@article {pmid39191191,
year = {2024},
author = {Middendorf, PS and Zomer, AL and Bergval, IL and Jacobs-Reitsma, WF and den Besten, HMW and Abee, T},
title = {Host associations of Campylobacter jejuni and Campylobacter coli isolates carrying the L-fucose or d-glucose utilization cluster.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110855},
doi = {10.1016/j.ijfoodmicro.2024.110855},
pmid = {39191191},
issn = {1879-3460},
abstract = {Campylobacter was considered asaccharolytic, but is now known to carry saccharide metabolization pathways for L-fucose and d-glucose. We hypothesized that these clusters are beneficial for Campylobacter niche adaptation and may help establish human infection. We investigated the distribution of d-glucose and L-fucose clusters among ∼9600 C. jejuni and C. coli genomes of different isolation sources in the Netherlands, the United Kingdom, the United States of America and Finland. The L-fucose utilization cluster was integrated at the same location in all C. jejuni and C. coli genomes, and was flanked by the genes rpoB, rpoC, rspL, repsG and fusA, which are associated with functions in transcription as well as translation and in acquired drug resistance. In contrast, the flanking regions of the d-glucose utilization cluster were variable among the isolates, and integration sites were located within one of the three different 16S23S ribosomal RNA areas of the C. jejuni and C. coli genomes. In addition, we investigated whether acquisition of the L-fucose utilization cluster could be due to horizontal gene transfer between the two species and found three isolates for which this was the case: one C. jejuni isolate carrying a C. coli L-fucose cluster, and two C. coli isolates which carried a C. jejuni L-fucose cluster. Furthermore, L-fucose utilization cluster alignments revealed multiple frameshift mutations, most of which were commonly found in the non-essential genes for L-fucose metabolism, namely, Cj0484 and Cj0489. These findings support our hypothesis that the L-fucose cluster was integrated multiple times across the C. coli/C. jejuni phylogeny. Notably, association analysis using the C. jejuni isolates from the Netherlands showed a significant correlation between human C. jejuni isolates and C. jejuni isolates carrying the L-fucose utilization cluster. This correlation was even stronger when the Dutch isolates were combined with the isolates from the UK, the USA and Finland. No such correlations were observed for C. coli or for the d-glucose cluster for both species. This research provides insight into the spread and host associations of the L-fucose and d-glucose utilization clusters in C. jejuni and C. coli, and the potential benefits in human infection and/or proliferation in humans, conceivably after transmission from any reservoir.},
}

@article {pmid39190937,
year = {2024},
author = {Wen, AX and Herman, C},
title = {Horizontal gene transfer and beyond: the delivery of biological matter by bacterial membrane vesicles to host and bacterial cells.},
journal = {Current opinion in microbiology},
volume = {81},
number = {},
pages = {102525},
doi = {10.1016/j.mib.2024.102525},
pmid = {39190937},
issn = {1879-0364},
abstract = {Membrane vesicles (MVs) are produced in all domains of life. In eukaryotes, extracellular vesicles have been shown to mediate the horizontal transfer of biological material between cells [1]. Therefore, bacterial MVs are also thought to mediate horizontal material transfer to host cells and other bacteria, especially in the context of cell stress. In this review, we discuss the mechanisms of bacterial MV production, evidence that their contents can be trafficked to host cells and other bacteria, and the biological relevance of horizontal material transfer by bacterial MVs.},
}

@article {pmid39190025,
year = {2024},
author = {Alav, I and Pordelkhaki, P and Rodriguez-Navarro, J and Neo, O and Kessler, C and Awodipe, RJ and Cliffe, P and Pulavan, N and Marton, HL and Gibbons, S and Buckner, MMC},
title = {Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {8},
pages = {},
doi = {10.1099/mic.0.001496},
pmid = {39190025},
issn = {1465-2080},
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; *Klebsiella pneumoniae/drug effects/genetics ; *Escherichia coli/genetics/drug effects ; *beta-Lactamases/genetics/metabolism ; *Biological Products/pharmacology ; Drug Resistance, Bacterial/genetics ; Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/drug effects/genetics ; Microbial Sensitivity Tests ; Food Microbiology ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum β-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum β-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.},
}

