosporins, is increasing worldwide. To characterize the penicillin-nonsusceptible (Pen[NS]) meningococci, we analyzed 491 meningococci and 724 commensal Neisseria isolates in Shanghai, China, during 1965-2020. The Pen[NS] proportion increased from 0.3% in 1965-1985 to 7.0% in 2005-2014 and to 33.3% in 2015-2020. Of the 26 Pen[NS] meningococci, 11 (42.3%) belonged to the CC4821 cluster; all possessed mutations in penicillin-binding protein 2, mostly from commensal Neisseria. Genetic analyses and transformation identified potential donors of 6 penA alleles. Three Pen[NS] meningococci were resistant to cefotaxime, 2 within the CC4821 cluster. With 96% of the Pen[NS] meningococci beyond the coverage of scheduled vaccination and the cefotaxime-resistant isolates all from toddlers, quinolone-resistant CC4821 has acquired penicillin and cefotaxime resistance closely related to the internationally disseminated ceftriaxone-resistant gonococcal FC428 clone, posing a greater threat especially to young children.}, }
@article {pmid36690118, year = {2023}, author = {Yue, Z and Zhang, J and Ding, C and Wang, Y and Zhou, Z and Yu, X and Zhang, T and Wang, X}, title = {Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161742}, doi = {10.1016/j.scitotenv.2023.161742}, pmid = {36690118}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Arachis ; Genes, Bacterial ; Manure/analysis ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.}, }
@article {pmid36689882, year = {2023}, author = {An, R and Qi, Y and Zhang, XX and Ma, L}, title = {Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects.}, journal = {Water research}, volume = {231}, number = {}, pages = {119629}, doi = {10.1016/j.watres.2023.119629}, pmid = {36689882}, issn = {1879-2448}, mesh = {Humans ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; Environmental Pollution ; }, abstract = {Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.}, }
@article {pmid36688638, year = {2023}, author = {Bhandari, M and Rathnayake, IU and Huygens, F and Jennison, AV}, title = {Clinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0263122}, pmid = {36688638}, issn = {2165-0497}, mesh = {Humans ; *Cholera/epidemiology/microbiology ; *Vibrio cholerae non-O1/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Serogroup ; Phylogeny ; Travel ; Genetic Variation ; Drug Resistance, Bacterial/genetics ; }, abstract = {Cholera caused by pathogenic Vibrio cholerae is still considered one of the major health problems in developing countries including those in Asia and Africa. Australia is known to have unique V. cholerae strains in Queensland waterways, resulting in sporadic cholera-like disease being reported in Queensland each year. We conducted virulence and antimicrobial genetic characterization of O1 and non-O1, non-O139 V. cholerae (NOVC) strains (1983 to 2020) from Queensland with clinical significance and compared these to environmental strains that were collected as part of a V. cholerae monitoring project in 2012 of Queensland waterways. In this study, 87 V. cholerae strains were analyzed where O1 (n = 5) and NOVC (n = 54) strains from Queensland and international travel-associated NOVC (n = 2) (61 in total) strains were sequenced, characterized, and compared with seven previously sequenced O1 strains and 18 other publicly available NOVC strains from Australia and overseas to visualize the genetic context among them. Of the 61 strains, three clinical and environmental NOVC serogroup strains had cholera toxin-producing genes, namely, the CTX phage (identified in previous outbreaks) and the complete Vibrio pathogenicity island 1. Phylogenetic analysis based on core genome analysis showed more than 10 distinct clusters and interrelatedness between clinical and environmental V. cholerae strains from Australia. Moreover, 30 (55%) NOVC strains had the cholix toxin gene (chxA) while only 11 (20%) strains had the mshA gene. In addition, 18 (34%) NOVC strains from Australia had the type three secretion system and discrete expression of type six secretion system genes. Interestingly, four NOVC strains from Australia and one NOVC strain from Indonesia had intSXT, a mobile genetic element. Several strains were found to have beta-lactamase (blaCARB-9) and chloramphenicol acetyltransferase (catB9) genes. Our study suggests that Queensland waterways can harbor highly divergent V. cholerae strains and serve as a reservoir for various V. cholerae-associated virulence genes which could be shared among O1 and NOVC V. cholerae strains via mobile genetic elements or horizontal gene transfer. IMPORTANCE Australia has its own V. cholerae strains, both toxigenic and nontoxigenic, that are associated with cholera disease. This study aimed to characterize a collection of clinical and environmental NOVC strains from Australia to understand their virulence and antimicrobial resistance profile and to place strains from Australia in the genetic context of international strains. The findings from this study suggest the toxigenic V. cholerae strains in the Queensland River water system are of public health concern. Therefore, ongoing monitoring and genomic characterization of V. cholerae strains from the Queensland environment are important and would assist public health departments to track the source of cholera infection early and implement prevention strategies for future outbreaks. Understanding the genomics of V. cholerae could also inform the natural ecology and evolution of this bacterium in natural environments.}, }
@article {pmid36685277, year = {2022}, author = {Gomis-Rüth, FX and Stöcker, W}, title = {Structural and evolutionary insights into astacin metallopeptidases.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {1080836}, pmid = {36685277}, issn = {2296-889X}, abstract = {The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.}, }
@article {pmid36684780, year = {2022}, author = {Wang, Y and Shahid, MQ}, title = {Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1035157}, pmid = {36684780}, issn = {1664-462X}, abstract = {Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.}, }
@article {pmid36680934, year = {2023}, author = {Tang, Y and Shi, Y and Jia, B and Zhang, Y and Wang, Q}, title = {Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa.}, journal = {Biochemical and biophysical research communications}, volume = {645}, number = {}, pages = {30-39}, doi = {10.1016/j.bbrc.2022.12.060}, pmid = {36680934}, issn = {1090-2104}, mesh = {Humans ; Glycerol/metabolism ; *Glycerol Kinase/genetics/metabolism ; Phosphorylation ; *Pseudomonas aeruginosa/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Pseudomonas aeruginosa is a Gram-negative bacterium capable of widespread niches, which is also one of the main bacteria that cause patient infection. The metabolic diversity of Pseudomonas aeruginosa is an essential factor in adapting to a variety of environments. Based on the previous studies, adaptive genetic variation in the glycerol kinase GlpK, the glycerol 3-phosphotransferase, contributes to the fitness of bacteria in human bodies, such as Mycobacterium tuberculosis and Escherichia coli. Thus, this study aimed to explore the molecular evolution and function of glpK in P. aeruginosa. Using extensive population genomic data, we have identified the prevalence of two glpK copies in P. aeruginosa that clustered into distinct branches, which were later known as Clade 1 and 2. The evolution analysis revealed that glpK in Clade 1 derived from an ancestral P. aeruginosa species and the other from an ancient horizontal gene transfer event. In addition, we confirmed that the GlpK in Clade 2 still retained glycerol kinase activity but was much weaker than that of GlpK in Clade 1. We demonstrated the importance of the critical amino acid Q70 in GlpK glycerol kinase activity by point mutation. Furthermore, Co-expression network analysis implied that the two glpK copies of P. aeruginosa regulate separate networks and may be a strategy to improve fitness in P. aeruginosa.}, }
@article {pmid36680256, year = {2023}, author = {Pchelin, IM and Tkachev, PV and Azarov, DV and Gorshkov, AN and Drachko, DO and Zlatogursky, VV and Dmitriev, AV and Goncharov, AE}, title = {A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680256}, issn = {1999-4915}, mesh = {Humans ; *Bacteriophages ; Enterococcus/genetics ; Genome, Viral ; Sequence Analysis, DNA ; Phylogeny ; Myoviridae/genetics ; }, abstract = {In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.}, }
@article {pmid36677319, year = {2022}, author = {Shivaramu, S and Tomasch, J and Kopejtka, K and Nupur,  and Saini, MK and Bokhari, SNH and Küpper, H and Koblížek, M}, title = {The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677319}, issn = {2076-2607}, abstract = {The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L[-1]. When grown at a lower concentration of calcium (2 mg CaCl2 L[-1]) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L[-1] to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.}, }
@article {pmid36676100, year = {2023}, author = {Lila, ASA and Rajab, AAH and Abdallah, MH and Rizvi, SMD and Moin, A and Khafagy, ES and Tabrez, S and Hegazy, WAH}, title = {Biofilm Lifestyle in Recurrent Urinary Tract Infections.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {36676100}, issn = {2075-1729}, abstract = {Urinary tract infections (UTIs) represent one of the most common infections that are frequently encountered in health care facilities. One of the main mechanisms used by bacteria that allows them to survive hostile environments is biofilm formation. Biofilms are closed bacterial communities that offer protection and safe hiding, allowing bacteria to evade host defenses and hide from the reach of antibiotics. Inside biofilm communities, bacteria show an increased rate of horizontal gene transfer and exchange of resistance and virulence genes. Additionally, bacterial communication within the biofilm allows them to orchestrate the expression of virulence genes, which further cements the infestation and increases the invasiveness of the infection. These facts stress the necessity of continuously updating our information and understanding of the etiology, pathogenesis, and eradication methods of this growing public health concern. This review seeks to understand the role of biofilm formation in recurrent urinary tact infections by outlining the mechanisms underlying biofilm formation in different uropathogens, in addition to shedding light on some biofilm eradication strategies.}, }
@article {pmid36675876, year = {2022}, author = {Li, Y and Qi, M and Zhang, Q and Xu, Z and Zhang, Y and Gao, Y and Qi, Y and Qiu, L and Wang, M}, title = {Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, pmid = {36675876}, issn = {2309-608X}, abstract = {The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.}, }
@article {pmid36671285, year = {2023}, author = {Canellas, ALB and de Oliveira, BFR and Laport, MS}, title = {Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671285}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations' Sustainable Development Goals and, due to its multisectoral character, a holistic approach is needed to tackle this issue. Thus, the investigation of environments beyond the clinic is of utmost importance. Here, we investigated thirteen strains of antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most strains carried at least one antimicrobial resistance gene and 11 carried at least one heavy metal resistance gene. Noteworthy, four (30.7%) strains carried the blaKPC gene, coding for a carbapenemase. In particular, the whole-genome sequence of Aeromonas hydrophila strain 34SFC-3 was determined, revealing not only the presence of antimicrobial and heavy metal resistance genes but also a versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative elements, and an IncQ1 plasmid were also detected. Considering the ubiquity of Aeromonas species, their genetic promiscuity, pathogenicity, and intrinsic features to endure environmental stress, our findings reinforce the concept that A. hydrophila truly is a "Jack of all trades'' that should not be overlooked under the One Health perspective.}, }
@article {pmid36671228, year = {2022}, author = {Selvarajan, R and Obize, C and Sibanda, T and Abia, ALK and Long, H}, title = {Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671228}, issn = {2079-6382}, abstract = {Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.}, }
@article {pmid36669850, year = {2023}, author = {Tonkin-Hill, G and Gladstone, RA and Pöntinen, AK and Arredondo-Alonso, S and Bentley, SD and Corander, J}, title = {Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.}, journal = {Genome research}, volume = {33}, number = {1}, pages = {129-140}, pmid = {36669850}, issn = {1549-5469}, support = {204016/Z/16/Z//Wellcome Trust/United Kingdom ; 206194//Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Phylogeny ; *Evolution, Molecular ; *Prokaryotic Cells ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.}, }
@article {pmid36669792, year = {2023}, author = {Breidenstein, A and Ter Beek, J and Berntsson, RP}, title = {Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.}, journal = {Life science alliance}, volume = {6}, number = {4}, pages = {}, pmid = {36669792}, issn = {2575-1077}, mesh = {*Escherichia coli Proteins/metabolism ; Type IV Secretion Systems ; Plasmids/genetics ; DNA ; Esterases/genetics ; }, abstract = {Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.}, }
@article {pmid36669117, year = {2023}, author = {Ishikawa, M and Fujiwara, A and Kosetsu, K and Horiuchi, Y and Kamamoto, N and Umakawa, N and Tamada, Y and Zhang, L and Matsushita, K and Palfalvi, G and Nishiyama, T and Kitasaki, S and Masuda, Y and Shiroza, Y and Kitagawa, M and Nakamura, T and Cui, H and Hiwatashi, Y and Kabeya, Y and Shigenobu, S and Aoyama, T and Kato, K and Murata, T and Fujimoto, K and Benfey, PN and Hasebe, M and Kofuji, R}, title = {GRAS transcription factors regulate cell division planes in moss overriding the default rule.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2210632120}, pmid = {36669117}, issn = {1091-6490}, support = {R35 GM131725/GM/NIGMS NIH HHS/United States ; }, mesh = {*Arabidopsis Proteins/metabolism ; *Arabidopsis/genetics ; Transcription Factors/genetics/metabolism ; Cell Division/genetics ; Plant Roots/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {Plant cells are surrounded by a cell wall and do not migrate, which makes the regulation of cell division orientation crucial for development. Regulatory mechanisms controlling cell division orientation may have contributed to the evolution of body organization in land plants. The GRAS family of transcription factors was transferred horizontally from soil bacteria to an algal common ancestor of land plants. SHORTROOT (SHR) and SCARECROW (SCR) genes in this family regulate formative periclinal cell divisions in the roots of flowering plants, but their roles in nonflowering plants and their evolution have not been studied in relation to body organization. Here, we show that SHR cell autonomously inhibits formative periclinal cell divisions indispensable for leaf vein formation in the moss Physcomitrium patens, and SHR expression is positively and negatively regulated by SCR and the GRAS member LATERAL SUPPRESSOR, respectively. While precursor cells of a leaf vein lacking SHR usually follow the geometry rule of dividing along the division plane with the minimum surface area, SHR overrides this rule and forces cells to divide nonpericlinally. Together, these results imply that these bacterially derived GRAS transcription factors were involved in the establishment of the genetic regulatory networks modulating cell division orientation in the common ancestor of land plants and were later adapted to function in flowering plant and moss lineages for their specific body organizations.}, }
@article {pmid36668832, year = {2022}, author = {Proctor, RH and Hao, G and Kim, HS and Whitaker, BK and Laraba, I and Vaughan, MM and McCormick, SP}, title = {A Novel Trichothecene Toxin Phenotype Associated with Horizontal Gene Transfer and a Change in Gene Function in Fusarium.}, journal = {Toxins}, volume = {15}, number = {1}, pages = {}, pmid = {36668832}, issn = {2072-6651}, mesh = {Phylogeny ; *Fusarium/metabolism ; Gene Transfer, Horizontal ; *Trichothecenes/metabolism ; *Mycotoxins/chemistry ; Phenotype ; }, abstract = {Fusarium trichothecenes are among the mycotoxins of most concern to food and feed safety. Production of these mycotoxins and presence of the trichothecene biosynthetic gene (TRI) cluster have been confirmed in only two multispecies lineages of Fusarium: the Fusarium incarnatum-equiseti (Incarnatum) and F. sambucinum (Sambucinum) species complexes. Here, we identified and characterized a TRI cluster in a species that has not been formally described and is represented by Fusarium sp. NRRL 66739. This fungus is reported to be a member of a third Fusarium lineage: the F. buharicum species complex. Cultures of NRRL 66739 accumulated only two trichothecenes, 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol. Although these are not novel trichothecenes, the production profile of NRRL 66739 is novel, because in previous reports 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol were components of mixtures of 6-8 trichothecenes produced by several Fusarium species in Sambucinum. Heterologous expression analysis indicated that the TRI13 gene in NRRL 66739 confers trichothecene 7-hydroxylation. This contrasts the trichothecene 4-hydroxylation function of TRI13 in other Fusarium species. Phylogenetic analyses suggest that NRRL 66739 acquired the TRI cluster via horizontal gene transfer from a close relative of Incarnatum and Sambucinum. These findings provide insights into evolutionary processes that have shaped the distribution of trichothecene production among Fusarium species and the structural diversity of the toxins.}, }
@article {pmid36655280, year = {2023}, author = {Shin, H and Kim, Y and Han, S and Hur, HG}, title = {Resistome Study in Aquatic Environments.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {3}, pages = {277-287}, pmid = {36655280}, issn = {1738-8872}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; }, abstract = {Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs (e.g., strA, sul1, int1) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.}, }
@article {pmid36653393, year = {2023}, author = {Couturier, A and Virolle, C and Goldlust, K and Berne-Dedieu, A and Reuter, A and Nolivos, S and Yamaichi, Y and Bigot, S and Lesterlin, C}, title = {Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {294}, pmid = {36653393}, issn = {2041-1723}, mesh = {DNA, Bacterial/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Conjugation, Genetic ; Plasmids/genetics ; DNA ; DNA, Single-Stranded/genetics ; Gene Transfer, Horizontal ; }, abstract = {Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.}, }
@article {pmid36653270, year = {2023}, author = {Murakami, H and Sano, K and Motomura, K and Kuroda, A and Hirota, R}, title = {Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system.}, journal = {Journal of bioscience and bioengineering}, volume = {135}, number = {3}, pages = {190-195}, doi = {10.1016/j.jbiosc.2022.12.002}, pmid = {36653270}, issn = {1347-4421}, mesh = {*Gene Transfer, Horizontal ; Ecosystem ; *Synechococcus/metabolism ; Phosphates/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.}, }
@article {pmid36641904, year = {2023}, author = {Alnahhas, RN and Dunlop, MJ}, title = {Advances in linking single-cell bacterial stress response to population-level survival.}, journal = {Current opinion in biotechnology}, volume = {79}, number = {}, pages = {102885}, pmid = {36641904}, issn = {1879-0429}, support = {R01 AI102922/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents ; *Bacteria/genetics ; Phenotype ; }, abstract = {Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.}, }
@article {pmid36639816, year = {2023}, author = {Zhu, J and Yang, F and Du, K and Wei, ZL and Wu, QF and Chen, Y and Li, WF and Li, Q and Zhou, CZ}, title = {Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {3}, pmid = {36639816}, issn = {2524-6372}, abstract = {BACKGROUND: Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.<br><br>RESULTS: Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0&#xa0;kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the &#x3b1;-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and &#x3b1;-proteobacteria.<br><br>CONCLUSION: In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.}, }
@article {pmid36638983, year = {2023}, author = {Yang, K and Chen, ML and Zhu, D}, title = {Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes.}, journal = {The Science of the total environment}, volume = {867}, number = {}, pages = {161527}, pmid = {36638983}, issn = {1879-1026}, mesh = {Humans ; Sewage/microbiology ; Benzalkonium Compounds/pharmacology ; Genes, Bacterial ; *Disinfectants ; *COVID-19 ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.}, }
@article {pmid36638546, year = {2023}, author = {Gibson, PS and Veening, JW}, title = {Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae.}, journal = {Current opinion in microbiology}, volume = {72}, number = {}, pages = {102261}, doi = {10.1016/j.mib.2022.102261}, pmid = {36638546}, issn = {1879-0364}, mesh = {Child ; Humans ; *Amoxicillin/pharmacology ; Streptococcus pneumoniae/genetics ; *Respiratory Tract Infections/microbiology ; Peptidoglycan ; Biology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.}, }
@article {pmid36634159, year = {2023}, author = {Ryan, MP and Carraro, N and Slattery, S and Pembroke, JT}, title = {Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/1040841X.2022.2161870}, pmid = {36634159}, issn = {1549-7828}, abstract = {Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.}, }
@article {pmid36629415, year = {2023}, author = {Finks, SS and Martiny, JBH}, title = {Plasmid-Encoded Traits Vary across Environments.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0319122}, pmid = {36629415}, issn = {2150-7511}, mesh = {Humans ; *Ecosystem ; Plasmids/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; }, abstract = {Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.}, }
@article {pmid36626782, year = {2022}, author = {Sundarraj, S and Sudarmani, DNP and Samuel, P and Sevarkodiyone, SP}, title = {Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxac019}, pmid = {36626782}, issn = {1365-2672}, abstract = {AIMS: Hexavalent chromium (Cr(VI)), a toxic heavy metal, is a serious pollutant from tannery effluent, and its accumulation in soil and water causes severe environmental concerns and increasing public health issues. The present study focuses on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Ps. putida and transferred to Escherichia coli DH5α for further studies.<br><br>METHODS AND RESULTS: The bacterial cultures were kept under controlled conditions for 72&#xa0;h to observe the growth rates and bacterial resistance to chromium. When strains wild-type and transformant E. coli DH5&#x3b1; were grown in chromium-supplemented media, they revealed significant growth, but strains cured type Ps. putida and E. coli DH5&#x3b1; recorded minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5&#x3b1; and wild Ps. putida was 42.52&#xa0;&#xb1;&#xa0;1.48% and 44.46&#xa0;&#xb1;&#xa0;0.55%, respectively. The culture supernatant of the wild Ps. putida and transformant E. coli DH5&#x3b1; showed an increased reduction of Cr(VI) compared with cell extract supernatant and cell debris due to the extracellular activity of chromium reductase being responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Ps. putida and transformant E. coli DH5&#x3b1;.<br><br>CONCLUSIONS: Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.<br><br>High Cr(VI) concentration resistance and high Cr(VI) reducing the strain's ability make it suitable for bioremediation. These possible horizontal gene transfer events indicated in this study may have enabled transformant E. coli DH5&#x3b1; as a good candidate for reducing the heavy metal pollution.}, }
@article {pmid36623672, year = {2023}, author = {Sazykin, IS and Sazykina, MA}, title = {The role of oxidative stress in genome destabilization and adaptive evolution of bacteria.}, journal = {Gene}, volume = {857}, number = {}, pages = {147170}, doi = {10.1016/j.gene.2023.147170}, pmid = {36623672}, issn = {1879-0038}, mesh = {*Oxidative Stress/genetics ; *Bacteria/genetics ; Mutagenesis ; Genome, Bacterial ; }, abstract = {The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.}, }
@article {pmid36623656, year = {2023}, author = {Wang, C and Jia, Y and Li, J and Wang, Y and Niu, H and Qiu, H and Li, X and Fang, W and Qiu, Z}, title = {Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance.}, journal = {The Science of the total environment}, volume = {867}, number = {}, pages = {161457}, doi = {10.1016/j.scitotenv.2023.161457}, pmid = {36623656}, issn = {1879-1026}, mesh = {Animals ; *Composting ; Manure ; Chickens ; Tetracyclines ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO3[-]-N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.}, }
@article {pmid36622346, year = {2023}, author = {Nieves, C and Vincent, AT and Zarantonelli, L and Picardeau, M and Veyrier, FJ and Buschiazzo, A}, title = {Horizontal transfer of the rfb cluster in Leptospira is a genetic determinant of serovar identity.}, journal = {Life science alliance}, volume = {6}, number = {2}, pages = {}, pmid = {36622346}, issn = {2575-1077}, mesh = {Humans ; *Leptospira/genetics ; Serogroup ; Lipopolysaccharides ; Phenotype ; }, abstract = {Leptospira bacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis-encoding genes reside within the chromosomic rfb gene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of the rfb cluster strongly correlates with Leptospira serovar designation. Whole-genome sequencing of pathogenic L. noguchii, including strains of different serogroups, reveals that the rfb cluster undergoes extensive horizontal gene transfer. The rfb clusters from several Leptospira species disclose a univocal correspondence between gene composition and serovar identity. This work paves the way to genetic typing of Leptospira serovars, and to pinpointing specific genes within the distinct rfb clusters, encoding host-specific virulence traits. Further research shall unveil the molecular mechanism of rfb transfer among Leptospira strains and species.}, }
@article {pmid36622251, year = {2023}, author = {Lindqvist, LL and Jarmusch, SA and Sonnenschein, EC and Strube, ML and Kim, J and Nielsen, MW and Kempen, PJ and Schoof, EM and Zhang, SD and Gram, L}, title = {Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae.}, journal = {mSphere}, volume = {8}, number = {1}, pages = {e0051722}, pmid = {36622251}, issn = {2379-5042}, mesh = {*Type IV Secretion Systems/metabolism ; *Rhodobacteraceae/genetics ; Anti-Bacterial Agents/metabolism ; }, abstract = {In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.}, }
@article {pmid36620013, year = {2022}, author = {Lieberman, LA}, title = {Outer membrane vesicles: A bacterial-derived vaccination system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1029146}, pmid = {36620013}, issn = {1664-302X}, abstract = {Outer membrane vesicles (OMVs) are non-living spherical nanostructures that derive from the cell envelope of Gram-negative bacteria. OMVs are important in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and in maintaining bacterial fitness. These structures can be modified to express antigens of interest using glycoengineering and genetic or chemical modification. The resulting OMVs can be used to immunize individuals against the expressed homo- or heterologous antigens. Additionally, cargo can be loaded into OMVs and they could be used as a drug delivery system. OMVs are inherently immunogenic due to proteins and glycans found on Gram negative bacterial outer membranes. This review focuses on OMV manipulation to increase vesiculation and decrease antigenicity, their utility as vaccines, and novel engineering approaches to extend their application.}, }
@article {pmid36611105, year = {2023}, author = {Aldaihani, R and Heath, LS}, title = {Connecting genomic islands across prokaryotic and phage genomes via protein families.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {344}, pmid = {36611105}, issn = {2045-2322}, mesh = {*Genomic Islands/genetics ; *Bacteriophages/genetics ; Prokaryotic Cells ; Proteins/genetics ; Bacteria/genetics ; Computational Biology/methods ; Gene Transfer, Horizontal ; Genome, Bacterial ; }, abstract = {Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.}, }
@article {pmid36610752, year = {2023}, author = {Botelho, J and Cazares, A and Schulenburg, H}, title = {The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements.}, journal = {Nucleic acids research}, volume = {51}, number = {1}, pages = {236-252}, pmid = {36610752}, issn = {1362-4962}, mesh = {Humans ; *Interspersed Repetitive Sequences/genetics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Gene Transfer, Horizontal/genetics ; Prophages/genetics ; }, abstract = {Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.}, }
@article {pmid36608829, year = {2023}, author = {Tan, Y and Cao, X and Chen, S and Ao, X and Li, J and Hu, K and Liu, S and Penttinen, P and Yang, Y and Yu, X and Liu, A and Liu, C and Zhao, K and Zou, L}, title = {Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161386}, doi = {10.1016/j.scitotenv.2023.161386}, pmid = {36608829}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents ; Sewage/microbiology ; Genes, Bacterial ; *Composting ; *Metals, Heavy ; Bacteria/genetics ; Manure ; }, abstract = {Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.}, }
@article {pmid36608658, year = {2023}, author = {Utter, DR and Orphan, VJ}, title = {Gifts hidden in shadowy genome islands.}, journal = {Cell}, volume = {186}, number = {1}, pages = {5-7}, doi = {10.1016/j.cell.2022.12.001}, pmid = {36608658}, issn = {1097-4172}, mesh = {Archaea/genetics ; *Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.}, }
@article {pmid36608657, year = {2023}, author = {Hackl, T and Laurenceau, R and Ankenbrand, MJ and Bliem, C and Cariani, Z and Thomas, E and Dooley, KD and Arellano, AA and Hogle, SL and Berube, P and Leventhal, GE and Luo, E and Eppley, JM and Zayed, AA and Beaulaurier, J and Stepanauskas, R and Sullivan, MB and DeLong, EF and Biller, SJ and Chisholm, SW}, title = {Novel integrative elements and genomic plasticity in ocean ecosystems.}, journal = {Cell}, volume = {186}, number = {1}, pages = {47-62.e16}, doi = {10.1016/j.cell.2022.12.006}, pmid = {36608657}, issn = {1097-4172}, mesh = {*Ecosystem ; *Genome, Bacterial/genetics ; Phylogeny ; Oceans and Seas ; Genomics ; }, abstract = {Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.}, }
@article {pmid36602323, year = {2023}, author = {Regmi, A and Tague, JG and Boas Lichty, KE and Boyd, EF}, title = {A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0187422}, pmid = {36602323}, issn = {1098-5336}, mesh = {*Adenylyl Cyclases/genetics/metabolism ; *Vibrio parahaemolyticus/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Phylogeny ; Cyclic AMP/metabolism ; Bacterial Proteins/genetics/metabolism ; Cyclic AMP Receptor Protein/genetics/metabolism ; Biofilms ; Polysaccharides ; }, abstract = {Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.}, }
@article {pmid36599855, year = {2023}, author = {Cho, CH and Park, SI and Huang, TY and Lee, Y and Ciniglia, C and Yadavalli, HC and Yang, SW and Bhattacharya, D and Yoon, HS}, title = {Genome-wide signatures of adaptation to extreme environments in red algae.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {10}, pmid = {36599855}, issn = {2041-1723}, mesh = {*Rhodophyta/genetics ; Genome/genetics ; Acclimatization ; *Hot Springs ; *Metals, Heavy ; Phylogeny ; }, abstract = {The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative Cyanidiophyceae species to study environmental adaptation at the genomic level. We find that subtelomeric gene duplication of functional genes and loss of canonical eukaryotic traits played a major role in environmental adaptation, in addition to horizontal gene transfer events. Shared responses to environmental stress exist in Cyanidiales and Galdieriales, however, most of the adaptive genes (e.g., for arsenic detoxification) evolved independently in these lineages. Our results underline the power of local selection to shape eukaryotic genomes that may face vastly different stresses in adjacent, extreme microhabitats.}, }
@article {pmid36598481, year = {2023}, author = {O'Leary, ML and Burbank, LP}, title = {Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0187322}, pmid = {36598481}, issn = {1098-5336}, mesh = {Crops, Agricultural ; DNA Methylation ; Gene Transfer, Horizontal ; Genomics ; *Plant Diseases/genetics/microbiology ; *Xylella/genetics/pathogenicity ; }, abstract = {Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.}, }
@article {pmid36598279, year = {2023}, author = {Xu, C and Rao, J and Xie, Y and Lu, J and Li, Z and Dong, C and Wang, L and Jiang, J and Chen, C and Chen, S}, title = {The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0350922}, pmid = {36598279}, issn = {2165-0497}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; DNA Restriction-Modification Enzymes/genetics ; DNA ; Gene Transfer, Horizontal ; }, abstract = {Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.}, }
@article {pmid36597348, year = {2023}, author = {Lai, CK and Lee, YC and Ke, HM and Lu, MR and Liu, WA and Lee, HH and Liu, YC and Yoshiga, T and Kikuchi, T and Chen, PJ and Tsai, IJ}, title = {The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {905-919}, doi = {10.1111/1755-0998.13752}, pmid = {36597348}, issn = {1755-0998}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Nematoda/genetics ; Phylogeny ; Plants/genetics/parasitology ; }, abstract = {Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.}, }
@article {pmid36592614, year = {2023}, author = {Liu, Y and Chen, J and Raj, K and Baerg, L and Nathan, N and Philpott, DJ and Mahadevan, R}, title = {A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses.}, journal = {ACS synthetic biology}, volume = {12}, number = {1}, pages = {319-328}, doi = {10.1021/acssynbio.2c00583}, pmid = {36592614}, issn = {2161-5063}, mesh = {Humans ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; HEK293 Cells ; Gram-Positive Bacteria ; Gram-Negative Bacteria ; Bacteria ; Immunity, Innate ; *Extracellular Vesicles ; }, abstract = {Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.}, }
@article {pmid36588930, year = {2022}, author = {Martinez-Vaz, BM and Dodge, AG and Lucero, RM and Stockbridge, RB and Robinson, AA and Tassoulas, LJ and Wackett, LP}, title = {Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1086261}, pmid = {36588930}, issn = {2296-4185}, abstract = {Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.}, }
@article {pmid36587809, year = {2023}, author = {Trissi, N and Troczka, BJ and Ozsanlav-Harris, L and Singh, KS and Mallott, M and Aishwarya, V and O'Reilly, A and Bass, C and Wilding, CS}, title = {Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae.}, journal = {Insect biochemistry and molecular biology}, volume = {153}, number = {}, pages = {103896}, doi = {10.1016/j.ibmb.2022.103896}, pmid = {36587809}, issn = {1879-0240}, mesh = {Animals ; *Aphids/physiology ; Lycopene/metabolism ; Pigmentation/genetics ; Carotenoids/metabolism ; }, abstract = {In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.}, }
@article {pmid36586689, year = {2023}, author = {Shi, H and Hu, X and Xu, J and Hu, B and Ma, L and Lou, L}, title = {Conjugation-mediated transfer of antibiotic resistance genes influenced by primary soil components and underlying mechanisms.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161232}, doi = {10.1016/j.scitotenv.2022.161232}, pmid = {36586689}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Bentonite ; Kaolin ; Quartz/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Plasmids ; }, abstract = {Soil is the main natural reservoir of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Their dissemination and proliferation were largely motivated by conjugative transfer, while the influence of soil components on bacterial conjugative transfer and the underlying mechanisms remain poorly understood. In the present study, two Escherichia coli strains were exposed to soil minerals (quartz, kaolinite and montmorillonite) and organic matters (humic acid, biochar and soot) respectively to investigate their impact on ARGs conjugation. The results showed that quartz had no significant effect on conjugation; montmorillonite promoted the growth of the donor, but inhibited the recipient and conjugant; kaolinite and three organic matters significantly promoted the production of conjugant, while biochar promoted and then inhibited it with time prolong. Within the range of bacterial concentration involved in this study, the concentration of conjugant increased with the ratio of the concentration of donor and recipient (RD/R), indicating that the variation of conjugant production was mainly mediated by changing RD/R. Further observation of biochar treatment group showed that the bacterial responses such as cell membrane permeability, cell surface hydrophobicity and biofilm formation ability shifted with the exposure time, which might be a potential factor affecting conjugative transfer. Collectively, our findings suggest that the type and exposure time of soil components jointly affected conjugation, while the change of RD/R and related bacterial responses are the main underlying mechanisms.}, }
@article {pmid36586329, year = {2023}, author = {Nnorom, MA and Saroj, D and Avery, L and Hough, R and Guo, B}, title = {A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130628}, doi = {10.1016/j.jhazmat.2022.130628}, pmid = {36586329}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Sewage/microbiology ; *Genes, Bacterial ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; }, abstract = {The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.}, }
@article {pmid36583227, year = {2023}, author = {Sloan, DB and Warren, JM and Williams, AM and Kuster, SA and Forsythe, ES}, title = {Incompatibility and Interchangeability in Molecular Evolution.}, journal = {Genome biology and evolution}, volume = {15}, number = {1}, pages = {}, pmid = {36583227}, issn = {1759-6653}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Hybridization, Genetic ; *Evolution, Molecular ; }, abstract = {There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.}, }
@article {pmid36582150, year = {2022}, author = {Manaia, CM and Aga, DS and Cytryn, E and Gaze, WH and Graham, DW and Guo, J and Leonard, AFC and Li, L and Murray, AK and Nunes, OC and Rodriguez-Mozaz, S and Topp, E and Zhang, T}, title = {The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/etc.5555}, pmid = {36582150}, issn = {1552-8618}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are important environmental contaminants. Nonetheless, what drives the evolution, spread, and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of ARB and ARGs is often elevated in human-impacted areas, especially in environments receiving fecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products. Self-replication, mutation, horizontal gene transfer, and adaptation to different environmental conditions contribute to the persistence and proliferation of ARB in habitats under strong anthropogenic influence. Our review discusses the interplay between chemical contaminants and ARB and their respective genes, specifically in reference to co-occurrence, potential biostimulation, and selective pressure effects, and gives an overview of mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human health risks due to environmental antibiotic resistance are also discussed. Environ Toxicol Chem 2023;00:1-16. © 2022 SETAC.}, }
@article {pmid36575565, year = {2023}, author = {Chen, H and Tao, S and Li, N and Zhu, Q and Liu, L and Fang, Y and Xu, Y and Liang, W}, title = {Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {2}, pages = {521-530}, doi = {10.1093/jac/dkac423}, pmid = {36575565}, issn = {1460-2091}, mesh = {Humans ; *Klebsiella pneumoniae ; Klebsiella/genetics ; *Klebsiella Infections/microbiology ; Molecular Epidemiology ; Bacterial Proteins/genetics ; beta-Lactamases/genetics/metabolism ; Plasmids ; }, abstract = {BACKGROUND: Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria.<br><br>OBJECTIVES: To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread.<br><br>METHODS: We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro.<br><br>RESULTS: We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P&#x200a;<&#x200a;0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules.<br><br>CONCLUSIONS: These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.}, }
@article {pmid36573357, year = {2023}, author = {Bethke, JH and Ma, HR and Tsoi, R and Cheng, L and Xiao, M and You, L}, title = {Vertical and horizontal gene transfer tradeoffs direct plasmid fitness.}, journal = {Molecular systems biology}, volume = {19}, number = {2}, pages = {e11300}, pmid = {36573357}, issn = {1744-4292}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 GM098642/GM/NIGMS NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.}, }
@article {pmid36572269, year = {2023}, author = {Beltrán de Heredia, I and Garbisu, C and Alkorta, I and Urra, J and González-Gaya, B and Ruiz-Romera, E}, title = {Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {319}, number = {}, pages = {120883}, doi = {10.1016/j.envpol.2022.120883}, pmid = {36572269}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; Seasons ; *Ecosystem ; Wastewater ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/analysis ; Water ; }, abstract = {There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.}, }
@article {pmid36571993, year = {2023}, author = {Su, Z and Wen, D and Gu, AZ and Zheng, Y and Tang, Y and Chen, L}, title = {Industrial effluents boosted antibiotic resistome risk in coastal environments.}, journal = {Environment international}, volume = {171}, number = {}, pages = {107714}, doi = {10.1016/j.envint.2022.107714}, pmid = {36571993}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Bacteria/genetics ; Genes, Bacterial ; Sewage ; }, abstract = {Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.}, }
@article {pmid36571495, year = {2023}, author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL}, title = {Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {800-810}, doi = {10.1111/1462-2920.16329}, pmid = {36571495}, issn = {1462-2920}, mesh = {Genes, Viral ; *Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; *Microbiota/genetics ; Soil ; }, abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.}, }
@article {pmid36568361, year = {2022}, author = {Nayar, G and Terrizzano, I and Seabolt, E and Agarwal, A and Boucher, C and Ruiz, J and Slizovskiy, IB and Kaufman, JH and Noyes, NR}, title = {ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1024577}, pmid = {36568361}, issn = {1664-8021}, abstract = {Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.}, }
@article {pmid36567403, year = {2023}, author = {Feng, R and Duan, L and Shen, S and Cheng, Y and Wang, Y and Wang, W and Yang, S}, title = {Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community.}, journal = {Ecotoxicology (London, England)}, volume = {32}, number = {1}, pages = {57-72}, doi = {10.1007/s10646-022-02616-5}, pmid = {36567403}, issn = {1573-3017}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Sulfanilamide ; }, abstract = {The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.}, }
@article {pmid36563663, year = {2022}, author = {Vatanen, T and Jabbar, KS and Ruohtula, T and Honkanen, J and Avila-Pacheco, J and Siljander, H and Stražar, M and Oikarinen, S and Hyöty, H and Ilonen, J and Mitchell, CM and Yassour, M and Virtanen, SM and Clish, CB and Plichta, DR and Vlamakis, H and Knip, M and Xavier, RJ}, title = {Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.}, journal = {Cell}, volume = {185}, number = {26}, pages = {4921-4936.e15}, pmid = {36563663}, issn = {1097-4172}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Mothers ; Breast Feeding ; Feces ; Interspersed Repetitive Sequences ; }, abstract = {The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.}, }
@article {pmid36561977, year = {2022}, author = {González-Villarreal, JA and González-Lozano, KJ and Aréchiga-Carvajal, ET and Morlett-Chávez, JA and Luévanos-Escareño, MP and Balagurusamy, N and Salinas-Santander, MA}, title = {Molecular mechanisms of multidrug resistance in clinically relevant enteropathogenic bacteria (Review).}, journal = {Experimental and therapeutic medicine}, volume = {24}, number = {6}, pages = {753}, pmid = {36561977}, issn = {1792-1015}, abstract = {Multidrug resistant (MDR) enteropathogenic bacteria are a growing problem within the clinical environment due to their acquired tolerance to a wide range of antibiotics, thus causing severe illnesses and a tremendous economic impact in the healthcare sector. Due to its difficult treatment, knowledge and understanding of the molecular mechanisms that confer this resistance are needed. The aim of the present review is to describe the mechanisms of antibiotic resistance from a genomic perspective observed in bacteria, including naturally acquired resistance. The present review also discusses common pharmacological and alternative treatments used in cases of infection caused by MDR bacteria, thus covering necessary information for the development of novel antimicrobials and adjuvant molecules inhibiting bacterial proliferation.}, }
@article {pmid36560776, year = {2022}, author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ}, title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560776}, issn = {1999-4915}, support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; *Clostridioides difficile ; Clostridioides ; Prophages/genetics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.}, }
@article {pmid36560636, year = {2022}, author = {Ács, N and Holohan, R and Dunne, LJ and Fernandes, AR and Clooney, AG and Draper, LA and Ross, RP and Hill, C}, title = {Comparing In Vitro Faecal Fermentation Methods as Surrogates for Phage Therapy Application.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560636}, issn = {1999-4915}, mesh = {Humans ; Fermentation ; *Phage Therapy ; Feces ; Gastrointestinal Tract ; *Bacteriophages/genetics ; }, abstract = {The human microbiome and its importance in health and disease have been the subject of numerous research articles. Most microbes reside in the digestive tract, with up to 10[12] cells per gram of faecal material found in the colon. In terms of gene number, it has been estimated that the gut microbiome harbours >100 times more genes than the human genome. Several human intestinal diseases are strongly associated with disruptions in gut microbiome composition. Less studied components of the gut microbiome are the bacterial viruses called bacteriophages that may be present in numbers equal to or greater than the prokaryotes. Their potential to lyse their bacterial hosts, or to act as agents of horizontal gene transfer makes them important research targets. In this study in vitro faecal fermentation systems were developed and compared for their ability to act as surrogates for the human colon. Changes in bacterial and viral composition occurred after introducing a high-titre single phage preparation both with and without a known bacterial host during the 24 h-long fermentation. We also show that during this timeframe 50 mL plastic tubes can provide data similar to that generated in a sophisticated faecal fermenter system. This knowledge can guide us to a better understanding of the short-term impact of bacteriophage transplants on the bacteriomes and viromes of human recipients.}, }
@article {pmid36558750, year = {2022}, author = {de Brito, FAE and de Freitas, APP and Nascimento, MS}, title = {Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36558750}, issn = {2076-0817}, abstract = {Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.}, }
@article {pmid36555178, year = {2022}, author = {Janczarek, M}, title = {The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555178}, issn = {1422-0067}, mesh = {Phylogeny ; Amino Acid Sequence ; *Bacterial Proteins/metabolism ; *Zinc Fingers/genetics ; Transcription Factors/genetics ; Bacteria/metabolism ; Zinc/metabolism ; }, abstract = {Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.}, }
@article {pmid36551459, year = {2022}, author = {Lienen, T and Grobbel, M and Tenhagen, BA and Maurischat, S}, title = {Plasmid-Coded Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus from Food and Livestock in Germany.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551459}, issn = {2079-6382}, abstract = {Resistance of methicillin-resistant Staphylococcus aureus (MRSA) from food and livestock to last resort antibiotics such as linezolid is highly concerning, since treatment options for infections in humans might be diminished. Known mechanisms of linezolid resistance include point mutations in the 23S rRNA gene and in the ribosomal proteins L3, L4 and L22 as well as an acquisition of the cfr, optrA or poxtA gene. The objective of our study was to characterize antimicrobial resistance (AMR) determinants and phylogenetic relationships among linezolid-resistant (LR-) MRSA from food and livestock. In total, from more than 4000 incoming isolates in the years 2012 to 2021, only two strains from 2015 originating from pig samples exhibited linezolid resistance in the antimicrobial susceptibility testing with MICs of ≥8 mg/L. These LR-MRSA were characterized in detail by whole-genome sequencing and phylogenetic analyses using cgMLST. The LR-MRSA strains showed resistances to ten and eight different antibiotics, respectively. Both strains harbored plasmid-coded cfr genes mediating the linezolid resistance. The cfr genes showed identical sequences in both strains. In addition to the cfr gene, genes for phenicol and clindamycin resistance were detected on the respective plasmids, opening the possibility for a co-selection. The LR-MRSA differed distantly in the phylogenetic analyses and also to other MRSA from pig samples in the year 2015. In conclusion, the occurrence of LR-MRSA in food and livestock seems to be very rare in Germany. However, carriage of plasmids with linezolid resistance determinants could lead to further linezolid-resistant strains by horizontal gene transfer.}, }
@article {pmid36549493, year = {2023}, author = {Abudureheman, M and Ailijiang, N and Mamat, A and Feng, Y and He, C and Pu, M}, title = {Enhanced biodegradation of fluoroquinolones and the changes of bacterial communities and antibiotic-resistant genes under intermittent electrical stimulation.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115127}, doi = {10.1016/j.envres.2022.115127}, pmid = {36549493}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Fluoroquinolones/pharmacology/analysis/metabolism ; Wastewater ; Bacteria/genetics/metabolism ; Electric Stimulation ; Genes, Bacterial ; }, abstract = {In this study, an anaerobic-aerobic coupling system under intermittent electrical stimulation was used to improve the biodegradation of synthetic wastewater containing fluoroquinolones (FQs). The effect of electrical stimulation on FQ removal performance is more pronounced with appropriate voltage and hydraulic retention time. In addition, the combination of anaerobic-anodic and aerobic-cathodic chambers is more conducive to improving the removal efficiency of FQs. Under 0.9 V, the removal efficiencies of ofloxacin, norfloxacin, ciprofloxacin, and enrofloxacin were significantly improved in the anaerobic-anodic and aerobic-cathodic system. The contribution of the anaerobic/aerobic anodic chambers to FQ removal was greater than that of the anaerobic/aerobic cathodic chambers. Electrical stimulation selectively enriched electroactive bacteria related to biodegradation (Desulfovibrio and Terrimonas), antibiotic-resistant bacteria (Atopobium and Neochlamydia), and nitrifying bacteria (SM1A02 and Reyranella). This study indicated the potential effectiveness of intermittent electrical stimulation in treating fluoroquinolone-containing wastewater in a biofilm reactor. However, electrical stimulation led to an increase in mobile genetic elements , induced horizontal gene transfer and enriched resistant bacteria, which accelerated the spread of antibiotic-resistant genes (ARGs) in the system, indicating that the diffusion of ARGs remains a challenge.}, }
@article {pmid36539881, year = {2022}, author = {Kwun, MJ and Ion, AV and Cheng, HC and D'Aeth, JC and Dougan, S and Oggioni, MR and Goulding, DA and Bentley, SD and Croucher, NJ}, title = {Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {144}, pmid = {36539881}, issn = {1756-994X}, support = {102169/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; BB/N002903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; 104169/Z/14/A/WT_/Wellcome Trust/United Kingdom ; MR/T016434/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Streptococcus pneumoniae/genetics ; Serogroup ; *Pneumococcal Infections/epidemiology/prevention &amp; control/microbiology ; Prophages/genetics ; Pneumococcal Vaccines ; Vaccines, Conjugate ; RNA, Untranslated/genetics/pharmacology ; }, abstract = {BACKGROUND: The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).<br><br>METHODS: A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics,&#xa0;and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain's evolution.<br><br>RESULTS: GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage &#x3d5;OXC141. Prior to the introduction of PCV13, this clade's composition shifted towards a &#x3d5;OXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also &#x3d5;OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage &#x3d5;OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation.<br><br>CONCLUSION: This interference with the quorum sensing needed to induce competence reduces the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.}, }