*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
*Klebsiella pneumoniae/drug effects/genetics
*Escherichia coli/genetics/drug effects
*beta-Lactamases/genetics/metabolism
*Biological Products/pharmacology
Drug Resistance, Bacterial/genetics
Conjugation, Genetic
Bacterial Proteins/genetics/metabolism
Enterobacteriaceae/drug effects/genetics
Microbial Sensitivity Tests
Food Microbiology
Gene Transfer, Horizontal

@article {pmid39189989,
year = {2024},
author = {Brewer, TE and Wagner, A},
title = {Horizontal gene transfer of a key translation factor and its role in polyproline proteome evolution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae180},
pmid = {39189989},
issn = {1537-1719},
abstract = {Prolines cause ribosomes to stall during translation due to their rigid structure. This phenomenon occurs in all domains of life and is exacerbated at polyproline motifs. Such stalling can be eased by the elongation factor P (EF-P) in bacteria. We discovered a potential connection between the loss of ancestral EF-P, the appearance of horizontally transferred EF-P variants, and genomic signs of EF-P dysfunction. Horizontal transfer of the efp gene has occurred several times among bacteria and is associated with the loss of highly conserved polyproline motifs. In this study, we pinpoint cases of horizontal EF-P transfer among a diverse set of bacteria and examine genomic features associated with these events in the phyla Thermotogota and Planctomycetes. In these phyla, horizontal EF-P transfer is also associated with the loss of entire polyproline motif containing proteins, whose expression is likely dependent on EF-P. In particular, three proteases (Lon, ClpC, and FtsH) and three tRNA synthetases (ValS, IleS1, IleS2) appear highly sensitive to EF-P transfer. The conserved polyproline motifs within these proteins all reside within close proximity to ATP-binding-regions, some of which are crucial for their function. Our work shows that an ancient EF-P dysfunction has left genomic traces that persist to this day, although it remains unclear whether this dysfunction was strictly due to loss of ancestral EF-P or was related to the appearance of an exogenous variant. The latter possibility would imply that the process of 'domesticating' a horizontally transferred efp gene can perturb the overall function of EF-P.},
}

@article {pmid39189956,
year = {2024},
author = {Zheng, X and Huang, L},
title = {Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099924},
doi = {10.1128/msystems.00999-24},
pmid = {39189956},
issn = {2379-5077},
abstract = {UNLABELLED: Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.

IMPORTANCE: The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.},
}

@article {pmid39189770,
year = {2024},
author = {Kopejtka, K and Tomasch, J and Shivaramu, S and Saini, MK and Kaftan, D and Koblížek, M},
title = {Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070624},
doi = {10.1128/msystems.00706-24},
pmid = {39189770},
issn = {2379-5077},
abstract = {UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64[T], received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m[-2] s[-1], while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m[-2] s[-1]) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.},
}

@article {pmid39189747,
year = {2024},
author = {Duchin Rapp, Y and Lipsman, V and Yuda, L and Kublanov, IV and Matsliyah, D and Segev, E},
title = {Algal exudates promote conjugation in marine Roseobacters.},
journal = {mBio},
volume = {},
number = {},
pages = {e0106224},
doi = {10.1128/mbio.01062-24},
pmid = {39189747},
issn = {2150-7511},
abstract = {UNLABELLED: Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.

IMPORTANCE: This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.},
}

@article {pmid39187833,
year = {2024},
author = {Yutin, N and Tolstoy, I and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV},
title = {DNA polymerase swapping in Caudoviricetes bacteriophages.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {200},
pmid = {39187833},
issn = {1743-422X},
mesh = {*DNA-Directed DNA Polymerase/genetics ; *Phylogeny ; *Viral Proteins/genetics/metabolism ; Evolution, Molecular ; Genome, Viral ; Caudovirales/genetics/classification ; DNA, Viral/genetics ; Bacteriophages/genetics/enzymology/classification ; DNA Replication ; },
abstract = {BACKGROUND: Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families.

METHODS: Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2.

RESULTS: We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.