@article {pmid36537743, year = {2022}, author = {Lisboa, MP and Canal, D and Filgueiras, JPC and Turchetto-Zolet, AC}, title = {Molecular evolution and diversification of phytoene synthase (PSY) gene family.}, journal = {Genetics and molecular biology}, volume = {45}, number = {4}, pages = {e20210411}, pmid = {36537743}, issn = {1415-4757}, abstract = {Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.}, }
@article {pmid36536072, year = {2023}, author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P}, title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {354-370}, pmid = {36536072}, issn = {1751-7370}, mesh = {*Ecosystem ; Brazil ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics/metabolism ; Plants/metabolism ; Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; }, abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.}, }
@article {pmid36532464, year = {2022}, author = {Li, P and Luo, W and Xiang, TX and Jiang, Y and Liu, P and Wei, DD and Fan, L and Huang, S and Liao, W and Liu, Y and Zhang, W}, title = {Horizontal gene transfer via OMVs co-carrying virulence and antimicrobial-resistant genes is a novel way for the dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {945972}, pmid = {36532464}, issn = {1664-302X}, abstract = {INTRODUCTION: The rapidly increased isolation rate of CR-HvKP worldwide has brought great difficulties in controlling clinical infection. Moreover, it has been demonstrated that the transmission of drug-resistant genes among bacteria can be mediated by outer membrane vesicles (OMVs), which is a new way of horizontal gene transfer (HGT). The transmission of virulence genes among bacteria has also been well studied; however, it remains unclear whether virulence and drug-resistant genes can be co-transmitted simultaneously. Co-transmission of virulence and drug-resistant genes is essential for the formation and prevalence of CR-HvKP.<br><br>METHODS: First, we isolated OMVs from CR-HvKP by cushioned-density gradient ultracentrifugation (C-DGUC). TEM and DLS were used to examine the morphology and size of bacterial OMVs. OMV-mediated gene transfer in liquid cultures and the acquisition of the carbapenem gene and virulence gene was confirmed using colony-PCR. Antimicrobial susceptibility testing, mCIM and eCIM were conducted for the resistance of transformant. Serum killing assay, assessment of the anti-biofilm effect and galleria mellonella infection model, mucoviscosity assay, extraction and quantification of capsules were verified the virulence of transformant. Pulsed-field gel electrophoresis (PFGE), S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting hybridization confirmed the plasmid of transformant.<br><br>RESULTS: Firstly, OMVs were isolated from CR-HvKP NUHL30457 (K2, ST86). TEM and DLS analyses revealed the spherical morphology of the vesicles. Secondly, our study demonstrated that CR-HvKP delivered genetic material, incorporated DNA within the OMVs, and protected it from degradation by extracellular exonucleases. Thirdly, the vesicular lumen DNA was delivered to the recipient cells after determining the presence of virulence and carbapenem-resistant genes in the CR-HvKP OMVs. Importantly, S1-PFGE and Southern hybridization analysis of the 700603 transformant strain showed that the transformant contained both drug-resistant and virulence plasmids.<br><br>DISCUSSION: In the present study, we aimed to clarify the role of CRHvKP-OMVs in transmitting CR-HvKP among K. pneumoniae. Collectively, our findings provided valuable insights into the evolution of CR-HvKP.}, }
@article {pmid36532424, year = {2022}, author = {Pillay, S and Calderón-Franco, D and Urhan, A and Abeel, T}, title = {Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1066995}, pmid = {36532424}, issn = {1664-302X}, abstract = {The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.}, }
@article {pmid36532220, year = {2022}, author = {Boury, N and Van den Bogaard, MED and Wasendorf, C and Amon, J and Judson, S and Maroushek, SR and Peters, NT}, title = {The Use of a Multimodal Case Study To Illustrate Microbial Genetics, Metabolism, and Evolution: The Emergence of VRSA-1.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {3}, pages = {}, pmid = {36532220}, issn = {1935-7877}, abstract = {Antibiotic Resistance (ABR) is a global concern and while many students are aware of this issue, many of them are unclear on the mechanisms by which ABR may emerge. The mechanism of horizontal gene transfer is something many students are not familiar with. In this curriculum contribution we present 2 versions of an 'interrupted case study' that is designed as an introduction to horizontal gene transfer for early major students and as a review case for advanced major students in biology and life sciences. The case is based on an authentic patient who developed infections with both methicillin resistant Staphylococcus aureus and vancomycin resistant S. aureus. The interrupted case study is appropriate for small and large groups and engages students while content is introduced in a highly structured way. This type of case study can be done by novice and seasoned instructors and lead to considerable learning gains in both introductory and intermediate microbiology courses.}, }
@article {pmid36528203, year = {2023}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {318}, number = {}, pages = {120867}, doi = {10.1016/j.envpol.2022.120867}, pmid = {36528203}, issn = {1873-6424}, mesh = {*Hexachlorocyclohexane/metabolism ; Biodegradation, Environmental ; *Pseudomonas putida/genetics ; Bacillus cereus/genetics ; Molecular Sequence Annotation ; }, abstract = {The contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due to its persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.}, }
@article {pmid36527364, year = {2023}, author = {Knoop, V}, title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.}, journal = {Journal of experimental botany}, volume = {74}, number = {7}, pages = {2273-2294}, doi = {10.1093/jxb/erac488}, pmid = {36527364}, issn = {1460-2431}, mesh = {*RNA Editing ; Uridine/genetics/metabolism ; *Organelles/genetics/metabolism ; Plants/genetics/metabolism ; Chloroplasts/metabolism ; RNA, Plant/genetics/metabolism ; Plant Proteins/metabolism ; }, abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts were not altered by site-specific cytidine-to-uridine (C-to-U) exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes, and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over >30 years. Lately new studies have revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that lately have contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.}, }
@article {pmid36525956, year = {2022}, author = {Liu, HW and Roisné-Hamelin, F and Beckert, B and Li, Y and Myasnikov, A and Gruber, S}, title = {DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.}, journal = {Molecular cell}, volume = {82}, number = {24}, pages = {4727-4740.e6}, doi = {10.1016/j.molcel.2022.11.015}, pmid = {36525956}, issn = {1097-4164}, mesh = {*Adenosine Triphosphatases/genetics/metabolism ; *DNA Cleavage ; Plasmids/genetics ; Chromosomes/metabolism ; DNA/genetics ; Cell Cycle Proteins/genetics ; Chromosomes, Bacterial/genetics/metabolism ; }, abstract = {Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.}, }
@article {pmid36525447, year = {2022}, author = {Zou, X and Nguyen, M and Overbeek, J and Cao, B and Davis, JJ}, title = {Classification of bacterial plasmid and chromosome derived sequences using machine learning.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279280}, pmid = {36525447}, issn = {1932-6203}, mesh = {Plasmids/genetics ; *Genome, Bacterial ; *Chromosomes, Bacterial/genetics ; Bacteria/genetics ; Machine Learning ; Nucleotides ; }, abstract = {Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer-including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements-were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.}, }
@article {pmid36523753, year = {2022}, author = {Alam, M and Bano, N and Upadhyay, TK and Binsuwaidan, R and Alshammari, N and Sharangi, AB and Kaushal, RS and Saeed, M}, title = {Enzymatic Activity and Horizontal Gene Transfer of Heavy Metals and Antibiotic Resistant Proteus vulgaris from Hospital Wastewater: An Insight.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {3399137}, pmid = {36523753}, issn = {1712-9532}, abstract = {Globally, the issue of microbial resistance to medicines and heavy metals is getting worse. There are few reports or data available for Proteus vulgaris (P. vulgaris), particularly in India. This investigation intends to reveal the bacteria's ability to transmit genes and their level of resistance as well. The wastewater samples were taken from several hospitals in Lucknow City, India, and examined for the presence of Gram-negative bacteria that were resistant to antibiotics and heavy metals. The microbial population count in different hospital wastewaters decreases with increasing concentrations of metal and antibiotics. Among all the examined metals, Ni and Zn had the highest viable counts, whereas Hg, Cd, and Co had the lowest viable counts. Penicillin, ampicillin, and amoxicillin, among the antibiotics, demonstrated higher viable counts, whereas tetracycline and erythromycin exhibited lower viable counts. The MIC values for the P. vulgaris isolates tested ranged from 50 to 16,00 μg/ml for each metal tested. The multiple metal resistance (MMR) index, which ranged from 0.04 to 0.50, showed diverse heavy metal resistance patterns in all P. vulgaris isolates (in the case of 2-7 metals in various combinations). All of the tested isolates had methicillin resistance, whereas the least number of isolates had ofloxacin, gentamycin, or neomycin resistance. The P. vulgaris isolates displayed multidrug resistance patterns (2-12 drugs) in various antibiotic combinations. The MAR indexes were shown to be between (0.02-0.7). From the total isolates, 98%, 84%, and 80% had urease, gelatinase, and amylase activity, whereas 68% and 56% displayed protease and beta-lactamase activity. Plasmids were present in all the selected resistant isolates and varied in size from 42.5 to 57.0 kb and molecular weight from 27.2 to 37.0 MD. The transmission of the antibiotic/metal resistance genes was evaluated between a total of 7 pairs of isolates. A higher transfer frequency (4.4 × 10[-1]) was observed among antibiotics, although a lower transfer frequency (1.0 × 10[-2]) was observed against metals in both the media from the entire site tested. According to exponential decay, the population of hospital wastewater declined in the following order across all sites: Site II > Site IV > Site III > Site I for antibiotics and site IV > site II > site I >site III for metal. Different metal and antibiotic concentrations have varying effects on the population. The metal-tolerant P. vulgaris from hospital wastewater was studied in the current study had multiple distinct patterns of antibiotic resistance. It could provide cutting-edge methods for treating infectious diseases, which are essential for managing and assessing the risks associated with hospital wastewater, especially in the case of P. vulgaris.}, }
@article {pmid36522135, year = {2023}, author = {Dorrell, RG and Kuo, A and Füssy, Z and Richardson, EH and Salamov, A and Zarevski, N and Freyria, NJ and Ibarbalz, FM and Jenkins, J and Pierella Karlusich, JJ and Stecca Steindorff, A and Edgar, RE and Handley, L and Lail, K and Lipzen, A and Lombard, V and McFarlane, J and Nef, C and Novák Vanclová, AM and Peng, Y and Plott, C and Potvin, M and Vieira, FRJ and Barry, K and de Vargas, C and Henrissat, B and Pelletier, E and Schmutz, J and Wincker, P and Dacks, JB and Bowler, C and Grigoriev, IV and Lovejoy, C}, title = {Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.}, journal = {Life science alliance}, volume = {6}, number = {3}, pages = {}, pmid = {36522135}, issn = {2575-1077}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microalgae/genetics ; Arctic Regions ; Oceans and Seas ; Ice Cover ; Bacteria ; }, abstract = {Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.}, }
@article {pmid36522081, year = {2023}, author = {Fan, X and Su, J and Zhou, S and An, X and Li, H}, title = {Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {508-518}, doi = {10.1016/j.jes.2022.06.006}, pmid = {36522081}, issn = {1001-0742}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil/chemistry ; Soil Microbiology ; Plants ; }, abstract = {The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.}, }
@article {pmid36522071, year = {2023}, author = {Yan, X and Liu, W and Wen, S and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {399-409}, doi = {10.1016/j.jes.2022.06.014}, pmid = {36522071}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Plasmids/genetics ; RNA, Messenger ; }, abstract = {As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10[-5], which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.}, }
@article {pmid36518176, year = {2022}, author = {Cangui-Panchi, SP and Ñacato-Toapanta, AL and Enríquez-Martínez, LJ and Reyes, J and Garzon-Chavez, D and Machado, A}, title = {Biofilm-forming microorganisms causing hospital-acquired infections from intravenous catheter: A systematic review.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100175}, pmid = {36518176}, issn = {2666-5174}, abstract = {The high prevalence of nosocomial infections is related to the use of medical insertion devices such as central venous catheters (CVCs). Most of the microorganisms causing nosocomial infections are biofilm producers, this characteristic allows them to adhere to abiotic surfaces and cause initial catheter infections that can lead to bloodstream infections. Our main goal in this systematic review was to evaluate the prevalence of biofilm among CVC-related infections, particularly among Intensive Care Unit (ICU) patients, in the studies applying different in vitro and in vivo methodologies. All studies reporting clinical isolates from patients with catheter-related nosocomial infections and biofilm evaluation published up to 24 June 2022 in the PubMed and Scopus databases were included. Twenty-five studies met the eligibility criteria and were included in this systematic review for analysis. Different methodologies were applied in the assessment of biofilm-forming microorganisms including in vitro assays, catheter-infected in vitro, and in vivo mouse models. The present study showed that between 59 and 100% of clinical isolates were able to form biofilms, and the prevalence rate of biofilm formation varied significantly between studies from different countries and regions. Among the clinical isolates collected in our study set, a wide variety of microorganisms including Gram-positive strains, Gram-negative strains, and Candida albicans were found. Many authors studied resistance mechanisms and genes related to biofilm development and surface adherence properties. In some cases, the studies also evaluated biofilm inhibition assays using various kinds of catheter coatings.}, }
@article {pmid36517909, year = {2022}, author = {Vasco, K and Guevara, N and Mosquera, J and Zapata, S and Zhang, L}, title = {Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {65}, pmid = {36517909}, issn = {2524-4671}, abstract = {BACKGROUND: Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.<br><br>RESULTS: The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.<br><br>CONCLUSION: Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.}, }
@article {pmid36517527, year = {2023}, author = {Dziuba, MV and Paulus, A and Schramm, L and Awal, RP and Pósfai, M and Monteil, CL and Fouteau, S and Uebe, R and Schüler, D}, title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {326-339}, pmid = {36517527}, issn = {1751-7370}, mesh = {*Magnetospirillum/genetics ; *Magnetosomes/genetics ; Bacteria/genetics ; Gram-Negative Bacteria/genetics ; Bacteria, Aerobic/genetics ; Multigene Family ; Magnetic Phenomena ; Bacterial Proteins/genetics ; }, abstract = {Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.}, }
@article {pmid36516783, year = {2022}, author = {Nishimoto, AT and Dao, TH and Jia, Q and Ortiz-Marquez, JC and Echlin, H and Vogel, P and van Opijnen, T and Rosch, JW}, title = {Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae.}, journal = {Cell reports}, volume = {41}, number = {11}, pages = {111835}, pmid = {36516783}, issn = {2211-1247}, support = {U01 AI124302/AI/NIAID NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Streptococcus pneumoniae/genetics ; Gene Transfer, Horizontal ; *Pneumococcal Infections ; Virulence/genetics ; Microbial Sensitivity Tests ; beta-Lactam Resistance/genetics ; Penicillin-Binding Proteins/genetics/metabolism ; Mutation/genetics ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology/metabolism ; }, abstract = {As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.}, }
@article {pmid36515883, year = {2023}, author = {Martins-Silva, P and Dias, CP and Vilar, LC and de Queiroz Silva, S and Rossi, CC and Giambiagi-deMarval, M}, title = {Dispersion and persistence of antimicrobial resistance genes among Staphylococcus spp. and Mammaliicoccus spp. isolated along a swine manure treatment plant.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {34709-34719}, pmid = {36515883}, issn = {1614-7499}, mesh = {Humans ; Swine ; Animals ; *Staphylococcus ; *Anti-Bacterial Agents/pharmacology ; Manure ; Drug Resistance, Bacterial/genetics ; Cefoxitin ; Microbial Sensitivity Tests ; }, abstract = {Staphylococcus spp. and Mammaliicoccus spp. colonize the skin and mucosa of humans and other animals and are responsible for several opportunistic infections. Staphylococci antibiotic resistance may be present in the environment due to the spread of treated and untreated manure from the livestock industry due to antibiotic use to disease control or growth promoter. In this work, we analyzed the species distribution and antimicrobial susceptibility of Staphylococcus and Mammaliicoccus species along different sites of a swine manure treatment plant from Southeastern Brazil. Bacterial colonies were obtained on mannitol salt agar, selected after catalase test and Gram staining, and finally identified by mass spectrometry and sequencing of the tuf gene. According to the results, S.cohnii and S. simulans were the most prevalent species. Antibiotic resistance test revealed that several strains were resistant to multiple drugs, with high levels of chloramphenicol resistance (98%), followed by erythromycin (79%), tetracycline (73%), gentamicin (46%), ciprofloxacin (42%), cefoxitin (18%), sulfamethoxazole + trimethoprim (12%), and linezolid (4%). In addition, gene detection by PCR showed that all strains carried at least 2 resistance genes and one of them carried all 11 genes investigated. Using the GTG5-PCR approach, a high genetic similarity was observed between some strains that were isolated from different points of the treatment plant. Although some were seemingly identical, differences in their resistance phenotype and genotype suggest horizontal gene transfer. The presence of resistant bacteria and resistance genes along the treatment system highlights the potential risk of contamination by people in direct contact with these animals and the soil since the effluent is used as a biofertilizer in the surrounding environment.}, }
@article {pmid36515719, year = {2022}, author = {Almalki, F and Choudhary, M and Azad, RK}, title = {Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {25}, pmid = {36515719}, issn = {1432-072X}, mesh = {*Genome, Bacterial ; Genomics ; Biological Evolution ; *Rhodobacter sphaeroides/genetics ; Evolution, Molecular ; Chromosomes, Bacterial/genetics ; }, abstract = {Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.}, }
@article {pmid36515529, year = {2023}, author = {Brennan, G and Stoian, AMM and Yu, H and Rahman, MJ and Banerjee, S and Stroup, JN and Park, C and Tazi, L and Rothenburg, S}, title = {Molecular Mechanisms of Poxvirus Evolution.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0152622}, pmid = {36515529}, issn = {2150-7511}, support = {R01 AI114851/AI/NIAID NIH HHS/United States ; R01 AI146915/AI/NIAID NIH HHS/United States ; R21 AI135257/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Evolution, Molecular ; *Poxviridae/genetics ; Host Specificity ; Gene Duplication ; }, abstract = {Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.}, }
@article {pmid36515045, year = {2023}, author = {de Morais Oliveira-Tintino, CD and Muniz, DF and Dos Santos Barbosa, CR and Silva Pereira, RL and Begnini, IM and Rebelo, RA and da Silva, LE and Mireski, SL and Nasato, MC and Lacowicz Krautler, MI and Barros Oliveira, CV and Pereira, PS and Rodrigues Teixeira, AM and Tintino, SR and de Menezes, IRA and Melo Coutinho, HD and da Silva, TG}, title = {NorA, Tet(K), MepA, and MsrA Efflux Pumps in Staphylococcus aureus, their Inhibitors and 1,8-Naphthyridine Sulfonamides.}, journal = {Current pharmaceutical design}, volume = {29}, number = {5}, pages = {323-355}, doi = {10.2174/1381612829666221212101501}, pmid = {36515045}, issn = {1873-4286}, mesh = {Humans ; *Staphylococcus aureus ; *Bacterial Proteins/genetics/chemistry ; Sulfonamides/pharmacology ; Bacteria ; Anti-Bacterial Agents/pharmacology ; Sulfanilamide/pharmacology ; Naphthyridines/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic resistance can be characterized, in biochemical terms, as an antibiotic's inability to reach its bacterial target at a concentration that was previously effective. Microbial resistance to different agents can be intrinsic or acquired. Intrinsic resistance occurs due to inherent functional or structural characteristics of the bacteria, such as antibiotic-inactivating enzymes, nonspecific efflux pumps, and permeability barriers. On the other hand, bacteria can acquire resistance mechanisms via horizontal gene transfer in mobile genetic elements such as plasmids. Acquired resistance mechanisms include another category of efflux pumps with more specific substrates, which are plasmid-encoded. Efflux pumps are considered one of the main mechanisms of bacterial resistance to antibiotics and biocides, presenting themselves as integral membrane transporters. They are essential in both bacterial physiology and defense and are responsible for exporting structurally diverse substrates, falling into the following main families: ATP-binding cassette (ABC), multidrug and toxic compound extrusion (MATE), major facilitator superfamily (MFS), small multidrug resistance (SMR) and resistance-nodulation-cell division (RND). The Efflux pumps NorA and Tet(K) of the MFS family, MepA of the MATE family, and MsrA of the ABC family are some examples of specific efflux pumps that act in the extrusion of antibiotics. In this review, we address bacterial efflux pump inhibitors (EPIs), including 1,8-naphthyridine sulfonamide derivatives, given the pre-existing knowledge about the chemical characteristics that favor their biological activity. The modification and emergence of resistance to new EPIs justify further research on this theme, aiming to develop efficient compounds for clinical use.}, }
@article {pmid36512900, year = {2023}, author = {Puxty, RJ and Millard, AD}, title = {Functional ecology of bacteriophages in the environment.}, journal = {Current opinion in microbiology}, volume = {71}, number = {}, pages = {102245}, doi = {10.1016/j.mib.2022.102245}, pmid = {36512900}, issn = {1879-0364}, mesh = {*Bacteriophages/genetics ; Bacteria/genetics ; Ecology ; }, abstract = {Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.}, }
@article {pmid36511859, year = {2022}, author = {Kim, SK and Kim, H and Woo, SG and Kim, TH and Rha, E and Kwon, KK and Lee, H and Lee, SG and Lee, DH}, title = {CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids.}, journal = {Nucleic acids research}, volume = {50}, number = {22}, pages = {13155-13171}, pmid = {36511859}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Escherichia coli/drug effects/genetics ; Plasmids/genetics ; *Microbiological Techniques/methods ; }, abstract = {Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.}, }
@article {pmid36511824, year = {2023}, author = {Liu, C and Li, Y and Chen, Y and Chen, XX and Huang, J and Rokas, A and Shen, XX}, title = {How has horizontal gene transfer shaped the evolution of insect genomes?.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {642-645}, doi = {10.1111/1462-2920.16311}, pmid = {36511824}, issn = {1462-2920}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Ecosystem ; Prokaryotic Cells ; Insecta ; Genome, Insect ; Phylogeny ; }, abstract = {As the most diverse group of animals on Earth, insects are key organisms in ecosystems. Horizontal gene transfer (HGT) refers to the transfer of genetic material between species by non-reproductive means. HGT is a major evolutionary force in prokaryotic genome evolution, but its importance in different eukaryotic groups, such as insects, has only recently begun to be understood. Genomic data from hundreds of insect species have enabled the detection of large numbers of HGT events and the elucidation of the functions of some of these foreign genes. Although quantification of the extent of HGT in insects broadens our understanding of its role in insect evolution, the scope of its influence and underlying mechanism(s) of its occurrence remain open questions for the field.}, }
@article {pmid36507660, year = {2023}, author = {Zheng, J and Liang, JL and Jia, P and Feng, SW and Lu, JL and Luo, ZH and Ai, HX and Liao, B and Li, JT and Shu, WS}, title = {Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0073622}, pmid = {36507660}, issn = {2379-5077}, mesh = {*Methylmercury Compounds/analysis ; Bacteria/genetics ; Phylogeny ; Metagenome ; Firmicutes/genetics ; }, abstract = {Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km[2] in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.}, }
@article {pmid36507655, year = {2023}, author = {Guan, Y and Ma, L and Wang, Q and Zhao, J and Wang, S and Wu, J and Liu, Y and Sun, H and Huang, J}, title = {Horizontally acquired fungal killer protein genes affect cell development in mosses.}, journal = {The Plant journal : for cell and molecular biology}, volume = {113}, number = {4}, pages = {665-676}, doi = {10.1111/tpj.16060}, pmid = {36507655}, issn = {1365-313X}, mesh = {*Bryophyta/metabolism ; Calcium/metabolism ; Fungal Proteins/genetics ; Fungi/metabolism ; *Bryopsida/genetics ; }, abstract = {The moss Physcomitrium patens is crucial for studying plant development and evolution. Although the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a toxin secreted by the phytopathogenic fungus Ustilago maydis that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here, we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer. Two paralogous copies of KP4 (PpKP4-1 and PpKP4-2) exist in P. patens. Knockout mutants ppkp4-1 and ppkp4-2 showed cell death at the protonemal stage, and ppkp4-2 also exhibited defects in tip growth. We provide experimental evidence indicating that PpKP4-1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. The present study provides additional insights into the role of horizontal gene transfer in land plant development and evolution.}, }
@article {pmid36506112, year = {2023}, author = {Alvarez-Molina, A and Trigal, E and Prieto, M and López, M and Alvarez-Ordóñez, A}, title = {Assessment of a plasmid conjugation procedure to monitor horizontal transfer of an extended-spectrum β-lactamase resistance gene under food chain scenarios.}, journal = {Current research in food science}, volume = {6}, number = {}, pages = {100405}, pmid = {36506112}, issn = {2665-9271}, abstract = {Plasmids are relevant reservoirs of antimicrobial resistance genes (ARGs) which confer adaptive advantages to their host and can be horizontally transferred. The aims of this study were to develop a conjugation procedure to monitor the horizontal transfer of a 193 kb plasmid containing the extended-spectrum β-lactamase production gene bla CTX-M-14 between two Escherichia coli strains under a range of food chain-related scenarios, including temperature (20-37 °C), pH (5.0-9.0) or the presence of some biocidal agents (benzalkonium chloride, sodium hypochlorite or peracetic acid). The average conjugation rate in LB broth after 18 h at 37 °C was 2.09e-04 and similar rates were observed in a food matrix (cow's milk). The conjugation was reduced at temperatures below 37 °C, at alkaline pH (especially at pH 9.0) or in the presence of benzalkonium chloride. Peracetic acid and sodium hypochlorite slightly increased conjugation rates, which reached 5.59e-04 and 6.77e-03, respectively. The conjugation procedure described can be used to identify risk scenarios leading to an enhanced ARGs transmission via plasmid conjugation, as well as to identify novel intervention strategies impairing plasmid conjugation and tackling antimicrobial resistance.}, }
@article {pmid36503799, year = {2023}, author = {Wang, S and Li, S and Du, D and Abass, OK and Nasir, MS and Yan, W}, title = {Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge.}, journal = {Journal of environmental sciences (China)}, volume = {126}, number = {}, pages = {742-753}, doi = {10.1016/j.jes.2022.03.011}, pmid = {36503799}, issn = {1001-0742}, mesh = {*Gene Transfer, Horizontal ; *Sewage ; Naphthalenes ; Tetracycline ; Anti-Bacterial Agents ; }, abstract = {The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.}, }
@article {pmid36502290, year = {2023}, author = {Kinateder, T and Drexler, L and Straub, K and Merkl, R and Sterner, R}, title = {Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis.}, journal = {Protein science : a publication of the Protein Society}, volume = {32}, number = {1}, pages = {e4536}, pmid = {36502290}, issn = {1469-896X}, mesh = {*Histidine/genetics/metabolism ; Phylogeny ; *Phosphoric Monoester Hydrolases/genetics/chemistry/metabolism ; Histidinol-Phosphatase/chemistry ; Escherichia coli/genetics ; }, abstract = {The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact subcluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N.}, }
@article {pmid36498841, year = {2022}, author = {Carpanzano, S and Santorsola, M and Nf-Core Community,  and Lescai, F}, title = {hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36498841}, issn = {1422-0067}, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; Prokaryotic Cells ; Bacteria/genetics ; Base Sequence ; Phylogeny ; Mammals/genetics ; }, abstract = {Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.}, }
@article {pmid36495587, year = {2023}, author = {Farghaly, M and Hynes, MF and Nazari, M and Checkley, S and Liljebjelke, K}, title = {Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multidrug resistance in Histophilus somni.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {3}, pages = {123-135}, doi = {10.1139/cjm-2021-0349}, pmid = {36495587}, issn = {1480-3275}, mesh = {*Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Pasteurellaceae ; Ciprofloxacin ; Tetracyclines ; Conjugation, Genetic ; }, abstract = {Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).}, }
@article {pmid36495352, year = {2022}, author = {Kim, J and Cha, IT and Lee, KE and Son, YK and Yu, J and Seol, D}, title = {Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {22}, pmid = {36495352}, issn = {1432-072X}, mesh = {*Flavobacterium/genetics ; *Genomics ; Genomic Islands ; Plants ; }, abstract = {Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.}, }
@article {pmid36472431, year = {2023}, author = {Brown, P and Kucerova, Z and Gorski, L and Chen, Y and Ivanova, M and Leekitcharoenphon, P and Parsons, C and Niedermeyer, J and Jackson, J and Kathariou, S}, title = {Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0274522}, pmid = {36472431}, issn = {2165-0497}, mesh = {Pregnancy ; Female ; Humans ; Aged ; *Listeria monocytogenes/genetics ; Serogroup ; Serotyping ; Gene Transfer, Horizontal ; *Listeriosis ; }, abstract = {Listeria monocytogenes is a Gram-positive, facultative intracellular foodborne pathogen capable of causing severe, invasive illness (listeriosis). Three serotypes, 1/2a, 1/2b, and 4b, are leading contributors to human listeriosis, with 4b including the major hypervirulent clones. The multiplex PCR scheme developed by Doumith and collaborators employs primers targeting specific lineages (e.g., lineage II-specific lmo0737, lineage I-specific LMOf2365_2059) or serotypes (e.g., serotype 4b-specific LMOf2365_1900). The Doumith scheme (DS) is extensively employed for molecular serotyping of L. monocytogenes due to its high accuracy, relative ease, and affordability. However, for certain strains, the DS serotype designations are in conflict with those relying on antibody-based schemes or whole-genome sequence (WGS) analysis. In the current study, all 27 tested serotype 4b strains with sequence type 782 (ST782) within the hypervirulent clonal complex 2 (CC2) were designated 1/2b/3b using the DS. These strains lacked the serotype 4b-specific gene LMOf2365_1900, while retaining LMOf2365_2059, which, together with prs, yields the DS 1/2b/3b profile. Furthermore, 15 serotype 1/2a strains of four STs, mostly from water, were designated 1/2b/3b using the DS. These strains lacked the lmo0737 cassette but harbored genomic islands with LMOf2365_2059, thus yielding the DS 1/2b/3b profile. Lastly, we investigated a novel, dual 1/2a-1/2b profile obtained using the DS with 21 serotype 1/2a strains of four STs harboring both the lmo0737 cassette and genomic islands with LMOf2365_2059. The findings suggest that for certain strains and clones of L. monocytogenes the DS designations should be viewed with caution and complemented with alternative tools, e.g., traditional serotyping or WGS analysis. IMPORTANCE Listeria monocytogenes is a foodborne pathogen responsible for severe illness (listeriosis), especially in pregnant women and their fetuses, immunocompromised individuals, and the elderly. Three serotypes, 1/2a, 1/2b, and 4b, account for most human listeriosis, with certain serotype 4b clonal complexes (CCs) overrepresented in human disease. Serotyping remains extensively employed in Listeria epidemiologic investigations, and a multiplex PCR-based serotyping scheme is widely used. However, the PCR gene targets can be lost or gained via horizontal gene transfer, leading to novel PCR profiles without known serotype designations or to incorrect serotype assignments. Thus, an entire serotype 4b clone of the hypervirulent CC2 would be misidentified as serotype 1/2b, and several strains of serotype 1/2a would be identified as serotype 1/2b. Such challenges are especially common in novel clones from underexplored habitats, e.g., wildlife and surface water. The findings suggest caution in application of molecular serotyping, while highlighting Listeria's diversity and potential for horizontal gene transfer.}, }
@article {pmid36471715, year = {2022}, author = {Wen, Y and Xie, X and Xu, P and Yang, C and Zhu, Z and Zhu, J and Lv, J and Zhang, H and Chen, L and Du, H}, title = {NDM-1 and OXA-48-Like Carbapenemases (OXA-48, OXA-181 and OXA-252) Co-Producing Shewanella xiamenensis from Hospital Wastewater, China.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6927-6938}, pmid = {36471715}, issn = {1178-6973}, abstract = {BACKGROUND: Shewanella genus, as an important carrier of resistance genes, has the potential to transmit resistance to many antimicrobials in many circumstances, especially in aquatic environment. The aim of the study was to describe the risk of Shewanella xiamenensis in hospital environment through analysis of genomic comparison and resistance status.<br><br>METHODS: Seven S. xiamenensis strains were isolated from hospital wastewater. PCR and Sanger sequencing were carried out for detection of common carbapenemase genes. Antimicrobial susceptibility testing was performed to determine the antimicrobial profile. Whole genome sequencing was applied, and sequences were further used for genomic analysis.<br><br>RESULTS: Seven Shewanella xiamenensis were all positive for bla NDM and bla OXA-48. Antimicrobial susceptibility testing showed all Shewanella xiamenensis were resistant to cefotaxime, ceftazidime, imipenem, meropenem, gentamycin and trimethoprim-sulfamethoxazole. Whole genome sequencing and phylogenetic analysis demonstrated the diversity of Shewanella xiamenensis despite isolating from one wastewater pool.<br><br>CONCLUSION: To the best of our knowledge, this is the first report of detection of three types bla OXA-48-like genes in one hospital in China. And we have detected multi-drug resistant S. xiamenensis from hospital wastewater. This emphasizes that the presence of naturally existing carbapenemases in the environment may be significantly overlooked and that the bla OXA-48-like genes in China may originate through the horizontal gene transfer from S. xiamenensis to Enterobacterales rather than import from other countries.}, }
@article {pmid36462475, year = {2023}, author = {Huang, Y and Wen, X and Li, J and Niu, Q and Tang, A and Li, Q}, title = {Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120795}, doi = {10.1016/j.envpol.2022.120795}, pmid = {36462475}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; *Composting ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Manure/microbiology ; }, abstract = {In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.}, }
@article {pmid36458228, year = {2022}, author = {Lal, D and Pandey, H and Lal, R}, title = {Phylogenetic Analyses of Microbial Hydrolytic Dehalogenases Reveal Polyphyletic Origin.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {651-657}, pmid = {36458228}, issn = {0046-8991}, abstract = {UNLABELLED: Hydrolytic dehalogenases form an important class of dehalogenases that include haloacid dehalogenase, haloalkane dehalogenase, haloacetate dehalogenase, and atrazine chlorohydrolase. These enzymes are involved in biodegradation of various environmental pollutants and therefore it is important to understand their phylogeny. In the present study, it was found that the enzymes haloalkane and haloacetate dehalogenases share a common ancestry with enzymes such as carboxyesterase, epoxide hydrolase, and lipases, which can be traced to ancestral α/β hydrolase fold enzyme. Haloacid dehalogenases and atrazine chlorohydrolases have probabaly evolved from ancestral enzymes with phosphatase and deaminases activity, respectively. These findings were supported by the similarities in the secondary structure, key catalytic motifs and placement of catalytic residues. The phylogeny of haloalkane dehalogenases and haloacid dehalogenases differs from 16S rRNA gene phylogeny, suggesting spread through horizontal gene transfer. Hydrolytic dehalogenases are polyphyletic and do not share a common evolutionay history, the functional similarities are due to convergent evolution. The present study also identifies key functional residues, mutating which, can help in generating better enzymes for clean up of the persistent environmental pollutants using enzymatic bioremediation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01043-8.}, }
@article {pmid36456543, year = {2022}, author = {Gaines, MC and Isupov, MN and Sivabalasarma, S and Haque, RU and McLaren, M and Mollat, CL and Tripp, P and Neuhaus, A and Gold, VAM and Albers, SV and Daum, B}, title = {Electron cryo-microscopy reveals the structure of the archaeal thread filament.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7411}, pmid = {36456543}, issn = {2041-1723}, mesh = {Cryoelectron Microscopy ; *Archaea ; *Electrons ; Cytoskeleton ; Software ; }, abstract = {Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.}, }
@article {pmid36455559, year = {2022}, author = {Ruan, C and Ramoneda, J and Gogia, G and Wang, G and Johnson, DR}, title = {Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion.}, journal = {Current biology : CB}, volume = {32}, number = {24}, pages = {5285-5294.e4}, doi = {10.1016/j.cub.2022.11.009}, pmid = {36455559}, issn = {1879-0445}, mesh = {*Hyphae/genetics ; *Bacteria/genetics ; Plasmids/genetics ; }, abstract = {The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.}, }
@article {pmid36455257, year = {2022}, author = {Zhang, X and Yao, MC and Chen, L and Sheng, GP}, title = {Lewis Acid-Base Interaction Triggering Electron Delocalization to Enhance the Photodegradation of Extracellular Antibiotic Resistance Genes Adsorbed on Clay Minerals.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {24}, pages = {17684-17693}, doi = {10.1021/acs.est.2c05785}, pmid = {36455257}, issn = {1520-5851}, mesh = {Clay ; *Kaolin/chemistry ; *Anti-Bacterial Agents ; Lewis Acids ; Electrons ; Photolysis ; Minerals/chemistry ; Drug Resistance, Microbial/genetics ; Adsorption ; }, abstract = {The transformation of extracellular antibiotic resistance genes (eARGs) is largely influenced by their inevitable photodegradation in environments where they tend to be adsorbed by ubiquitous clay minerals instead of being in a free form. However, the photodegradation behaviors and mechanisms of the adsorbed eARGs may be quite different from those of the free form and still remain unclear. Herein, we found that kaolinite, a common 1:1-type clay, markedly enhanced eARG photodegradation and made eARGs undergo direct photodegradation under UVA. The decrease in the transformation efficiency of eARGs caused by photodegradation was also promoted. Spectroscopy methods combined with density functional theory calculations revealed that the Lewis acid-base interaction between P-O in eARGs and Al-OH on kaolinite delocalized electrons of eARGs, thus resulting in increased photon absorption ability of eARGs. This ultimately led to enhanced photodegradation of kaolinite-adsorbed eARGs. Additionally, divalent Ca[2+] could reduce the Lewis acid-base interaction-mediated adsorption of eARGs by kaolinite, thereby weakening the enhanced photodegradation of eARGs caused by electron delocalization. In contrast, the 2:1-type clay montmorillonite without strong Lewis acid sites was unable to delocalize the electrons to enhance the photodegradation of eARGs. This work allowed us to better evaluate eARGs' fate and risk in real aqueous environments.}, }
@article {pmid36451580, year = {2023}, author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A}, title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {454-472}, doi = {10.1111/1462-2920.16292}, pmid = {36451580}, issn = {1462-2920}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Cyclitols ; *Burkholderia/genetics ; Symbiosis/genetics ; Endophytes/genetics ; Plants/microbiology ; Plant Leaves/microbiology ; Phylogeny ; }, abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.}, }
@article {pmid36451084, year = {2022}, author = {Jones, CT and Susko, E and Bielawski, JP}, title = {Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {140}, pmid = {36451084}, issn = {2730-7182}, mesh = {*Gene Transfer, Horizontal ; *RNA ; Referral and Consultation ; }, abstract = {BACKGROUND: The number of interactions between a transferable gene or its protein product and genes or gene products native to its microbial host is referred to as connectivity. Such interactions impact the tendency of the gene to be retained by evolution following horizontal gene transfer (HGT) into a microbial population. The complexity hypothesis posits that the protein product of a transferable gene with lower connectivity is more likely to function in a way that is beneficial to a new microbial host compared to the protein product of a transferable gene with higher connectivity. A gene with lower connectivity is consequently more likely to be fixed in any microbial population it enters by HGT. The more recently proposed simplicity hypothesis posits that the connectivity of a transferable gene might increase over time within any single microbial population due to gene-host coevolution, but that differential rates of colonization of microbial populations by HGT in accordance with differences in connectivity might act to counter this and even reduce connectivity over time, comprising an evolutionary trade-off.<br><br>RESULTS: We present a theoretical model that can be used to predict the conditions under which gene-host coevolution might increase or decrease the connectivity of a transferable gene over time. We show that the opportunity to enter new microbial populations by HGT can cause the connectivity of a transferable gene to evolve toward lower values, particularly in an environment that is unstable with respect to the function of the gene's protein product. We also show that a lack of such opportunity in a stable environment can cause the connectivity of a transferable gene to evolve toward higher values.<br><br>CONCLUSION: Our theoretical model suggests that the connectivity of a transferable gene can change over time toward higher values corresponding to a more sessile state of lower transferability or lower values corresponding to a more itinerant state of higher transferability, depending on the ecological milieu in which the gene exists. We note, however, that a better understanding of gene-host coevolutionary dynamics in natural microbial systems is required before any further conclusions about the veracity of the simplicity hypothesis can be drawn.}, }
@article {pmid36448285, year = {2022}, author = {Hao, C and Dewar, AE and West, SA and Ghoul, M}, title = {Gene transferability and sociality do not correlate with gene connectivity.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1987}, pages = {20221819}, pmid = {36448285}, issn = {1471-2954}, support = {834164/ERC_/European Research Council/International ; }, mesh = {*Social Behavior ; *Gene Transfer, Horizontal ; Prokaryotic Cells ; RNA ; }, abstract = {The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.}, }
@article {pmid36447017, year = {2023}, author = {Nieuwenhuis, M and Groeneveld, J and Aanen, DK}, title = {Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA.}, journal = {Current genetics}, volume = {69}, number = {1}, pages = {55-65}, pmid = {36447017}, issn = {1432-0983}, mesh = {*DNA, Mitochondrial/genetics ; DNA, Fungal/genetics ; *Mitochondria/genetics ; Plasmids/genetics ; RNA, Transfer/genetics ; Gene Transfer, Horizontal ; }, abstract = {Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.}, }
@article {pmid36446404, year = {2022}, author = {Sengupta, S and Azad, RK}, title = {Reconstructing horizontal gene flow network to understand prokaryotic evolution.}, journal = {Open biology}, volume = {12}, number = {11}, pages = {220169}, pmid = {36446404}, issn = {2046-2441}, mesh = {*Gene Flow ; Phylogeny ; *Prokaryotic Cells ; Gene Regulatory Networks ; Computational Biology ; }, abstract = {Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.}, }
@article {pmid36445094, year = {2022}, author = {Yu, Y and Cheng, W and Chen, X and Guo, Q and Cao, H}, title = {Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0319422}, pmid = {36445094}, issn = {2165-0497}, mesh = {Phylogeny ; *Lakes/microbiology ; *Cyanobacteria/genetics ; Harmful Algal Bloom ; Water ; }, abstract = {Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.}, }
@article {pmid36443412, year = {2022}, author = {Ekhlas, D and Soro, AB and Leonard, FC and Manzanilla, EG and Burgess, CM}, title = {Examining the impact of zinc on horizontal gene transfer in Enterobacterales.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20503}, pmid = {36443412}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; Zinc/pharmacology ; *Gammaproteobacteria ; Conjugation, Genetic ; Ampicillin ; Escherichia coli/genetics ; }, abstract = {Antimicrobial resistance is one of the main international health concerns for humans, animals, and the environment, and substantial efforts have focused on reducing its development and spread. While there is evidence for correlations between antimicrobial usage and antimicrobial resistance development, specific information on the effect of heavy metal/antimicrobial usage on bacterial conjugation is more limited. The aim of this study was to investigate the effects of zinc and antimicrobials in different concentrations on horizontal gene transfer of an ampicillin resistance gene, using a multi-drug resistant Escherichia coli donor strain and three different Salmonella enterica serovars as recipient strains. Differences in conjugation frequencies for the different Salmonella recipients were observed, independent of the presence of zinc or the antimicrobials. Selective pressure on the recipient strains, in the form of ampicillin, resulted in a decrease in conjugation frequencies, while, the presence of rifampicin resulted in increases. Zinc exposure affected conjugation frequencies of only one of the three recipient strains, thus the effect of zinc on conjugation frequencies seemed to be concentration and strain dependent. Furthermore, differences in growth rates due to plasmid carriage were observed for one of the Salmonella strains.}, }
@article {pmid36442505, year = {2022}, author = {Ares-Arroyo, M and Coluzzi, C and P C Rocha, E}, title = {Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1079}, pmid = {36442505}, issn = {1362-4962}, abstract = {Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.}, }
@article {pmid36439225, year = {2022}, author = {Hosseini-Giv, N and Basas, A and Hicks, C and El-Omar, E and El-Assaad, F and Hosseini-Beheshti, E}, title = {Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {962216}, pmid = {36439225}, issn = {2235-2988}, mesh = {Humans ; Anti-Bacterial Agents/metabolism ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; *Extracellular Vesicles/metabolism ; *Neoplasms/therapy/metabolism ; }, abstract = {Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.}, }
@article {pmid36437887, year = {2023}, author = {Adyari, B and Hou, L and Zhang, L and Chen, N and Ju, F and Zhu, L and Yu, CP and Hu, A}, title = {Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome.}, journal = {Environmental science and ecotechnology}, volume = {13}, number = {}, pages = {100223}, pmid = {36437887}, issn = {2666-4984}, abstract = {Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.}, }
@article {pmid36436581, year = {2023}, author = {Cuetero-Martínez, Y and Flores-Ramírez, A and De Los Cobos-Vasconcelos, D and Aguirre-Garrido, JF and López-Vidal, Y and Noyola, A}, title = {Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137383}, doi = {10.1016/j.chemosphere.2022.137383}, pmid = {36436581}, issn = {1879-1298}, mesh = {Humans ; *Sewage/microbiology ; Anaerobiosis ; Hydrolysis ; *Angiotensin Receptor Antagonists ; Biosolids ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Salmonella ; Escherichia coli ; Drug Resistance, Microbial ; Digestion ; Bacteria, Anaerobic ; }, abstract = {Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.}, }
@article {pmid36436244, year = {2023}, author = {Sun, W and Qian, X and Wang, X and Gu, J}, title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {326}, number = {Pt B}, pages = {116864}, doi = {10.1016/j.jenvman.2022.116864}, pmid = {36436244}, issn = {1095-8630}, mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.}, }
@article {pmid36425127, year = {2022}, author = {Memili, A and Kutchy, N and Braimah, OA and Morenikeji, OB}, title = {Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci.}, journal = {Veterinary world}, volume = {15}, number = {10}, pages = {2407-2413}, pmid = {36425127}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis.<br><br>MATERIALS AND METHODS: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro.<br><br>RESULTS: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium.<br><br>CONCLUSION: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.}, }
@article {pmid36425042, year = {2022}, author = {Andersson, T and Makenga, G and Francis, F and Minja, DTR and Overballe-Petersen, S and Tang, ME and Fuursted, K and Baraka, V and Lood, R}, title = {Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1049110}, pmid = {36425042}, issn = {1664-302X}, abstract = {Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with bla CTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.}, }