CONCLUSIONS: Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.},
}

*DNA-Directed DNA Polymerase/genetics
*Phylogeny
*Viral Proteins/genetics/metabolism
Evolution, Molecular
Genome, Viral
Caudovirales/genetics/classification
DNA, Viral/genetics
Bacteriophages/genetics/enzymology/classification
DNA Replication

@article {pmid39186748,
year = {2024},
author = {Pradel, N and Bartoli, M and Koenen, M and Bale, N and Neumann-Schaal, M and Spröer, C and Bunk, B and Rohde, M and Pester, M and Spring, S},
title = {Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308405},
pmid = {39186748},
issn = {1932-6203},
mesh = {*Methanospirillum/genetics/metabolism ; *Phylogeny ; *Genome, Archaeal ; Sulfides/metabolism ; Iron/metabolism ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; },
abstract = {The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.},
}

*Methanospirillum/genetics/metabolism
*Phylogeny
*Genome, Archaeal
Sulfides/metabolism
Iron/metabolism
RNA, Ribosomal, 16S/genetics
Methane/metabolism

@article {pmid39184916,
year = {2024},
author = {Han, H and He, T and Wu, Y and He, T and Zhou, W},
title = {Multidimensional analysis of tumor stem cells: from biological properties, metabolic adaptations to immune escape mechanisms.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1441081},
pmid = {39184916},
issn = {2296-634X},
abstract = {As a key factor in tumorigenesis, progression, recurrence and metastasis, the biological properties, metabolic adaptations and immune escape mechanisms of CSCs are the focus of current oncological research. CSCs possess self-renewal, multidirectional differentiation and tumorigenicity, and their mechanisms of action can be elucidated by the clonal evolution, hierarchical model and the dynamic CSCs model, of which the dynamic model is widely recognized due to its better explanation of the function and origin of CSCs. The origin hypothesis of CSCs involves cell-cell fusion, horizontal gene transfer, genomic instability and microenvironmental regulation, which together shape the diversity of CSCs. In terms of classification, CSCs include primary CSCs (pri-CSCs), precancerous stem cells (pre-CSCs), migratory CSCs (mig-CSCs), and chemo-radiotherapy-resistant CSCs (cr-CSCs and rr-CSCs), with each type playing a specific role in tumor progression. Surface markers of CSCs, such as CD24, CD34, CD44, CD90, CD133, CD166, EpCAM, and LGR5, offer the possibility of identifying, isolating, and targeting CSCs, but the instability and heterogeneity of their expression increase the difficulty of treatment. CSCs have adapted to their survival needs through metabolic reprogramming, showing the ability to flexibly switch between glycolysis and oxidative phosphorylation (OXPHOS), as well as adjustments to amino acid and lipid metabolism. The Warburg effect typifies their metabolic profiles, and altered glutamine and fatty acid metabolism further contributes to the rapid proliferation and survival of CSCs. CSCs are able to maintain their stemness by regulating the metabolic networks to maintain their stemness characteristics, enhance antioxidant defences, and adapt to therapeutic stress. Immune escape is another strategy for CSCs to maintain their survival, and CSCs can effectively evade immune surveillance through mechanisms such as up-regulating PD-L1 expression and promoting the formation of an immunosuppressive microenvironment. Together, these properties reveal the multidimensional complexity of CSCs, underscoring the importance of a deeper understanding of the biology of CSCs for the development of more effective tumor therapeutic strategies. In the future, therapies targeting CSCs will focus on precise identification of surface markers, intervention of metabolic pathways, and overcoming immune escape, with the aim of improving the relevance and efficacy of cancer treatments, and ultimately improving patient prognosis.},
}

@article {pmid39184814,
year = {2024},
author = {Chen, N and Li, Y and Liang, X and Qin, K and Zhang, Y and Wang, J and Wu, Q and Gupta, TB and Ding, Y},
title = {Bacterial extracellular vesicle: A non-negligible component in biofilm life cycle and challenges in biofilm treatments.},
journal = {Biofilm},
volume = {8},
number = {},
pages = {100216},
pmid = {39184814},
issn = {2590-2075},
abstract = {Bacterial biofilms, especially those formed by pathogens, have been increasingly impacting human health. Bacterial extracellular vesicle (bEV), a kind of spherical membranous structure released by bacteria, has not only been reported to be a component of the biofilm matrix but also plays a non-negligible role in the biofilm life cycle. Nevertheless, a comprehensive overview of the bEVs functions in biofilms remains elusive. In this review, we summarize the biogenesis and distinctive features characterizing bEVs, and consolidate the current literature on their functions and proposed mechanisms in the biofilm life cycle. Furthermore, we emphasize the formidable challenges associated with vesicle interference in biofilm treatments. The primary objective of this review is to raise awareness regarding the functions of bEVs in the biofilm life cycle and lay the groundwork for the development of novel therapeutic strategies to control or even eliminate bacterial biofilms.},
}