@article {pmid36423222, year = {2023}, author = {Balparda, M and Schmitz, J and Duemmel, M and Wuthenow, IC and Schmidt, M and Alseekh, S and Fernie, AR and Lercher, MJ and Maurino, VG}, title = {Viridiplantae-specific GLXI and GLXII isoforms co-evolved and detoxify glucosone in planta.}, journal = {Plant physiology}, volume = {191}, number = {2}, pages = {1214-1233}, pmid = {36423222}, issn = {1532-2548}, mesh = {Magnesium Oxide ; *Lactoylglutathione Lyase/chemistry/genetics/metabolism ; Protein Isoforms/genetics ; *Arabidopsis/genetics/metabolism ; }, abstract = {Reactive carbonyl species (RCS) such as methylglyoxal (MGO) and glyoxal (GO) are highly reactive, unwanted side-products of cellular metabolism maintained at harmless intracellular levels by specific scavenging mechanisms.MGO and GO are metabolized through the glyoxalase (GLX) system, which consists of two enzymes acting in sequence, GLXI and GLXII. While plant genomes encode a number of different GLX isoforms, their specific functions and how they arose during evolution are unclear. Here, we used Arabidopsis (Arabidopsis thaliana) as a model species to investigate the evolutionary history of GLXI and GLXII in plants and whether the GLX system can protect plant cells from the toxicity of RCS other than MGO and GO. We show that plants possess two GLX systems of different evolutionary origins and with distinct structural and functional properties. The first system is shared by all eukaryotes, scavenges MGO and GO, especially during seedling establishment, and features Zn2+-type GLXI proteins with a metal cofactor preference that were present in the last eukaryotic common ancestor. GLXI and GLXII of the second system, featuring Ni2+-type GLXI, were acquired by the last common ancestor of Viridiplantae through horizontal gene transfer from proteobacteria and can together metabolize keto-D-glucose (KDG, glucosone), a glucose-derived RCS, to D-gluconate. When plants displaying loss-of-function of a Viridiplantae-specific GLXI were grown in KDG, D-gluconate levels were reduced to 10%-15% of those in the wild type, while KDG levels showed an increase of 48%-67%. In contrast to bacterial GLXI homologs, which are active as dimers, plant Ni2+-type GLXI proteins contain a domain duplication, are active as monomers, and have a modified second active site. The acquisition and neofunctionalization of a structurally, biochemically, and functionally distinct GLX system indicates that Viridiplantae are under strong selection to detoxify diverse RCS.}, }
@article {pmid36422324, year = {2022}, author = {Khayi, S and Chan, KG and Faure, D}, title = {Patterns of Genomic Variations in the Plant Pathogen Dickeya solani.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422324}, issn = {2076-2607}, abstract = {The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani.}, }
@article {pmid36422323, year = {2022}, author = {Belova, SE and Naumoff, DG and Suzina, NE and Kovalenko, VV and Loiko, NG and Sorokin, VV and Dedysh, SN}, title = {Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82[T].}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422323}, issn = {2076-2607}, abstract = {Acidisarcina polymorpha SBC82[T] is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82[T] and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82[T] by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82[T] was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.}, }
@article {pmid36422313, year = {2022}, author = {Tavares, RDS and Tacão, M and Ramalheira, E and Ferreira, S and Henriques, I}, title = {Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422313}, issn = {2076-2607}, abstract = {BACKGROUND: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in blaNDM-5 dissemination.<br><br>METHODS: After blaNDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed.<br><br>RESULTS: blaNDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that blaNDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of blaNDM and mcr genes. Regardless, comparative genomics confirmed the presence of blaNDM in similar complex integrons in plasmids (48/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20/41 blaNDM-positive genomes).<br><br>CONCLUSIONS: blaNDM-5 and other blaNDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of blaNDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons.}, }
@article {pmid36421375, year = {2022}, author = {Ding, H and Bi, D and Zhang, S and Han, S and Ye, Y and Yi, R and Yang, J and Liu, B and Wu, L and Zhuo, R and Kan, X}, title = {The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications.}, journal = {Biology}, volume = {11}, number = {11}, pages = {}, pmid = {36421375}, issn = {2079-7737}, abstract = {As the largest family within the order Saxifragales, Crassulaceae contains about 34 genera with 1400 species. Mitochondria play a critical role in cellular energy production. Since the first land plant mitogenome was reported in Arabidopsis, more than 400 mitogenomic sequences have been deposited in a public database. However, no entire mitogenome data have been available for species of Crassulaceae to date. To better understand the evolutionary history of the organelles of Crassulaceae, we sequenced and performed comprehensive analyses on the mitogenome of Sedum plumbizincicola. The master mitogenomic circle is 212,159 bp in length, including 31 protein-coding genes (PCGs), 14 tRNA genes, and 3 rRNA genes. We further identified totally 508 RNA editing sites in PCGs, and demonstrated that the second codon positions of mitochondrial genes are most prone to RNA editing events. Notably, by neutrality plot analyses, we observed that the mitochondrial RNA editing events have large effects on the driving forces of plant evolution. Additionally, 4 MTPTs and 686 NUMTs were detected in the mitochondrial and nuclear genomes of S. plumbizincicola, respectively. Additionally, we conducted further analyses on gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications. Therefore, the findings presented here will be helpful for future investigations on plant mitogenomes.}, }
@article {pmid36419429, year = {2022}, author = {Ding, M and Ye, Z and Liu, L and Wang, W and Chen, Q and Zhang, F and Wang, Y and Sjöling, &#xc5; and Martín-Rodríguez, AJ and Hu, R and Chen, W and Zhou, Y}, title = {Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1017092}, pmid = {36419429}, issn = {1664-302X}, abstract = {Horizontal gene transfer plays an important role in the spread of antibiotic resistance, in which plasmid-mediated conjugation transfer is the most important mechanism. While sub-minimal inhibitory concentrations (sub-MIC) of antibiotics could promote conjugation frequency, the mechanism by which sub-MIC levels of antibiotics affect conjugation frequency is not clear. Here, we used Klebsiella pneumoniae SW1780 carrying the multi-drug resistance plasmid pSW1780-KPC as the donor strain, to investigate the effects of sub-MICs of meropenem (MEM), ciprofloxacin (CIP), cefotaxime (CTX), and amikacin (AK) on conjugational transfer of pSW1780-KPC from SW1780 to Escherichia coli J53. Our results showed that the transfer frequencies increased significantly by treating SW1780 strain with sub-MIC levels of MEM, CIP, CTX and AK. Transfer frequencies at sub-MIC conditions in a Galleria mellonella were significantly higher than in vitro. To investigate gene expression and metabolic effects, RT-qPCR and LC-MS-based metabolome sequencing were performed. Transcript levels of T4SS genes virB1, virB2, virB4, virB8, and conjugation-related genes traB, traK, traE, and traL were significantly upregulated by exposure to sub-MICs of MEM, CIP, CTX, and AK. Metabolome sequencing revealed nine differentially regulated metabolites. Our findings are an early warning for a wide assessment of the roles of sub-MIC levels of antibiotics in the spread of antibiotic resistance.}, }
@article {pmid36418956, year = {2022}, author = {Lu, J and Duan, J and Han, Y and Gou, M and Li, J and Li, Q and Pang, Y}, title = {A novel serum spherical lectin from lamprey reveals a more efficient mechanism of immune initiation and regulation in jawless vertebrates.}, journal = {Cellular &amp; molecular biology letters}, volume = {27}, number = {1}, pages = {102}, pmid = {36418956}, issn = {1689-1392}, mesh = {Animals ; *Lampreys/metabolism ; *Lectins/metabolism ; Phylogeny ; Mannose-Binding Protein-Associated Serine Proteases/genetics/metabolism ; Mannose-Binding Lectins ; Mammals ; }, abstract = {The innate immune system is the body's first line of defense against pathogens and involves antibody and complement system-mediated antigen removal. Immune-response-related complement molecules have been identified in lamprey, and the occurrence of innate immune response via the mannose-binding lectin-associated serine proteases of the lectin cascade has been reported. We have previously shown that lamprey (Lampetra japonica) serum can efficiently and specifically eliminate foreign pathogens. Therefore, we aimed to understand the immune mechanism of lamprey serum in this study. We identified and purified a novel spherical lectin (LSSL) from lamprey serum. LSSL had two structural calcium ions coordinated with conserved amino acids, as determined through cryogenic electron microscopy. LSSL showed high binding capacity with microbial and mammalian glycans and demonstrated agglutination activity against bacteria. Phylogenetic analysis revealed that LSSL was transferred from phage transposons to the lamprey genome via horizontal gene transfer. Furthermore, LSSL was associated with mannose-binding lectin-associated serine protease 1 and promoted the deposition of the C3 fragment on the surface of target cells upon binding. These results led us to conclude that LSSL initiates and regulates agglutination, resulting in exogenous pathogen and tumor cell eradication. Our observations will give a greater understanding of the origin and evolution of the complement system in higher vertebrates and lead to the identification of novel immune molecules and pathways for defense against pathogens and tumor cells.}, }
@article {pmid36417430, year = {2022}, author = {Gozashti, L and Roy, SW and Thornlow, B and Kramer, A and Ares, M and Corbett-Detig, R}, title = {Transposable elements drive intron gain in diverse eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2209766119}, pmid = {36417430}, issn = {1091-6490}, support = {R35 GM145266/GM/NIGMS NIH HHS/United States ; R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Introns/genetics ; *Eukaryota/genetics ; *DNA Transposable Elements/genetics ; Phylogeny ; Eukaryotic Cells ; }, abstract = {There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.}, }
@article {pmid36416260, year = {2022}, author = {Stanton, IC and Tipper, HJ and Chau, K and Klümper, U and Subirats, J and Murray, AK}, title = {Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/etc.5498}, pmid = {36416260}, issn = {1552-8618}, support = {MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; }, abstract = {The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2022;00:1-14. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, }
@article {pmid36414122, year = {2023}, author = {Oyanedel, D and Rojas, R and Brokordt, K and Schmitt, P}, title = {Crassostrea gigas oysters from a non-intensive farming area naturally harbor potentially pathogenic vibrio strains.}, journal = {Journal of invertebrate pathology}, volume = {196}, number = {}, pages = {107856}, doi = {10.1016/j.jip.2022.107856}, pmid = {36414122}, issn = {1096-0805}, mesh = {Animals ; *Crassostrea ; *Vibrio ; Virulence ; Virulence Factors ; Aquaculture ; }, abstract = {Farming intensification and climate change are inevitably linked to pathogen emergence in aquaculture. In this context, infectious diseases associated with vibrios span all developmental stages of the Pacific Oyster Crassostrea gigas. Moreover, virulence factors associated with pathogenicity spread among the vibrio community through horizontal gene transfer as part of the natural eco-evolutive dynamic of this group. Therefore, risk factors associated with the emergence of pathogens should be assessed before the appearance of mass mortalities in developing rearing areas. In this context, we characterized the vibrios community associated with oysters cultured in a non-intensive area free of massive mortalities located at Tongoy bay, Chile, through a culture-dependent approach. We taxonomically affiliated our isolates at the species level through the partial sequencing of the heat shock protein 60 gene and estimated their virulence potential through experimental infection of juvenile C. gigas. The vibrio community belonged almost entirely to the Splendidus clade, with Vibrio lentus being the most abundant species. The virulence potential of selected isolates was highly contrasted with oyster survival ranging between 100 and 30 %. Moreover, different vibrio species affected oyster survival at different rates, for instance V. splendidus TO2_12 produced most mortalities just 24 h after injection, while the V. lentus the most virulent strain TO6_11 produced sustained mortalities reaching 30 % of survival at day 4 after injection. Production of enzymes associated with pathogenicity was detected and hemolytic activity was positive for 50 % of the virulent strains and negative for 90 % of non-virulent strains, representing the phenotype that better relates to the virulence status of strains. Overall, results highlight that virulence is a trait present in the absence of disease expression, and therefore the monitoring of potentially pathogenic groups such as vibrios is essential to anticipate and manage oyster disease emergence in both established and under-development rearing areas.}, }
@article {pmid36412071, year = {2023}, author = {Shimpi, GG and Bentlage, B}, title = {Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200190}, doi = {10.1002/bies.202200190}, pmid = {36412071}, issn = {1521-1878}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Phylogeny ; Evolution, Molecular ; }, abstract = {In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.}, }
@article {pmid36410487, year = {2023}, author = {Deng, Y and Jiang, J and Huang, Y and Cheng, C and Lin, Z and Liu, G and Guo, Z and Feng, J}, title = {Hypoxia triggers the proliferation of antibiotic resistance genes in a marine aquaculture system.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160305}, doi = {10.1016/j.scitotenv.2022.160305}, pmid = {36410487}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/analysis ; *Genes, Bacterial ; RNA, Ribosomal, 16S ; Drug Resistance, Microbial/genetics ; Aquaculture ; Hypoxia ; Cell Proliferation ; }, abstract = {The transmission of antibiotic resistance genes (ARGs) affects the safety of aquaculture animals. Dissolved oxygen (DO) can affect the transmission of ARGs, but its mechanism of action in this process is unclear. We conducted laboratory breeding experiment with low and control DO groups. Combined quantitative PCR and 16S rRNA sequencing to study the effect of DO on the spread of ARGs. Hypoxia treatment significantly increased the accumulation of ammonium and nitrite in aquaculture water, and it increased the relative abundances of ARGs and mobile genetic elements (MGEs), especially the ARGs resistant to drugs in the categories of sulfonamide, (flor)/(chlor)/(am)phenicol, and MLSB (macrolide, lincosamide and streptogramin B) and the MGE intI-1(clinic), by 2.39-95.69 % in 28 days relative to the control DO treatment. Though the abundance of ARG carries, especially the Rhodocyclaceae, Caldilineaceae, Cyclobacteriaceae, Saprospiraceae, Enterobacteriaceae, Sphingomonadaceae families, showed higher abundance in low DO groups, relating to the vertical transmission of ARGs. Hypoxia treatment is more likely to promote the horizontal gene transfer (HGT)-related pathways, including ABC transporters, two component system, and quorum sensing, thus to induce the HGT of ARGs. The changed bacterial proliferation also altered the abundance of MGEs, especially intI-1(clinic), which induced HGT of ARGs as well. Additionally, pearson correlation results revealed that the succession of bacterial community function played the strongest role in ARG proliferation, followed by bacterial community structure and MGEs. Our results highlight the importance of suitable DO concentration in controlling the spread of ARGs especially the HGT of ARGs. In the context of global attention to food safety, our results provide important information for ensuring the safety of aquatic products and the sustainable development of aquaculture.}, }
@article {pmid36409903, year = {2022}, author = {Liu, B and Liu, Y and Yang, B and Wang, Q and Liu, X and Qin, J and Zhao, K and Li, F and Feng, X and Li, L and Wu, P and Liu, M and Zhu, S and Feng, L and Wang, L}, title = {Escherichia coli O157:H7 senses microbiota-produced riboflavin to increase its virulence in the gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2212436119}, pmid = {36409903}, issn = {1091-6490}, mesh = {Animals ; Humans ; Mice ; *Enterohemorrhagic Escherichia coli/genetics ; *Escherichia coli O157/genetics ; *Microbiota ; Riboflavin ; Virulence/genetics ; Intestines ; }, abstract = {Riboflavin is produced by most commensal bacteria in the human colon, where enterohemorrhagic Escherichia coli (EHEC) colonizes and causes diseases. Sensing environmental signals to site-specifically express the type-III secretion system (T3SS), which injects effectors into host cells leading to intestinal colonization and disease, is key to the pathogenesis of EHEC. Here, we reveal that EHEC O157:H7, a dominant EHEC serotype frequently associated with severe diseases, acquired a previously uncharacterized two-component regulatory system rbfSR, which senses microbiota-produced riboflavin to directly activate the expression of LEE genes encoding the T3SS in the colon. rbfSR is present in O157:H7 and O145:H28 but absent from other EHEC serotypes. The binding site of RbfR through which it regulates LEE gene expression was identified and is conserved in all EHEC serotypes and Citrobacter rodentium, a surrogate for EHEC in mice. Introducing rbfSR into C. rodentium enabled bacteria to sense microbiota-produced riboflavin in the mouse colon to increase the expression of LEE genes, causing increased disease severity in mice. Phylogenic analysis showed that the O55:H7 ancestor of O157:H7 obtained rbfSR which has been kept in O157:H7 since then. Thus, acquiring rbfSR represents an essential step in the evolution of the highly pathogenic O157:H7. The expression of LEE genes and cell attachment ability of other EHEC serotypes in the presence of riboflavin significantly increased when rbfSR was introduced into them, indicating that those serotypes are ready to use RbfSR to increase their pathogenicity. This may present a potential public health issue as horizontal gene transfer is frequent in enteric bacteria.}, }
@article {pmid36407614, year = {2022}, author = {Li, L and Peng, S and Wang, Z and Zhang, T and Li, H and Xiao, Y and Li, J and Liu, Y and Yin, H}, title = {Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1025122}, pmid = {36407614}, issn = {1664-462X}, abstract = {Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na[+]/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.}, }
@article {pmid36406448, year = {2022}, author = {Hinnekens, P and Fayad, N and Gillis, A and Mahillon, J}, title = {Conjugation across Bacillus cereus and kin: A review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1034440}, pmid = {36406448}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. Bacillus cereus and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of B. cereus sensu lato (s.l.) 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from B. cereus isolates have been reported as conjugative. However, with the increasing number of genomic data available, in silico analyses indicate that more plasmids from B. cereus s.l. genomes present self-transfer potential. B. cereus s.l. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of B. cereus s.l., it is of prime importance to consider the impact of conjugation within this bacterial group.}, }
@article {pmid36404338, year = {2022}, author = {Orata, FD and Hussain, NAS and Liang, KYH and Hu, D and Boucher, YF}, title = {Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {42}, pmid = {36404338}, issn = {1757-4749}, abstract = {BACKGROUND: Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).<br><br>RESULTS: The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (<&#x2009;3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).<br><br>CONCLUSION: V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.}, }
@article {pmid36400772, year = {2022}, author = {Kim, HJ and Black, M and Edwards, RA and Peillard-Fiorente, F and Panigrahi, R and Klingler, D and Eidelpes, R and Zeindl, R and Peng, S and Su, J and Omar, AR and MacMillan, AM and Kreutz, C and Tollinger, M and Charpentier, X and Attaiech, L and Glover, JNM}, title = {Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7076}, pmid = {36400772}, issn = {2041-1723}, mesh = {*RNA-Binding Proteins/metabolism ; *RNA, Small Untranslated/genetics ; }, abstract = {The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail.}, }
@article {pmid36400617, year = {2023}, author = {Zhai, Z and Cui, C and Li, X and Yan, J and Sun, E and Wang, C and Guo, H and Hao, Y}, title = {Prevalence, antimicrobial susceptibility, and antibiotic resistance gene transfer of Bacillus strains isolated from pasteurized milk.}, journal = {Journal of dairy science}, volume = {106}, number = {1}, pages = {75-83}, doi = {10.3168/jds.2022-22199}, pmid = {36400617}, issn = {1525-3198}, mesh = {Animals ; *Milk/microbiology ; Prevalence ; Drug Resistance, Microbial ; *Bacillus/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests/veterinary ; }, abstract = {Pasteurization is carried out in dairy industries to kill harmful bacteria present in raw milk. However, endospore-forming bacteria, such as Bacillus, cannot be completely eliminated by pasteurization. In this study, a total of 114 Bacillus strains were isolated from 133 pasteurized milk samples. Antibiotic susceptibility tests showed that the percentage of Bacillus with intrinsic resistance to ampicillin and penicillin were 80 and 86%, respectively. Meanwhile, some Bacillus isolates had acquired resistance, including trimethoprim-sulfamethoxazole resistance (10 isolates), clindamycin resistance (8 isolates), erythromycin resistance (2 isolates), and tetracycline resistance (1 isolate). To further locate these acquired resistance genes, the plasmids were investigated in these 16 Bacillus strains. The plasmid profile indicated that Bacillus cereus BA008, BA117, and BA119 harbored plasmids, respectively. Subsequently, the Illumina Novaseq PE150 was applied for the genomic and plasmid DNA sequencing. Notably, the gene tetL encoding tetracycline efflux protein was found to be located on plasmid pBC46-TL of B. cereus BA117. In vitro conjugative transfer indicated that pBC46-TL can be transferred into Bacillus invictae BA142, Bacillus safensis BA143, and Bacillus licheniformis BA130. The frequencies were of 1.5 × 10[-7] to 1.7 × 10[-5] transconjugants per donor cells. Therefore, Bacillus strains with acquired antibiotic resistance may represent a potential risk for the spread of antibiotic resistance between Bacillus and other clinical pathogens via horizontal gene transfer.}, }
@article {pmid36386695, year = {2022}, author = {Gerlach, D and Sieber, RN and Larsen, J and Krusche, J and De Castro, C and Baumann, J and Molinaro, A and Peschel, A}, title = {Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951333}, pmid = {36386695}, issn = {1664-302X}, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones.}, }
@article {pmid36386682, year = {2022}, author = {Pan, X and Zhou, Z and Liu, B and Wu, Z}, title = {A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1037389}, pmid = {36386682}, issn = {1664-302X}, abstract = {Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a "reservoir" of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.}, }
@article {pmid36386654, year = {2022}, author = {Guzman-Otazo, J and Joffré, E and Agramont, J and Mamani, N and Jutkina, J and Boulund, F and Hu, YOO and Jumilla-Lorenz, D and Farewell, A and Larsson, DGJ and Flach, CF and Iñiguez, V and Sjöling, &#xc5;}, title = {Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {997849}, pmid = {36386654}, issn = {1664-302X}, abstract = {Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.}, }
@article {pmid36386652, year = {2022}, author = {de la Higuera, I and Lázaro, E}, title = {Viruses in astrobiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032918}, pmid = {36386652}, issn = {1664-302X}, abstract = {Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.}, }
@article {pmid36384846, year = {2022}, author = {Wang, YJ and Tang, YJ and Zhang, YP and Zhang, MY and Chu, SS and Qiu, RL}, title = {[Retarding potential of biochar on antibiotic resistance genes in soil and the mechanisms: A review.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {11}, pages = {3116-3126}, doi = {10.13287/j.1001-9332.202211.014}, pmid = {36384846}, issn = {1001-9332}, mesh = {Humans ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/analysis ; Bacteria/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) in soil pose a major challenge to global environment and health. The development of effective technologies to reduce their negative effects has implications for maintaining soil health and human health. Biochar would be a suitable control material due to its characteristics of high carbon content, large surface area, excellent adsorption capacity, and economic advantages. There are three mechanisms underlying its negative effects on the abundance of ARGs: 1) adsorption of certain pollutants (e.g., antibiotics and heavy metals) to reduce the co-selective pressure of ARGs; 2) alteration of microbial composition through altering soil physico-chemical properties, and thereby limiting the ability of bacteria to undergo horizontal transfer of ARGs; 3) direct impairment of horizontal gene transfer by the adsorption of horizontal transfer vectors such as plasmids, transposons, and integrons. However, the negative effect of biochar depends on the source of material, pyrolysis process, and its amount added. Furthermore, field aging of biochar may reduce its ability to block ARGs. Endogenous contaminants of biochar, such as polycyclic aromatic hydrocarbons and heavy metals, may cause the enrichment of specific antibiotic-resistant bacteria in the environment or induce horizontal gene transfer. In further studies, suitable biochar should be selected according to soil environments, and biochar aging control measures should be taken to improve its retarding effect on ARGs.}, }
@article {pmid36384625, year = {2022}, author = {Wang, YJ and Si, YM and Li, YJ}, title = {[Research progress on the application of quorum sensing in the colonization and degradation enhancement of bioaugmentation functional bacteria].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {10}, pages = {2871-2880}, doi = {10.13287/j.1001-9332.202210.031}, pmid = {36384625}, issn = {1001-9332}, mesh = {Quorum Sensing/physiology ; Sewage ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants/metabolism ; }, abstract = {Due to the impacts of refractory organic pollutants and environment on the water treatment system, the sewage quality can not reach the standard. It is an effective measure to improve the efficiency of wastewater treatment by introducing exogenous engineering strains with relevant functional genes and the ability of horizontal gene transfer. In sewage treatment system, there are bacteria secreting signal molecules with quorum sensing. When population density reaches induction threshold, the bacteria would activate the related genes expression (such as biofilm formation, bioluminescent, antibiotics synthesis and virulence factor expression, etc.) through releasing signaling molecules, and thus trigger the behavior of other groups. Previously, researches about quorum sensing mainly concentrated on signal transduction, microbial social behavior, and medical microbiology. In recent years, stu-dies found that quorum sensing plays an important role in wastewater biological treatment and affects the colonization of the microorganism strain and pollutants degradation. Therefore, the regulation of quorum-sensing behavior is the key factor in the bioaugmentation performance. Here, we review the signaling molecules mechanism, the release of signaling molecules and its influence factors, the colonization of microbial community and the removal of pollutants. We further discussed the research from the perspective of quorum sensing biological process. The aim was to provide new idea for the effective implementation of bioaugmentation technology and the improvement of wastewater treatment efficiency, and to provide a theoretical reference for the in-depth understanding of quorum sensing regulation behavior in the process of bioaugmentation.}, }
@article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, }
@article {pmid36381231, year = {2022}, author = {Benites, LF and Stephens, TG and Bhattacharya, D}, title = {Multiple waves of viral invasions in Symbiodiniaceae algal genomes.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac101}, pmid = {36381231}, issn = {2057-1577}, abstract = {Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.}, }
@article {pmid36377945, year = {2022}, author = {Aytan-Aktug, D and Grigorjev, V and Szarvas, J and Clausen, PTLC and Munk, P and Nguyen, M and Davis, JJ and Aarestrup, FM and Lund, O}, title = {SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0264122}, pmid = {36377945}, issn = {2165-0497}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Genome, Bacterial ; *Bacteriophages/genetics ; Plasmids/genetics ; Chromosomes, Bacterial/genetics ; Machine Learning ; }, abstract = {High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.}, }
@article {pmid36375055, year = {2022}, author = {Wu, C and Tang, D and Dai, J and Tang, X and Bao, Y and Ning, J and Zhen, Q and Song, H and St Leger, RJ and Fang, W}, title = {Bioremediation of mercury-polluted soil and water by the plant symbiotic fungus Metarhizium robertsii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {47}, pages = {e2214513119}, pmid = {36375055}, issn = {1091-6490}, mesh = {Biodegradation, Environmental ; Water ; *Mercury/toxicity ; *Methylmercury Compounds ; Phylogeny ; Ecosystem ; *Metarhizium/genetics ; Soil ; }, abstract = {Fungi are central to every terrestrial and many aquatic ecosystems, but the mechanisms underlying fungal tolerance to mercury, a global pollutant, remain unknown. Here, we show that the plant symbiotic fungus Metarhizium robertsii degrades methylmercury and reduces divalent mercury, decreasing mercury accumulation in plants and greatly increasing their growth in contaminated soils. M. robertsii does this by demethylating methylmercury via a methylmercury demethylase (MMD) and using a mercury ion reductase (MIR) to reduce divalent mercury to volatile elemental mercury. M. robertsii can also remove methylmercury and divalent mercury from fresh and sea water even in the absence of added nutrients. Overexpression of MMD and MIR significantly improved the ability of M. robertsii to bioremediate soil and water contaminated with methylmercury and divalent mercury. MIR homologs, and thereby divalent mercury tolerance, are widespread in fungi. In contrast, MMD homologs were patchily distributed among the few plant associates and soil fungi that were also able to demethylate methylmercury. Phylogenetic analysis suggests that fungi could have acquired methylmercury demethylase genes from bacteria via two independent horizontal gene transfer events. Heterologous expression of MMD in fungi that lack MMD homologs enabled them to demethylate methylmercury. Our work reveals the mechanisms underlying mercury tolerance in fungi, and may provide a cheap and environmentally friendly means of cleaning up mercury pollution.}, }
@article {pmid36374836, year = {2022}, author = {Kurlovs, AH and De Beer, B and Ji, M and Vandenhole, M and De Meyer, T and Feyereisen, R and Clark, RM and Van Leeuwen, T}, title = {Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae.}, journal = {PLoS genetics}, volume = {18}, number = {11}, pages = {e1010333}, pmid = {36374836}, issn = {1553-7404}, mesh = {Animals ; *Tetranychidae/genetics ; Herbivory ; Gene Transfer, Horizontal ; Adaptation, Physiological ; Plants ; *Pesticides ; }, abstract = {The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness as is commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, or in some cases synergism of cis and trans, in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggests modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects.}, }
@article {pmid36374047, year = {2022}, author = {Kogay, R and Zhaxybayeva, O}, title = {Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0089222}, pmid = {36374047}, issn = {2379-5077}, mesh = {Bacteria ; *Viruses ; DNA ; *Alphaproteobacteria ; }, abstract = {Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.}, }
@article {pmid36371907, year = {2022}, author = {Zhao, CX and Su, XX and Xu, MR and An, XL and Su, JQ}, title = {Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114282}, doi = {10.1016/j.ecoenv.2022.114282}, pmid = {36371907}, issn = {1090-2414}, mesh = {Humans ; *Integrons/genetics ; *Endophytes/genetics ; Vegetables/genetics ; Anti-Bacterial Agents/pharmacology ; Integrases/genetics ; }, abstract = {Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.}, }
@article {pmid36371221, year = {2022}, author = {Uruén, C and García, C and Fraile, L and Tommassen, J and Arenas, J}, title = {How Streptococcus suis escapes antibiotic treatments.}, journal = {Veterinary research}, volume = {53}, number = {1}, pages = {91}, pmid = {36371221}, issn = {1297-9716}, mesh = {Humans ; Swine ; Animals ; *Streptococcus suis/genetics ; *Streptococcal Infections/drug therapy/veterinary ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Macrolides ; *Swine Diseases/drug therapy/prevention &amp; control ; }, abstract = {Streptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.}, }
@article {pmid36370776, year = {2023}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Charles, S and Srinivasan, V and Sajith, V and Subila, KP and Haritha, P}, title = {Metagenomics indicates abundance of biofilm related genes and horizontal transfer of multidrug resistant genes among bacterial communities in nano zinc oxide polluted soil.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160032}, doi = {10.1016/j.scitotenv.2022.160032}, pmid = {36370776}, issn = {1879-1026}, mesh = {*Zinc Oxide/toxicity ; Soil ; *Nanoparticles ; Biofilms ; *Metal Nanoparticles/toxicity ; Oxides ; }, abstract = {The unsafe and reckless disposal of metal oxide nanoparticles like ZnO (nZnO) into the soil could seriously impact bacterial behavioural responses and functions. Under such stress, biofilm formation is considered to be a robust mechanism for bacterial survival in soil. We examined the response of bacterial metagenomes in soils exposed to varying levels of Zn (50, 200, 500 and 1000 mg kg[-1]) as nano Zn oxide (nZnO) in terms of biofilm genesis and regulation and their co-occurrences with multidrug resistance genes (MDRGs) and mobile genetic elements (MGEs). The size-specific effects of nZnO were verified using its bulk counterpart (bZnO). Both nZnO and bZnO facilitated profusion of biofilm related genes (BGs) especially at higher Zn levels (500 and 1000 mg kg[-1] Zn), though maximum abundance was registered at a comparatively lower level under nZnO. In general, nZnO favoured an enhancement of genes involved in exopolysaccharide biosynthesis and attachment, while bZnO favoured genes related to capsule formation, chemotaxis and biofilm dispersion. Co-occurrence network analysis revealed significant positive correlations between abundances of BGs, MDRGs and MGEs, indicating an enhanced probability for horizontal gene transfer of MDRGs in nZnO polluted soils.}, }
@article {pmid36370236, year = {2022}, author = {Kerber-Diaz, JC and Leos-Ramírez, MA and Flores-Ceron, AA and Ponce-Mendoza, A and Estrada-de Los Santos, P and Ibarra, JA}, title = {Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {703}, pmid = {36370236}, issn = {1432-072X}, mesh = {CRISPR-Cas Systems ; *Burkholderiaceae/genetics ; Plasmids ; Computational Biology ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function of these systems. Their function has been mostly related to "genetic immunity" against foreign genetic material, among other roles. Interest in them increased after their use in genetic manipulation was uncovered and surveys to find and classify them have been done in several bacterial groups. To determine the presence of these genetic elements in the Burkholderiaceae family members, a bioinformatic approach was followed. Attention in this family comes as it is formed by a great diversity of microorganisms that include opportunistic and true pathogens, and symbiotic and saprophytic organisms, among others. Results show that, in contrast to other bacterial groups, only 8.4% of family members harbor complete CRISPR-Cas systems and the rest either do not have one or have remains or sections of one. Analyses of the spacer sequences indicated that most of them have identity to sections of the same genomes they were found, while a few had identities with either plasmids or phages. The genus with the higher proportion of self-directed spacers is Ralstonia, and their possible roles are discussed. Most of the systems (60%) belong to the class I subtype I-E and a few to subtypes I-C (13.3%), I-F (18.3%), II-C (5%), IV-A (1.7%) and V-C (1.7%). To the best of our knowledge, this is the first study to uncover the CRISPR-Cas system for the whole Burkholderiaceae family.}, }
@article {pmid36368125, year = {2022}, author = {Ropars, J and Giraud, T}, title = {Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102236}, doi = {10.1016/j.mib.2022.102236}, pmid = {36368125}, issn = {1879-0364}, mesh = {Humans ; *Cheese/microbiology ; Fungi/genetics ; Meat ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.}, }
@article {pmid36361992, year = {2022}, author = {Larrea, E and Fernández-Rubio, C and Peña-Guerrero, J and Guruceaga, E and Nguewa, PA}, title = {The BRCT Domain from the Homologue of the Oncogene PES1 in Leishmania major (LmjPES) Promotes Malignancy and Drug Resistance in Mammalian Cells.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361992}, issn = {1422-0067}, mesh = {Animals ; Humans ; Mice ; Adaptor Proteins, Signal Transducing/metabolism ; CARD Signaling Adaptor Proteins/metabolism ; HEK293 Cells ; *Leishmania major/genetics/metabolism ; Mammals/metabolism ; Oncogenes ; Proteins/metabolism ; *RNA-Binding Proteins/genetics ; Leishmaniasis/complications ; *Drug Resistance, Neoplasm/genetics ; *Carcinogenesis/genetics ; }, abstract = {Around 15% of cancer cases are attributable to infectious agents. Epidemiological studies suggest that an association between leishmaniasis and cancer does exist. Recently, the homologue of PES1 in Leishmania major (LmjPES) was described to be involved in parasite infectivity. Mammalian PES1 protein has been implicated in cellular processes like cell cycle regulation. Its BRCT domain has been identified as a key factor in DNA damage-responsive checkpoints. This work aimed to elucidate the hypothetical oncogenic implication of BRCT domain from LmjPES in host cells. We generated a lentivirus carrying this BRCT domain sequence (lentiBRCT) and a lentivirus expressing the luciferase protein (lentiLuc), as control. Then, HEK293T and NIH/3T3 mammalian cells were infected with these lentiviruses. We observed that the expression of BRCT domain from LmjPES conferred to mammal cells in vitro a greater replication rate and higher survival. In in vivo experiments, we observed faster tumor growth in mice inoculated with lentiBRCT respect to lentiLuc HEK293T infected cells. Moreover, the lentiBRCT infected cells were less sensitive to the genotoxic drugs. Accordingly, gene expression profiling analysis revealed that BRCT domain from LmjPES protein altered the expression of proliferation- (DTX3L, CPA4, BHLHE41, BMP2, DHRS2, S100A1 and PARP9), survival- (BMP2 and CARD9) and chemoresistance-related genes (DPYD, Dok3, DTX3L, PARP9 and DHRS2). Altogether, our results reinforced the idea that in eukaryotes, horizontal gene transfer might be also achieved by parasitism like Leishmania infection driving therefore to some crucial biological changes such as proliferation and drug resistance.}, }
@article {pmid36360308, year = {2022}, author = {Bernelot-Moens, R and Beatty, JT}, title = {DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360308}, issn = {2073-4425}, mesh = {*Rhodobacter capsulatus/genetics/metabolism ; Topoisomerase II Inhibitors/pharmacology ; Gene Expression Regulation, Bacterial ; *Bacteriophages ; Novobiocin/pharmacology/metabolism ; Ecosystem ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.}, }
@article {pmid36360197, year = {2022}, author = {Yushchuk, O and Binda, E and Fedorenko, V and Marinelli, F}, title = {Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360197}, issn = {2073-4425}, mesh = {*Bacteria ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Glycopeptides ; Firmicutes ; *Actinobacteria/genetics ; }, abstract = {Clinically relevant glycopeptide antibiotics remain among the most successful classes of natural antibacterials. This success, however, is endangered by the spread of glycopeptide resistance genes, also known as van genes. Thus, it is important to trace and comprehend possible routes of van gene dissemination. In the current work, we present a comprehensive bioinformatic analysis aimed at mapping the occurrence of van genes beyond the Actinobacteria phylum-the most likely natural reservoir of van genes. We show that two additional classes of Gram-positive bacteria, Erysipelotrichia and Ktedonobacteria, as well as one class of Gram-negative bacteria, Anaerolineae, carry van genes. Additionally, we demonstrate that various new genera belonging to the classes Clostridia and Bacilli also carry van genes. The majority of discovered van loci are co-localized with MGE-related genes of various types. Finally, we propose a phylogeny-based scenario for the spread of van genes, unraveling a network of consequential horizontal gene transfer events linking the phylum Actinobacteria with the five other bacterial classes carrying van genes.}, }
@article {pmid36357451, year = {2022}, author = {Downing, T and Rahm, A}, title = {Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19203}, pmid = {36357451}, issn = {2045-2322}, mesh = {*Protein Interaction Maps/genetics ; Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Bacterial Proteins/genetics ; }, abstract = {Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.}, }
@article {pmid36356515, year = {2023}, author = {Jin, X and Liu, S and Zhang, Z and Liu, T and Li, N and Liang, Y and Zheng, J and Peng, N}, title = {Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130261}, doi = {10.1016/j.jhazmat.2022.130261}, pmid = {36356515}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Astacoidea/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Ecosystem ; Enrofloxacin/pharmacology ; Genes, Bacterial ; *Ponds/analysis ; Geologic Sediments ; }, abstract = {Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.}, }
@article {pmid36354153, year = {2023}, author = {Wang, H and Li, Y and Zhang, Z and Zhong, B}, title = {Horizontal gene transfer: Driving the evolution and adaptation of plants.}, journal = {Journal of integrative plant biology}, volume = {65}, number = {3}, pages = {613-616}, doi = {10.1111/jipb.13407}, pmid = {36354153}, issn = {1744-7909}, mesh = {Phylogeny ; Gene Transfer, Horizontal ; Plants/genetics ; *Embryophyta/genetics ; *Viridiplantae ; }, abstract = {Horizontal gene transfer greatly contributes to the diversification and long-term evolution of green plants. Recent studies suggest that horizontal gene transfer events drove the evolution and adaptation of charophyte green algae and land plants.}, }
@article {pmid36351400, year = {2022}, author = {Hua, M and Dai, D and Du, P and Chen, N and Duan, A and Yue, J and Jia, H and Rong, C and Li, A and Zeng, H and Chen, C}, title = {A chromosome-encoded T4SS independently contributes to horizontal gene transfer in Enterococcus faecalis.}, journal = {Cell reports}, volume = {41}, number = {6}, pages = {111609}, doi = {10.1016/j.celrep.2022.111609}, pmid = {36351400}, issn = {2211-1247}, mesh = {*Enterococcus faecalis/genetics/metabolism ; *Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; Type IV Secretion Systems/metabolism ; Chromosomes/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial type IV secretion systems (T4SSs) are the specific devices that mediate the dissemination of antibiotic resistant genes via horizontal gene transfer (HGT). Multi-drug-resistant Enterococcus faecalis (E. faecalis) represents a clinical public health threat because of its transferable plasmid with a functional plasmid-encoded (PE)-T4SS. Here, we report a chromosome-encoded (CE)-T4SS that exists in 40% of E. faecalis isolates. Compared with the PE-T4SS, CE-T4SS displays distinct characteristics in protein architecture and is capable of mediating large and genome-wide gene transfer in an imprecise manner. Reciprocal exchange of CE-T4SS- or PE-T4SS-associated origin of transfer (oriT) could disrupt HGT function, indicating that CE-T4SS is an independent system compared with PE-T4SS. Taken together, the CE-T4SS sheds light on the knowledge of HGT in gram-positive bacteria and triggers us to explore more evolutionary mechanisms in E. faecalis.}, }
@article {pmid36350852, year = {2022}, author = {Koutsovoulos, GD and Granjeon Noriot, S and Bailly-Bechet, M and Danchin, EGJ and Rancurel, C}, title = {AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers.}, journal = {PLoS computational biology}, volume = {18}, number = {11}, pages = {e1010686}, pmid = {36350852}, issn = {1553-7358}, mesh = {*Gene Transfer, Horizontal/genetics ; Phylogeny ; *Biological Evolution ; Genome ; Software ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.}, }
@article {pmid36350849, year = {2022}, author = {Coyte, KZ and Stevenson, C and Knight, CG and Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Horizontal gene transfer and ecological interactions jointly control microbiome stability.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001847}, pmid = {36350849}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics ; }, abstract = {Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.}, }
@article {pmid36350646, year = {2023}, author = {Choi, Y and Ahn, S and Park, M and Lee, S and Cho, S and Kim, H}, title = {HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1010-D1018}, pmid = {36350646}, issn = {1362-4962}, mesh = {*Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; *Genome, Bacterial/genetics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.}, }
@article {pmid36350115, year = {2022}, author = {Koppenhöfer, S and Tomasch, J and Lang, AS}, title = {Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36350115}, issn = {2057-5858}, mesh = {*Alphaproteobacteria/genetics ; Gene Transfer, Horizontal ; *Rhodobacter capsulatus/genetics ; Prophages/genetics ; Genomics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.}, }
@article {pmid36346786, year = {2022}, author = {Lang, AS}, title = {Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001874}, pmid = {36346786}, issn = {1545-7885}, mesh = {Prophages/genetics ; Gene Transfer, Horizontal ; *Caulobacter crescentus ; *Bacteriophages/genetics ; DNA Repair ; }, abstract = {The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.}, }
@article {pmid36345550, year = {2022}, author = {Shokrollahi, P and Hasani, A and Aghazadeh, M and Memar, MY and Hasani, A and Zaree, M and Rezaee, MA and Sadeghi, J}, title = {Contribution of Arginine Catabolic Mobile Element and Copper and Mercury Resistance Element in Methicillin-Resistant Staphylococcus aureus: A Vantage Point.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {9916255}, pmid = {36345550}, issn = {1712-9532}, abstract = {Different clones of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are dominating geographically. One of the significant, hypervirulent, CA-MRSA and a significant health concern clones is USA3000, found worldwide regionally with varying frequencies. The clone harbors several mobile genetic elements (MGEs) including, arginine catabolic mobile element (ACME) and copper and mercury resistance genes (COMER), accomplished by horizontal gene transfer from S. epidermidis. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. This review highlights the comprehensive view on ACME and COMER structure, their distribution, and the mechanism of action along with pathogenetic features of USA3000 encompassing their role in biofilm formation, adhesion, quorum sensing, resistance to antibiotics, chemotaxis, and nutrient uptake. We also provided an insight into the role of ACME and COMER genes in the survival of bacterium. Our results shed light on the emergence of two independent clones possessing ACME (North American) and COMER (South American) elements which later disseminated to other regions. ACME and COMER both are adjacent to staphylococcal cassette chromosome mec type IV (SCCmec IV). The acquisition of mecA, followed by COMER or ACME has been shown as a significant factor in the rise and fall of MRSA strains and their complex ability to adapt to hostile environments. The presence of ACME increases fitness, thereby allowing bacteria to colonize the skin and mucous membrane while COMER contributes to genetic stability by knocking over the copper-mediated killing in macrophages. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. Interestingly, ACME strains have been shown to possess the ability to counteract skin acidity, thereby allowing increased skin colonization. A profound understanding of MGEs in S. aureus plays an important role in the prevention of epidemic clones.}, }
@article {pmid36343341, year = {2023}, author = {Wang, R and Xiao, J and Wang, Q and Zhao, W and Liu, X and Liu, Y and Fu, S}, title = {Genomic analysis of a new type VI secretion system in Vibrio parahaemolyticus and its implications for environmental adaptation in shrimp ponds.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {1}, pages = {53-61}, doi = {10.1139/cjm-2022-0096}, pmid = {36343341}, issn = {1480-3275}, mesh = {*Type VI Secretion Systems/genetics ; *Vibrio parahaemolyticus/genetics ; Ponds ; Genomics ; Anti-Bacterial Agents/pharmacology ; *Vibrio cholerae/genetics ; Bacterial Proteins/genetics ; }, abstract = {The type VI secretion system (T6SS) in Vibrio spp. is often used to kill heteroclonal neighbors by direct injection of toxic effectors, but its strategies in aquacultural environments receive limited attention. In this study, we conducted genomic analysis for a T6SS-harboring plasmid in V. parahaemolyticus strain VP157. Coculture assays were further conducted to verify its antibacterial function. The results showed that strain VP157 harbored a 132-kb plasmid, pVP157-1, which consists of two fragments: an 87.8-kb fragment identical to plasmid pTJ114-1 and a 44.2-kb T6SS gene cluster with only 4% DNA identity to T6SS1 in the V. parahaemolyticus reference genome. Gene-by-gene analysis of six genes representing core T6SS components suggested that each gene has distinct evolutionary origins. In vitro experimental evolution revealed that pVP157-1 can excise from the VP157 genome with an excision rate of 4%. A coculture assay suggested that strain VP157 had significantly higher antibacterial activity against Bacillus pumilus and V. cholerae than the strain without pVP157-1(VP157[∆T6SS]). In contrast, a rapid decline was observed for the proportion of VP157[∆] [T6SS] in a mock microbial community, which decreased from 10.7% to 2.1% in 5 days. The results highlighted that the acquisition of T6SS fostered the fitness of V . parahaemolyticus in a complex environment.}, }
@article {pmid36342184, year = {2022}, author = {Tran, F and Gangan, MS and Weaver, BP and Boedicker, JQ}, title = {Membrane-Binding Biomolecules Influence the Rate of Vesicle Exchange between Bacteria.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {23}, pages = {e0134622}, pmid = {36342184}, issn = {1098-5336}, mesh = {*Bacteria/genetics/metabolism ; Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; Membranes ; Eukaryota ; }, abstract = {The exchange of bacterial extracellular vesicles facilitates molecular exchange between cells, including the horizontal transfer of genetic material. Given the implications of such transfer events on cell physiology and adaptation, some bacterial cells have likely evolved mechanisms to regulate vesicle exchange. Past work has identified mechanisms that influence the formation of extracellular vesicles, including the production of small molecules that modulate membrane structure; however, whether these mechanisms also modulate vesicle uptake and have an overall impact on the rate of vesicle exchange is unknown. Here, we show that membrane-binding molecules produced by microbes influence both the formation and uptake of extracellular vesicles and have the overall impact of increasing the vesicle exchange rate within a bacterial coculture. In effect, production of compounds that increase vesicle exchange rates encourage gene exchange between neighboring cells. The ability of several membrane-binding compounds to increase vesicle exchange was demonstrated. Three of these compounds, nisin, colistin, and polymyxin B, are antimicrobial peptides added at sub-inhibitory concentrations. These results suggest that a potential function of exogenous compounds that bind to membranes may be the regulation of vesicle exchange between cells. IMPORTANCE The exchange of bacterial extracellular vesicles is one route of gene transfer between bacteria, although it was unclear if bacteria developed strategies to modulate the rate of gene transfer within vesicles. In eukaryotes, there are many examples of specialized molecules that have evolved to facilitate the production, loading, and uptake of vesicles. Recent work with bacteria has shown that some small molecules influence membrane curvature and induce vesicle formation. Here, we show that similar compounds facilitate vesicle uptake, thereby increasing the overall rate of vesicle exchange within bacterial populations. The addition of membrane-binding compounds, several of them antibiotics at subinhibitory concentrations, to a bacterial coculture increased the rate of horizontal gene transfer via vesicle exchange.}, }
@article {pmid36342139, year = {2022}, author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL}, title = {Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0163522}, pmid = {36342139}, issn = {1098-5336}, support = {R35 GM130355/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Aliivibrio fischeri/genetics ; *Decapodiformes/microbiology ; Symbiosis ; Phosphates ; Biofilms ; }, abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates after 72 h. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research. IMPORTANCE From soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between V. fischeri and its squid host, Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.}, }
@article {pmid36341518, year = {2023}, author = {Kessler, C and Hou, J and Neo, O and Buckner, MMC}, title = {In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {1}, pages = {}, pmid = {36341518}, issn = {1574-6976}, support = {MR/V009885/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Gene Transfer, Horizontal ; Conjugation, Genetic ; }, abstract = {Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.}, }
@article {pmid36340844, year = {2022}, author = {Lynch, T and Nandi, T and Jayaprakash, T and Gregson, D and Church, DL}, title = {Genomic analysis of group A Streptococcus isolated during a correctional facility outbreak of MRSA in 2004.}, journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada}, volume = {7}, number = {1}, pages = {23-35}, pmid = {36340844}, issn = {2371-0888}, abstract = {BACKGROUND: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus.<br><br>METHODS: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes.<br><br>RESULTS: Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections.<br><br>CONCLUSIONS: GAS recovered from invasive and non-invasive sources were not genetically distinguishable. Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.}, }
@article {pmid36338125, year = {2022}, author = {Yu, W and Li, S and Zhang, G and Xu, HHK and Zhang, K and Bai, Y}, title = {New frontiers of oral sciences: Focus on the source and biomedical application of extracellular vesicles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1023700}, pmid = {36338125}, issn = {2296-4185}, abstract = {Extracellular vesicles (EVs) are a class of nanoparticles that are derived from almost any type of cell in the organism tested thus far and are present in all body fluids. With the capacity to transfer "functional cargo and biological information" to regulate local and distant intercellular communication, EVs have developed into an attractive focus of research for various physiological and pathological conditions. The oral cavity is a special organ of the human body. It includes multiple types of tissue, and it is also the beginning of the digestive tract. Moreover, the oral cavity harbors thousands of bacteria. The importance and particularity of oral function indicate that EVs derived from oral cavity are quite complex but promising for further research. This review will discuss the extensive source of EVs in the oral cavity, including both cell sources and cell-independent sources. Besides, accumulating evidence supports extensive biomedical applications of extracellular vesicles in oral tissue regeneration and development, diagnosis and treatment of head and neck tumors, diagnosis and therapy of systemic disease, drug delivery, and horizontal gene transfer (HGT). The immune cell source, odontoblasts and ameloblasts sources, diet source and the application of EVs in tooth development and HGT were reviewed for the first time. In conclusion, we concentrate on the extensive source and potential applications offered by these nanovesicles in oral science.}, }
@article {pmid36338046, year = {2022}, author = {Yang, C and Han, J and Berglund, B and Zou, H and Gu, C and Zhao, L and Meng, C and Zhang, H and Ma, X and Li, X}, title = {Dissemination of bla NDM-5 and mcr-8.1 in carbapenem-resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae in an animal breeding area in Eastern China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1030490}, pmid = {36338046}, issn = {1664-302X}, abstract = {Animal farms have become one of the most important reservoirs of carbapenem-resistant Klebsiella spp. (CRK) owing to the wide usage of veterinary antibiotics. "One Health"-studies observing animals, the environment, and humans are necessary to understand the dissemination of CRK in animal breeding areas. Based on the concept of "One-Health," 263 samples of animal feces, wastewater, well water, and human feces from 60 livestock and poultry farms in Shandong province, China were screened for CRK. Five carbapenem-resistant Klebsiella pneumoniae (CRKP) and three carbapenem-resistant Klebsiella quasipneumoniae (CRKQ) strains were isolated from animal feces, human feces, and well water. The eight strains were characterized by antimicrobial susceptibility testing, plasmid conjugation assays, whole-genome sequencing, and bioinformatics analysis. All strains carried the carbapenemase-encoding gene bla NDM-5, which was flanked by the same core genetic structure (IS5-bla NDM-5-ble MBL-trpF-dsbD-IS26-ISKox3) and was located on highly related conjugative IncX3 plasmids. The colistin resistance gene mcr-8.1 was carried by three CRKP and located on self-transmissible IncFII(K)/IncFIA(HI1) and IncFII(pKP91)/IncFIA(HI1) plasmids. The genetic context of mcr-8.1 consisted of IS903-orf-mcr-8.1-copR-baeS-dgkA-orf-IS903 in three strains. Single nucleotide polymorphism (SNP) analysis confirmed the clonal spread of CRKP carrying-bla NDM-5 and mcr-8.1 between two human workers in the same chicken farm. Additionally, the SNP analysis showed clonal expansion of CRKP and CRKQ strains from well water in different farms, and the clonal CRKP was clonally related to isolates from animal farms and a wastewater treatment plant collected in other studies in the same province. These findings suggest that CRKP and CRKQ are capable of disseminating via horizontal gene transfer and clonal expansion and may pose a significant threat to public health unless preventative measures are taken.}, }
@article {pmid36338036, year = {2022}, author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA}, title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {995418}, pmid = {36338036}, issn = {1664-302X}, abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.}, }
@article {pmid36335713, year = {2022}, author = {Newson, JP and Gaissmaier, MS and McHugh, SC and Hardt, WD}, title = {Studying antibiotic persistence in vivo using the model organism Salmonella Typhimurium.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102224}, doi = {10.1016/j.mib.2022.102224}, pmid = {36335713}, issn = {1879-0364}, mesh = {Animals ; *Salmonella typhimurium/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Gene Transfer, Horizontal ; Virulence ; }, abstract = {Antibiotic persistence permits a subpopulation of susceptible bacteria to survive lethal concentrations of bactericidal antibiotics. This prolongs antibiotic therapy, promotes the evolution of antibiotic-resistant pathogen strains and can select for pathogen virulence within infected hosts. Here, we review the literature exploring antibiotic persistence in vivo, and describe the consequences of recalcitrant subpopulations, with a focus on studies using the model pathogen Salmonella Typhimurium. In vitro studies have established a concise set of features distinguishing true persisters from other forms of bacterial recalcitrance to bactericidal antibiotics. We discuss how animal infection models are useful for exploring these features in vivo, and describe how technical challenges can sometimes prevent the conclusive identification of true antibiotic persistence within infected hosts. We propose using two complementary working definitions for studying antibiotic persistence in vivo: the strict definition for studying the mechanisms of persister formation, and an operative definition for functional studies assessing the links between invasive virulence and persistence as well as the consequences for horizontal gene transfer, or the emergence of antibiotic-resistant mutants. This operative definition will enable further study of how antibiotic persisters arise in vivo, and of how surviving populations contribute to diverse downstream effects such as pathogen transmission, horizontal gene transfer and the evolution of virulence and antibiotic resistance. Ultimately, such studies will help to improve therapeutic control of antibiotic- recalcitrant populations.}, }
@article {pmid36334179, year = {2022}, author = {Tripathi, S and Purchase, D and Govarthanan, M and Chandra, R and Yadav, S}, title = {Regulatory and innovative mechanisms of bacterial quorum sensing-mediated pathogenicity: a review.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {75}, pmid = {36334179}, issn = {1573-2959}, mesh = {Humans ; *Quorum Sensing/physiology ; Virulence ; Environmental Monitoring ; Bacteria ; Biofilms ; Anti-Bacterial Agents/toxicity/metabolism ; *Anti-Infective Agents/metabolism ; }, abstract = {Quorum sensing (QS) is a system of bacteria in which cells communicate with each other; it is linked to cell density in the microbiome. The high-density colony population can provide enough small molecular signals to enable a range of cellular activities, gene expression, pathogenicity, and antibiotic resistance that cause damage to the hosts. QS is the basis of chronic illnesses in human due to microbial sporulation, expression of virulence factors, biofilm formation, secretion of enzymes, or production of membrane vesicles. The transfer of antimicrobial resistance gene (ARG) among antibiotic resistance bacteria is a major public health concern. QS-mediated biofilm is a hub for ARG horizontal gene transfer. To develop innovative approach to prevent microbial pathogenesis, it is essential to understand the role of QS especially in response to environmental stressors such as exposure to antibiotics. This review provides the latest knowledge on the relationship of QS and pathogenicity and explore the novel approach to control QS via quorum quenching (QQ) using QS inhibitors (QSIs) and QQ enzymes. The state-of-the art knowledge on the role of QS and the potential of using QQ will help to overcome the threats of rapidly emerging bacterial pathogenesis.}, }
@article {pmid36332408, year = {2022}, author = {Zhou, M and Cai, Q and Zhang, C and Ouyang, P and Yu, L and Xu, Y}, title = {Antibiotic resistance bacteria and antibiotic resistance genes survived from the extremely acidity posing a risk on intestinal bacteria in an in vitro digestion model by horizontal gene transfer.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114247}, doi = {10.1016/j.ecoenv.2022.114247}, pmid = {36332408}, issn = {1090-2414}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Angiotensin Receptor Antagonists ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Digestion ; }, abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants posing risk to human health. To investigate the pathogenic ARBs and the horizontal gene transfer (HGT) via both extracellular ARGs (eARGs) and intracellular ARGs (iARGs), an in vitro digestion simulation system was established to monitoring the ARB and ARGs passing through the artificial digestive tract. The results showed that ARB was mostly affected by the acidity of the gastric fluid with about 99% ARB (total population of 2.45 × 10[9]-2.54 × 10[9]) killed at pH 2.0 and severe damage of bacterial cell membrane. However, more than 80% ARB (total population of 2.71 × 10[9]-3.90 × 10[9]) survived the challenge when the pH of the gastric fluid was 3.0 and above. Most ARB died from the high acidity, but its ARGs, intI1 and 16 S rRNA could be detected. The eARGs (accounting for 0.03-24.56% of total genes) were less than iARGs obviously. The eARGs showed greater HGT potential than that of iARGs, suggesting that transformation occurred more easily than conjugation. The transferring potential followed: tet (100%) > sul (75%) > bla (58%), related to the high correlation of intI1 with tetA and sul2 (p < 0.01). Moreover, gastric juice of pH 1.0 could decrease the transfer frequency of ARGs by 2-3 order of magnitude compared to the control, but still posing potential risks to human health. Under the treatment of digestive fluid, ARGs showed high gene horizontal transfer potential, suggesting that food-borne ARBs pose a great risk of horizontal transfer of ARGs to intestinal bacteria.}, }
@article {pmid36328265, year = {2023}, author = {Li, H and Dechesne, A and He, Z and Jensen, MM and Song, HL and Smets, BF}, title = {Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159846}, doi = {10.1016/j.scitotenv.2022.159846}, pmid = {36328265}, issn = {1879-1026}, mesh = {*Disinfection ; Gene Transfer, Horizontal ; Angiotensin Receptor Antagonists/pharmacology ; Reactive Oxygen Species ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Plasmids ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Current in the milliampere range can be used for electrochemical inactivation of bacteria. Yet, bacteria-including antibiotic resistant bacteria (ARB) may be subjected to sublethal conditions due to imperfect mixing or energy savings measures during electrochemical disinfection. It is not known whether such sublethal current intensities have the potential to stimulate plasmid transfer from ARB. In this study, conjugal transfer of plasmid pKJK5 was investigated between Pseudomonas putida strains under conditions reflecting electrochemical disinfection. Although the abundance of culturable and membrane-intact donor and recipient cells decreased with applied current (0-60 mA), both transconjugant density and transconjugant frequency increased. Both active chlorine and superoxide radicals were generated electrolytically, and ROS generation was induced. In addition, we detected significant over expression of a core oxidative stress defense gene (ahpCF) with current. Expression of selected conjugation related genes (traE, traI, trbJ, and trbL) also significantly correlated with current intensity. ROS accumulation, SOS response and subsequent derepression of conjugation are therefore the plausible consequence of sublethal current exposure. These findings suggest that sublethal intensities of current can enhance conjugal plasmid transfer, and that it is essential that conditions of electrochemical disinfection (applied voltage, current density, time and mixing) are carefully controlled to avoid conjugal ARG transmission.}, }
@article {pmid36327832, year = {2023}, author = {Kothari, A and Kumar, P and Gaurav, A and Kaushal, K and Pandey, A and Yadav, SRM and Jain, N and Omar, BJ}, title = {Association of antibiotics and heavy metal arsenic to horizontal gene transfer from multidrug-resistant clinical strains to antibiotic-sensitive environmental strains.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130260}, doi = {10.1016/j.jhazmat.2022.130260}, pmid = {36327832}, issn = {1873-3336}, mesh = {Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Arsenic/toxicity ; Drug Resistance, Multiple, Bacterial/genetics ; *Metals, Heavy/toxicity ; Plasmids ; Bacteria/genetics ; Water ; }, abstract = {The emergence of multidrug-resistant bacteria is currently posing a significant threat to global public health. By testing for resistance to different antibiotic classes, we discovered that the majority of clinical bacteria are multidrug-resistant. These clinical multidrug-resistant species have antibiotic resistance genes on their plasmids that can be horizontally transferred to various antibiotic susceptible environmental bacterial species, resulting in antibiotic-resistant transconjugates. Furthermore, we discovered that the presence of an optimal concentration of antibiotics or heavy metal (arsenic) facilitates horizontal gene transfer through the formation of transconjugants. Notably, the addition of a conjugation inhibitor (2-hexadecynoic acid, a synthetic fatty acid) completely blocked the formation of antibiotic or arsenic-induced transconjugants. We discovered a high level of arsenic in water from the Shukratal region, Uttarakhand, India, which corresponded to a high serum level of arsenic in clinically infected individuals from the Shukratal region compared to other locations in Uttarakhand. Importantly, bacterial strains isolated from infected people who drink water from the Shukratal region with high arsenic levels were found to be more antibiotic-resistant than strains isolated from other sites. We discovered that bacterial strains isolated from individuals with high serum arsenic levels are significantly more resistant to antibiotics than individuals with low serum arsenic levels within the Shurkratal. This research sheds light on imminent threats to global health in which improper clinical, industrial, and other waste disposal, increased antibiotic concentrations in the environment, and increased human interference can easily transform commensal and pathogenic bacteria found in environmental niches into life-threatening multidrug-resistant superbugs.}, }
@article {pmid36327744, year = {2022}, author = {Carr, M and Leadbeater, BSC}, title = {Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species.}, journal = {Protist}, volume = {173}, number = {6}, pages = {125924}, doi = {10.1016/j.protis.2022.125924}, pmid = {36327744}, issn = {1618-0941}, mesh = {*Choanoflagellata/genetics ; Phylogeny ; }, abstract = {Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.}, }
@article {pmid36327213, year = {2022}, author = {Gozzi, K and Tran, NT and Modell, JW and Le, TBK and Laub, MT}, title = {Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001790}, pmid = {36327213}, issn = {1545-7885}, support = {BBS/E/J/000PR9791/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM082899/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Prophages/genetics/metabolism ; *Caulobacter crescentus/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; DNA Repair/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.}, }
@article {pmid36326505, year = {2022}, author = {Wilson, A and Molinar, J and Aldrich, J and Chintala, G and Smit, K and Miller, K and Bollivar, DW and Alvey, RM}, title = {Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes.}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0087922}, pmid = {36326505}, issn = {2576-098X}, abstract = {We report the genome sequences of 24 newly discovered bacteriophages that infect Rhodobacter capsulatus, a model for photosynthesis and horizontal gene transfer studies. All have substantial relatedness to previously reported siphovirus bacteriophages. Most are categorized in known clusters (RcB, RcC, RcD, and RcF), with one forming a new cluster, RcG.}, }
@article {pmid36325933, year = {2022}, author = {Corning, PA}, title = {The synergism hypothesis (revisited): a theory whose time has come?.}, journal = {Theoretical biology forum}, volume = {115}, number = {1-2}, pages = {85-97}, doi = {10.19272/202211402006}, pmid = {36325933}, issn = {2282-2593}, mesh = {*Biological Evolution ; Selection, Genetic ; *Heredity ; Hybridization, Genetic ; Gene Transfer, Horizontal ; }, abstract = {A major theoretical issue in evolutionary biology over the past two decades has concerned the rise of complexity over time in the natural world, and a search has been underway for "a Grand Unified Theory" - as biologist Daniel McShea characterized it - that is consistent with Darwin's great vision. As it happens, such a theory already exists. It was first proposed many years ago in The Synergism Hypothesis: A Theory of Progressive Evolution, and it involves an economic (or perhaps bioeconomic) theory of complexity. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects - synergies - with functional advantages that may, in turn, become direct causes of natural selection. In other words, the Synergism Hypothesis is a theory about the unique combined effects produced by the relationships between things. I refer to it as Holistic Darwinism; it is entirely con - sistent with natural selection theory, properly understood. Because the Synergism Hypothesis was first proposed during a time when the genecentric, neo-Darwinist paradigm was domi nant in evolutionary biology, it was largely overlooked. But times have changed. Biologist Richard Michod has concluded that "cooperation is now seen as the primary creative force behind ever greater levels of complexity and organization in all of biology." And Martin Nowak has called cooperation "the master architect of evolution." Here I will revisit this theory in the light of the many theoretical developments and research findings in recent years that are supportive of it, including the role of symbiogenesis in evolution, the phenomenon of hybridization, lateral gene transfer in prokaryotes, "developmental plasticity" (evo-devo), epigenetic inheritance, the role of behaviour (and teleonomy) in evolution, and gene-culture coevolution. The Synergism Hypothesis is especially relevant to the evolution of humankind.}, }
@article {pmid36324140, year = {2022}, author = {Slizovskiy, IB and Oliva, M and Settle, JK and Zyskina, LV and Prosperi, M and Boucher, C and Noyes, NR}, title = {Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {185}, pmid = {36324140}, issn = {2049-2618}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).<br><br>RESULTS: Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher&#xa0;ARG&#xa0;recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.<br><br>CONCLUSIONS: TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.}, }
@article {pmid36322896, year = {2022}, author = {Huang, H and Lin, L and Bu, F and Su, Y and Zheng, X and Chen, Y}, title = {Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {22}, pages = {15594-15606}, doi = {10.1021/acs.est.2c04276}, pmid = {36322896}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida ; Oxidation-Reduction ; Conjugation, Genetic ; }, abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg[2+] by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.}, }
@article {pmid36314801, year = {2022}, author = {Jiang, W and Zhang, M and Gao, S and Zhu, Q and Qiu, J and Yan, X and Xin, F and Jiang, M and Hong, Q}, title = {Comparative Genomic Analysis of Carbofuran-Degrading Sphingomonads Reveals the Carbofuran Catabolism Mechanism in Sphingobium sp. Strain CFD-1.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0102422}, pmid = {36314801}, issn = {1098-5336}, mesh = {*Carbofuran/metabolism ; *Insecticides/metabolism ; Biodegradation, Environmental ; *Sphingomonadaceae/metabolism ; Genomics ; Phenols/metabolism ; }, abstract = {The worldwide use of the carbamate insecticide carbofuran has caused considerable concern about its environmental fate. Degradation of carbofuran by Sphingobium sp. strain CFD-1 is initiated via the hydrolysis of its ester bond by carbamate hydrolase CehA to form carbofuran phenol. In this study, another carbofuran-degrading strain, Sphingobium sp. CFD-2, was isolated. Subsequently, a cfd gene cluster responsible for the catabolism of carbofuran phenol was predicted by comparing the genomes of strains CFD-1, CFD-2, and Novosphingobium sp. strain KN65.2. The key genes verified to be involved in the catabolism of carbofuran phenol within the cfd cluster include the hydroxylase gene cfdC, epoxide hydrolase gene cfdF, and ring cleavage dioxygenase gene cfdE and are responsible for the successive conversion of carbofuran phenol, resulting in complete ring cleavage. These carbofuran-catabolic genes (cehA and the cfd cluster) are distributed on two plasmids in strain CFD-1 and are highly conserved among the carbofuran-degrading sphingomonad strains. The mobile genetic element IS6100 flanks cehA and the cfd gene cluster, indicating the importance of horizontal gene transfer in the formation of carbofuran degradation gene clusters. The elucidation of the molecular mechanism of carbofuran catabolism provides insights into the evolutionary scenario of the conserved carbofuran catabolic pathway. IMPORTANCE Owing to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. In this study, the cfd gene cluster, responsible for the catabolism of carbofuran phenol, was predicted by comparing sphingomonad genomes. The function of key enzymatic genes in this gene cluster was identified. Furthermore, the carbamate hydrolase gene cehA and the cfd gene cluster are highly conserved in different carbofuran-degrading strains. Additionally, the horizontal gene transfer elements flanking the cfd gene cluster were investigated. These findings help elucidate the molecular mechanism of microbial carbofuran degradation and enhance our understanding of the evolutionary mechanism of the carbofuran catabolic pathway.}, }
@article {pmid36313567, year = {2022}, author = {Cellier, MFM}, title = {Nramp: Deprive and conquer?.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {988866}, pmid = {36313567}, issn = {2296-634X}, abstract = {Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H[+])-dependent manganese (Mn[2+]) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)'s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries 'eukaryotic signature' marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H[+]-dependent Mn[2+] acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn[2+]-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn[2+] sequestering defense perhaps favoring intracellular growth-competent bacteria.}, }
@article {pmid36312970, year = {2022}, author = {Wang, X and Wang, T and Guo, M and Zhang, C and Bo, Z and Wu, Y and Chao, G}, title = {The large plasmid carried class 1 integrons mediated multidrug resistance of foodborne Salmonella Indiana.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {991326}, pmid = {36312970}, issn = {1664-302X}, abstract = {Salmonella enterica serovar Indiana (S. Indiana) has aroused widespread concern as an important zoonotic pathogen. The molecular mechanism of multidrug resistance (MDR) in S. Indiana is not known and should be assessed. We aim to investigate the molecular mechanism of MDR and the importance of large plasmids carried class 1 integrons in the MDR of foodborne S. Indiana. Class 1 integrons in 48 S. Indiana isolates and 200 isolates of 7 other Salmonella serotypes were detected by polymerase chain reaction (PCR). To analyze the antimicrobial resistance genes (ARGs) of two S. Indiana isolates, designated S. Indiana 15 and S. Indiana 222, next-generation sequencing (NGS) was performed, and the resulting sequences were compared with the complete nucleotide sequences of S. Indiana D90 and S. Indiana C629. Comparative functional analysis was conducted between the intI1 (1,014 bp) of S. Indiana 222 and the intI1 (699 bp) of S. Indiana 15. Plasmid conjugation transfer analysis was performed to analyze the horizontal gene transfer of the integrons-related resistance genes with integron-positive and integron-negative Salmonella isolates. 64.58% of S. Indiana isolates carried class 1 integrons, which was significantly higher than that of other Salmonella serotypes (p < 0.001). The NGS results showed that the S. Indiana 15 and S. Indiana 222 isolates carried a large plasmid with a class 1 integron and multiple ARGs, similar to S. Indiana D90 and S. Indiana C629. Two integrases found in S. Indiana isolates belong to class 1 integrases and could integrate resistance genes into specific integration sites of the integrons. The conjugation frequency of intI1 (1,014 bp) was 6.08 × 10[-5], which was significantly higher than that of intI1 (699 bp) (p < 0.01). The large plasmids carrying a class 1 integron and the number of ARGs were strongly correlated (p < 0.001). The conjugation frequency of integron-positive S. Indiana recipient isolates was significantly higher than that of integron-negative recipient isolates (p < 0.05). S. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones. Graphical abstractS. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones.}, }
@article {pmid36309447, year = {2023}, author = {Alonso García, E and Benomar, N and Lavilla Lerma, L and de la Fuente Ordoñez, JJ and Knapp, CW and Abriouel, H}, title = {Changes in resistome profile of potential probiotic Lactiplantibacillus pentosus in response to edible oil adaptation.}, journal = {Food microbiology}, volume = {109}, number = {}, pages = {104148}, doi = {10.1016/j.fm.2022.104148}, pmid = {36309447}, issn = {1095-9998}, mesh = {Food Microbiology ; Fermentation ; *Lactobacillus pentosus/metabolism ; *Probiotics/metabolism ; *Olea ; Anti-Bacterial Agents/pharmacology/metabolism ; Oils ; }, abstract = {Despite increasing interest to investigate horizontal gene transfer as a leading cause of antibiotic resistance spread, the resistome is not only influenced by the influx and efflux of genes in different environments. Rather, the expression of existing genes under different stress conditions requires special attention. This study determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils influence their phenotypic and genotypic responses to antibiotics. This has significant diet, food matrix, gut health, and food safety concerns. Pre-adapting L. pentosus strains to oils significantly changed their susceptibility profile to antibiotics. However, results generally differed among the three strains; although changes in the Minimum Inhibitory Concentration (MIC) of antibiotics occurred, it depended on the L. pentosus strain and the oil used for adaptation. The pre-adaptation of L. pentosus strains with olive, sunflower, argan and linseed oils induced gene expressions (e.g., rpsL, recA and uvrB) in several stress responses. Thus, to analyze this fact in-depth, transcriptional changes were reported in the selected potential probiotic L. pentosus CF2-10 adapted with olive or sunflower, rerouting its metabolic pathways to export toxic molecules through efflux pumps and ABC transporters. Pre-adaptation of some lactobacilli with olive or sunflower oils may represent a novel approach for manufacturing probiotic products with improved stability, functionality and robustness.}, }
@article {pmid36308932, year = {2023}, author = {Ye, C and Zhang, K and Wu, X and Wan, K and Cai, WF and Feng, M and Yu, X}, title = {Uncovering novel disinfection mechanisms of solar light/periodate system: The dominance of singlet oxygen and metabolomic insights.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130177}, doi = {10.1016/j.jhazmat.2022.130177}, pmid = {36308932}, issn = {1873-3336}, mesh = {Humans ; Disinfection ; Singlet Oxygen ; Escherichia coli ; Pandemics ; *COVID-19 ; *Water Purification ; Water/pharmacology ; }, abstract = {Disinfection plays an essential role in waterborne pathogen control and disease prevention, especially during the COVID-19 pandemic. Catalyst-free solar light/periodate (PI) system has recently presented great potential in water disinfection, whereas the in-depth chemical and microbiological mechanisms for efficient bacterial inactivation remain unclear. Our work delineated firstly the critical role of singlet oxygen, instead of reported hydroxyl radicals and superoxide radicals, in dominating bacterial inactivation by the PI/simulated sunlight (SSL) system. Multi-evidence demonstrated the prominent disinfection performance of this system for Staphylococcus aureus in terms of culturability (> 6 logs CFU), cellular integrity, and metabolic activity. Particularly, the excellent intracellular DNA removal (> 95%) indicated that PI/SSL system may function as a selective disinfection strategy to diminish bacterial culturability without damaging the cell membrane. The PI/SSL system could also effectively inhibit bacterial regrowth for > 5 days and horizontal gene transfer between E. coli genera. Nontargeted metabolomic analysis suggested that PI/SSL system inactivated bacteria by triggering the accumulation of intracellular reactive oxygen species and the depletion of reduced glutathione. Additionally, the PI/SSL system could accomplish simultaneous micropollutant removal and bacterial inactivation, suggesting its versatility in water decontamination. Overall, this study deciphers more comprehensive antibacterial mechanisms of this environmentally friendly disinfection system, facilitating the technical development and application of the selective disinfection strategy in environmental pathogen control.}, }
@article {pmid36308328, year = {2022}, author = {Golparian, D and Jacobsson, S and Sánchez-Busó, L and Bazzo, ML and Lan, PT and Galarza, P and Ohnishi, M and Unemo, M}, title = {GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {1}, pages = {150-154}, doi = {10.1093/jac/dkac366}, pmid = {36308328}, issn = {1460-2091}, mesh = {Male ; Humans ; Anti-Bacterial Agents/pharmacology ; *Gonorrhea ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; *Anti-Infective Agents/pharmacology ; Neisseria gonorrhoeae/genetics ; Mutation ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; }, abstract = {OBJECTIVES: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global threat and novel treatment alternatives are imperative. Herein, susceptibility to the novel antimicrobial zoliflodacin, currently in a global Phase 3 randomized controlled clinical trial for gonorrhoea treatment, was investigated by screening for zoliflodacin GyrB target mutations in publicly available gonococcal genomes and, where feasible, determination of the associated zoliflodacin MIC.<br><br>METHODS: The European Nucleotide Archive was queried using the search term 'Taxon: 485'. DNA sequences from 27&#x200a;151 gonococcal isolates were analysed and gyrB, gyrA, parC and parE alleles characterized.<br><br>RESULTS: GyrB amino acid alterations were rare (97.0% of isolates had a wild-type GyrB sequence). GyrB V470L (2.7% of isolates) was the most prevalent alteration, followed by S467N (0.12%), N. meningitidis GyrB (0.092%), V470I (0.059%), Q468R/P (0.015%), A466T (0.0074%), L425I&#x200a;+&#x200a;L465I (0.0037%), L465I (0.0037%), G482S (0.0037%) and D429V (0.0037%). Only one isolate (0.0037%) carried a substitution in a resistance-associated GyrB codon (D429V), resulting in a zoliflodacin MIC of 8&#x2005;mg/L. None of the other detected gyrB, gyrA, parC or parE mutations caused a zoliflodacin MIC outside the wild-type MIC distribution.<br><br>CONCLUSIONS: The zoliflodacin target GyrB was highly conserved among 27&#x200a;151 global gonococcal isolates cultured in 1928-2021. The single zoliflodacin-resistant clinical isolate (0.0037%) was cultured from a male patient in Japan in 2000. Evidently, this strain has not clonally expanded nor has the gyrB zoliflodacin-resistance mutation disseminated through horizontal gene transfer to other strains. Phenotypic and genomic surveillance, including gyrB mutations, of zoliflodacin susceptibility are imperative.}, }
@article {pmid36307484, year = {2022}, author = {Tran, HNH and Thu, TNH and Nguyen, PH and Vo, CN and Doan, KV and Nguyen Ngoc Minh, C and Nguyen, NT and Ta, VND and Vu, KA and Hua, TD and Nguyen, TNT and Van, TT and Pham Duc, T and Duong, BL and Nguyen, PM and Hoang, VC and Pham, DT and Thwaites, GE and Hall, LJ and Slade, DJ and Baker, S and Tran, VH and Chung The, H}, title = {Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {87}, pmid = {36307484}, issn = {2055-5008}, support = {BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 215515/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 218726/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Fusobacterium/genetics ; Genomics ; *Microbiota ; *Colorectal Neoplasms/microbiology ; Asian People ; }, abstract = {Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.}, }
@article {pmid36306437, year = {2023}, author = {Kronmiller, BA and Feau, N and Shen, D and Tabima, JF and Ali, SS and Armitage, AD and Arredondo, F and Bailey, BA and Bollmann, SR and Dale, A and Harrison, RJ and Hrywkiw, K and Kasuga, T and McDougal, R and Nellist, CF and Panda, P and Tripathy, S and Williams, NM and Ye, W and Wang, Y and Hamelin, RC and Grünwald, NJ}, title = {Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {36}, number = {1}, pages = {26-46}, doi = {10.1094/MPMI-06-22-0133-R}, pmid = {36306437}, issn = {0894-0282}, mesh = {*Phytophthora/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Genome ; Genomics ; Plants/genetics ; }, abstract = {Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid36303123, year = {2022}, author = {Vaughan, AL and Altermann, E and Glare, TR and Hurst, MRH}, title = {Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {728}, pmid = {36303123}, issn = {1471-2164}, mesh = {Animals ; *Serratia/genetics ; Virulence/genetics ; Plasmids ; *Coleoptera/genetics ; Larva ; Serratia marcescens/genetics ; }, abstract = {BACKGROUND: Isolates of Serratia entomophila and S. proteamaculans (Yersiniaceae) cause disease specific to the endemic New Zealand pasture pest, Costelytra giveni (Coleoptera: Scarabaeidae). Previous genomic profiling has shown that S. entomophila isolates appear to have conserved genomes and, where present, conserved plasmids. In the absence of C. giveni larvae, S. entomophila prevalence reduces in the soil over time, suggesting that S. entomophila has formed a host-specific relationship with C. giveni. To help define potential genetic mechanisms driving retention of the chronic disease of S. entomophila, the genome of the isolate 626 was sequenced, enabling the identification of unique chromosomal properties, and defining the gain/loss of accessory virulence factors relevant to pathogenicity to C. giveni larvae.<br><br>RESULTS: We report the complete sequence of S. entomophila isolate 626, a causal agent of amber disease in C. giveni larvae. The genome of S. entomophila 626 is 5,046,461&#xa0;bp, with 59.1% G&#x2009;+&#x2009;C content and encoding 4,695 predicted CDS. Comparative analysis with five previously sequenced Serratia species, S. proteamaculans 336X, S. marcescens Db11, S. nematodiphila DH-S01, S. grimesii BXF1, and S. ficaria NBRC 102596, revealed a core of 1,165 genes shared. Further comparisons between S. entomophila 626 and S. proteamaculans 336X revealed fewer predicted phage-like regions and genomic islands in 626, suggesting less horizontally acquired genetic material. Genomic analyses revealed the presence of a four-gene itaconate operon, sharing a similar gene order as the Yersinia pestis ripABC complex. Assessment of a constructed 626::RipC mutant revealed that the operon confer a possible metabolic advantage to S. entomophila in the initial stages of C. giveni infection.<br><br>CONCLUSIONS: Evidence is presented where, relative to S. proteamaculans 336X, S. entomophila 626 encodes fewer genomic islands and phages, alluding to limited horizontal gene transfer in S. entomophila. Bioassay assessments of a S. entomophila-mutant with a targeted mutation of the itaconate degradation region unique to this species, found the mutant to have a reduced capacity to replicate post challenge of the C. giveni larval host, implicating the itaconate operon in establishment within the host.}, }
@article {pmid36301081, year = {2022}, author = {Castro-Gutierrez, V and Fuller, E and Garcillán-Barcia, MP and Helgason, T and Hassard, F and Moir, J}, title = {Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36301081}, issn = {2057-5858}, mesh = {*Proteobacteria/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; DNA Transposable Elements/genetics ; *Sphingomonadaceae/genetics ; Escherichia coli/genetics ; }, abstract = {Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders Acinetobacter calcoaceticus E1 and Sphingobium CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In A. calcoaceticus E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For Sphingobium CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in Escherichia coli alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.}, }
@article {pmid36298845, year = {2022}, author = {Harrison, RL and Rowley, DL}, title = {The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298845}, issn = {1999-4915}, mesh = {Animals ; *Nucleopolyhedroviruses ; Phylogeny ; Genome, Viral ; GTP Phosphohydrolases/genetics ; Open Reading Frames ; *Moths ; Nucleotides ; }, abstract = {We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.}, }
@article {pmid36298721, year = {2022}, author = {Lal, A and Kil, EJ and Vo, TTB and Wira Sanjaya, IGNP and Qureshi, MA and Nattanong, B and Ali, M and Shuja, MN and Lee, S}, title = {Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298721}, issn = {1999-4915}, mesh = {*Geminiviridae/genetics ; DNA, Viral/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Pakistan ; Plant Diseases ; *Begomovirus ; Sequence Analysis, DNA ; Genome, Viral ; }, abstract = {Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name 'Chenopodium leaf distortion virus' (CLDV).}, }
@article {pmid36296271, year = {2022}, author = {Navarro, A and Rodea, GE and Castelán-Sánchez, HG and Saucedo-Pastrana, HA and Licona-Moreno, D and Eslava-Campos, C and Tirado-Gómez, LL and Vilchis-Reyes, A and García de la Torre, G and Cruz-Licea, V}, title = {Importance of Microbiome of Fecal Samples Obtained from Adolescents with Different Weight Conditions on Resistance Gene Transfer.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296271}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is a relevant public health problem worldwide, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. The microbiome of fecal samples from Mexican adolescents were analyzed and correlated with eating habits, and the presence of AMR genes on bacteria in the microbiome was evaluated. Fecal samples from adolescents were collected and processed to extract genomic DNA. An Illumina HiSeq 1500 system was used to determine resistance genes and the microbiome of adolescents through the amplification of gene resistance and the V3-V4 regions of RNA, respectively. Analysis of the microbiome from fecal samples taken from 18 obese, overweight, and normal-weight adolescents revealed that the Firmicutes was the most frequent phylum, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The following species were detected as the most frequent in the samples: F. prausnitzii, P. cori, B. adolescentis, E. coli and A. muciniphila. The presence of Bacteroides, Prevotella and Ruminococcus was used to establish the enterotype; enterotype 1 was more common in women and enterotype 2 was more common in men. Twenty-nine AMR genes were found for β-lactamases, fluoroquinolones, aminoglycosides, macrolide, lincosamides, streptogramin (MLS), tetracyclines and sulfonamides. The presence of microorganisms in fecal samples that harbor AMR genes that work against antimicrobials frequently used for the treatment of microbial infections such as b-lactams, macrolides, aminoglycosides, MLS, and tetracyclines is of great concern, as these organisms may be an important reservoir for horizontal AMR gene transfer.}, }
@article {pmid36292780, year = {2022}, author = {Li, M and Chen, Q and Wu, C and Li, Y and Wang, S and Chen, X and Qiu, B and Li, Y and Mao, D and Lin, H and Yu, D and Cao, Y and Huang, Z and Cui, C and Zhong, Z}, title = {A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292780}, issn = {2073-4425}, mesh = {*Azorhizobium caulinodans/genetics ; Gene Transfer, Horizontal ; *Sesbania/microbiology ; Integrases/metabolism ; Flavonoids/metabolism ; Soil ; }, abstract = {Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICE[Ac]) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICE[Ac], but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICE[Ac] and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host's flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICE[Ac] by 18.5%. We propose the feasibility of constructing a minimal ICE[Ac] element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.}, }
@article {pmid36291676, year = {2022}, author = {Mocchetti, E and Morette, L and Mulliert, G and Mathiot, S and Guillot, B and Dehez, F and Chauvat, F and Cassier-Chauvat, C and Brochier-Armanet, C and Didierjean, C and Hecker, A}, title = {Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291676}, issn = {2218-273X}, mesh = {*Glutathione Transferase/metabolism ; *Synechocystis/genetics/metabolism ; Pyruvaldehyde ; Glutathione/metabolism ; Protein Structure, Secondary ; }, abstract = {Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site ([10]SRAS[13] in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.}, }
@article {pmid36289972, year = {2022}, author = {Cherak, Z and Loucif, L and Bendjama, E and Moussi, A and Benbouza, A and Grainat, N and Rolain, JM}, title = {Dissemination of Carbapenemases and MCR-1 Producing Gram-Negative Bacteria in Aquatic Environments in Batna, Algeria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289972}, issn = {2079-6382}, abstract = {Antibiotic-resistant-bacteria are being considered as emerging environmental contaminants where the importance of the surrounding environment in their emergence and dissemination has been emphasized. The aim of this study was to screen for the presence and diversity of carbapenem- and colistin-resistant Gram-negative bacteria (GNBs) in different aquatic environments. Water samples were collected in Batna, Algeria. Carbapenem- and colistin-resistant GNBs were selectively isolated and then identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. After phenotypic antibiotic susceptibility testing, the molecular mechanisms of β-lactams and colistin-resistance were investigated by PCR and sequencing. The clonality of mcr-1 positive Escherichia coli was determined by multi-locus sequence typing. We noticed a high level of resistance in both tap water and wastewater. The most commonly found carbapenem-resistance mechanism was the OXA-48 enzyme, but other carbapenemases were also detected. In addition, the mcr-1 gene was detected in 18 E. coli of different sequence types. Our findings highlight the role of aquatic environments in the dissemination of resistant-bacteria, especially considering that water is a connecting medium between different ecological systems and can easily transmit resistant-bacteria and promote horizontal gene transfer. Thus, the development of effective treatment strategies for eliminating antibiotic-resistance is seriously needed.}, }
@article {pmid36289941, year = {2022}, author = {Sekizuka, T and Tanaka, R and Hashino, M and Yatsu, K and Kuroda, M}, title = {Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289941}, issn = {2079-6382}, abstract = {To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.}, }
@article {pmid36287061, year = {2022}, author = {Li, Y and Shi, X and Zuo, Y and Li, T and Liu, L and Shen, Z and Shen, J and Zhang, R and Wang, S}, title = {Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0229722}, pmid = {36287061}, issn = {2165-0497}, mesh = {Humans ; *Metagenome ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Sewage ; Metagenomics/methods ; }, abstract = {Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 10[4]-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.}, }
@article {pmid36286524, year = {2022}, author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL}, title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0121922}, pmid = {36286524}, issn = {1098-5336}, mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.}, }
@article {pmid36285389, year = {2023}, author = {Hulin, MT and Rabiey, M and Zeng, Z and Vadillo Dieguez, A and Bellamy, S and Swift, P and Mansfield, JW and Jackson, RW and Harrison, RJ}, title = {Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface.}, journal = {The New phytologist}, volume = {237}, number = {3}, pages = {959-973}, pmid = {36285389}, issn = {1469-8137}, mesh = {Pseudomonas syringae/genetics ; Gene Transfer, Horizontal ; *Bacteriophages/genetics ; Genomics ; Genome, Bacterial ; *Prunus avium ; Plant Diseases/genetics ; }, abstract = {Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.}, }
@article {pmid36282569, year = {2022}, author = {Cerqueira de Araujo, A and Josse, T and Sibut, V and Urabe, M and Asadullah, A and Barbe, V and Nakai, M and Huguet, E and Periquet, G and Drezen, JM}, title = {Chelonus inanitus bracovirus encodes lineage-specific proteins and truncated immune IκB-like factors.}, journal = {The Journal of general virology}, volume = {103}, number = {10}, pages = {}, doi = {10.1099/jgv.0.001791}, pmid = {36282569}, issn = {1465-2099}, mesh = {Humans ; Animals ; *Polydnaviridae/genetics ; Phylogeny ; *Wasps/genetics ; Viral Proteins/genetics ; Biological Evolution ; }, abstract = {Bracoviruses and ichnoviruses are endogenous viruses of parasitic wasps that produce particles containing virulence genes expressed in host tissues and necessary for parasitism success. In the case of bracoviruses the particles are produced by conserved genes of nudiviral origin integrated permanently in the wasp genome, whereas the virulence genes can strikingly differ depending on the wasp lineage. To date most data obtained on bracoviruses concerned species from the braconid subfamily of Microgastrinae. To gain a broader view on the diversity of virulence genes we sequenced the genome packaged in the particles of Chelonus inanitus bracovirus (CiBV) produced by a wasp belonging to a different subfamily: the Cheloninae. These are egg-larval parasitoids, which means that they oviposit into the host egg and the wasp larvae then develop within the larval stages of the host. We found that most of CiBV virulence genes belong to families that are specific to Cheloninae. As other bracoviruses and ichnoviruses however, CiBV encode v-ank genes encoding truncated versions of the immune cactus/IκB factor, which suggests these proteins might play a key role in host-parasite interactions involving domesticated endogenous viruses. We found that the structures of CiBV V-ANKs are different from those previously reported. Phylogenetic analysis supports the hypothesis that they may originate from a cactus/IκB immune gene from the wasp genome acquired by the bracovirus. However, their evolutionary history is different from that shared by other V-ANKs, whose common origin probably reflects horizontal gene transfer events of virus sequences between braconid and ichneumonid wasps.}, }
@article {pmid36282171, year = {2022}, author = {Koonin, EV and Krupovic, M}, title = {A life LINE for large viruses.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36282171}, issn = {2050-084X}, mesh = {*Retroelements ; *Poxviridae/genetics ; Vaccinia virus/genetics ; Virus Replication ; }, abstract = {As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.}, }
@article {pmid36280316, year = {2022}, author = {Paul, D and Das, B}, title = {Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens.}, journal = {Progress in molecular biology and translational science}, volume = {192}, number = {1}, pages = {1-31}, doi = {10.1016/bs.pmbts.2022.07.009}, pmid = {36280316}, issn = {1878-0814}, mesh = {Humans ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Ecosystem ; Bacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {The human gastrointestinal tract is home to a complex and dynamic community of microorganisms known as gut microbiota, which provide the host with important metabolic, signaling, and immunomodulatory functions. Both the commensal and pathogenic members of the gut microbiome serve as reservoirs of antimicrobial-resistance genes (ARG), which can cause potential health threats to the host and can transfer the ARGs to the susceptible microbes and into the environment. Antimicrobial resistance is becoming a major burden on human health and is widely recognized as a global challenge. The diversity and abundance of ARGs in the gut microbiome are variable and depend on the exposure to healthcare-associated antibiotics, usage of antibiotics in veterinary and agriculture, and the migration of the population. The transfer frequency of the ARGs through horizontal gene transfer (HGT) with the help of mobile genetic elements (MGEs) like plasmids, transposons, or phages is much higher among bacteria living in the GI tract compared to other microbial ecosystems. HGT in gut bacteria is facilitated through multiple gene transfer mechanisms, including transformation, conjugation, transduction, and vesicle fusion. It is the need of the hour to implement strict policies to limit indiscriminate antibiotic usage when needed. Developing rapid diagnostic tests for resistance determination and alternatives to antibiotics like vaccination, probiotics, and bacteriophage therapy should have the highest priority in the research and development sectors. Collective actions for sustainable development against resistant pathogens by promoting endogenous gut microbial growth and diversity through interdisciplinary research and findings are key to overcoming the current antimicrobial resistance crisis.}, }
@article {pmid36279613, year = {2022}, author = {Yang, J and Xiang, J and Xie, Y and Yu, K and Li, J and Wang, H and Li, P and Gin, KY and He, Y}, title = {Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants.}, journal = {Water research}, volume = {226}, number = {}, pages = {119239}, doi = {10.1016/j.watres.2022.119239}, pmid = {36279613}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; Bioreactors ; Bacteria/genetics ; }, abstract = {Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10[9] copies/mL in raw leachate to 10[3]-10[5] copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.}, }
@article {pmid36275512, year = {2022}, author = {Wang, X and Yoo, E and Lee, S and Cho, GT and Lee, GA and Yi, JY and Du, X and Han, S and Hyun, DY and Ro, N and Kim, KM}, title = {Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {984825}, pmid = {36275512}, issn = {1664-462X}, abstract = {Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative spec