@article {pmid39182428,
year = {2024},
author = {Ando, S and Tanaka, R and Ito, H},
title = {Activity examination of plant Mg-dechelatase and its bacterial homolog in plants and in vitro.},
journal = {Plant physiology and biochemistry : PPB},
volume = {215},
number = {},
pages = {109073},
doi = {10.1016/j.plaphy.2024.109073},
pmid = {39182428},
issn = {1873-2690},
abstract = {Chlorophyll a serves as a photosynthetic pigment in plants. Its degradation is initiated by the extraction of the central Mg by the Mg-dechelatase enzyme, which is encoded by Stay-Green (SGR). Plant SGR is believed to be derived from bacterial SGR homolog obtained through horizontal gene transfer into photosynthetic eukaryotes. However, it is not known how the bacterial SGR homolog was modified to function in plants. To assess its adaptation mechanism in plants, a bacterial SGR homolog derived from the Anaerolineae bacterium SM23_63 was introduced into plants. It was found that the bacterial SGR homolog metabolized chlorophyll in plants. However, its chlorophyll catabolic activity was lower than that of plant SGR. Recombinant proteins of the bacterial SGR homolog exhibited higher activity than those of the plant SGR. The reduced chlorophyll catabolic activity of bacterial SGR homologs in plants may be associated with low hydrophobicity of the entrance to the catalytic site compared to that of plant SGR. This hinders the enzyme access to chlorophyll, which is localized in hydrophobic environments. This study offers insights into the molecular changes underlying the optimization of enzyme function.},
}

@article {pmid39107250,
year = {2024},
author = {Barragan, AC and Latorre, SM and Malmgren, A and Harant, A and Win, J and Sugihara, Y and Burbano, HA and Kamoun, S and Langner, T},
title = {Multiple Horizontal Mini-chromosome Transfers Drive Genome Evolution of Clonal Blast Fungus Lineages.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39107250},
issn = {1537-1719},
support = {//Gatsby Charitable Foundation/ ; UKRI-BBSRC//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; /ERC_/European Research Council/International ; 743165//BLASTOFF/ ; 101077853//PANDEMIC/ ; RSWF\R1\191011//Royal Society/ ; },
mesh = {*Gene Transfer, Horizontal ; *Evolution, Molecular ; Chromosomes, Fungal/genetics ; Ascomycota/genetics ; Plant Diseases/microbiology ; Genome, Fungal ; },
abstract = {Crop disease pandemics are often driven by asexually reproducing clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb accessory mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.},
}

*Gene Transfer, Horizontal
*Evolution, Molecular
Chromosomes, Fungal/genetics
Ascomycota/genetics
Plant Diseases/microbiology
Genome, Fungal

@article {pmid39089095,
year = {2024},
author = {Zhuang, M and Yan, W and Xiong, Y and Wu, Z and Cao, Y and Sanganyado, E and Siame, BA and Chen, L and Kashi, Y and Leung, KY},
title = {Horizontal plasmid transfer promotes antibiotic resistance in selected bacteria in Chinese frog farms.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108905},
doi = {10.1016/j.envint.2024.108905},
pmid = {39089095},
issn = {1873-6750},
mesh = {Animals ; *Plasmids/genetics ; China ; *Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; Rana catesbeiana/microbiology/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; },
abstract = {The emergence and dissemination of antibiotic resistance genes (ARGs) in the ecosystem are global public health concerns. One Health emphasizes the interconnectivity between different habitats and seeks to optimize animal, human, and environmental health. However, information on the dissemination of antibiotic resistance genes (ARGs) within complex microbiomes in natural habitats is scarce. We investigated the prevalence of antibiotic resistant bacteria (ARB) and the spread of ARGs in intensive bullfrog (Rana catesbeiana) farms in the Shantou area of China. Antibiotic susceptibilities of 361 strains, combined with microbiome analyses, revealed Escherichia coli, Edwardsiella tarda, Citrobacter and Klebsiella sp. as prevalent multidrug resistant bacteria on these farms. Whole genome sequencing of 95 ARB identified 250 large plasmids that harbored a wide range of ARGs. Plasmid sequences and sediment metagenomes revealed an abundance of tetA, sul1, and aph(3″)-Ib ARGs. Notably, antibiotic resistance (against 15 antibiotics) highly correlated with plasmid-borne rather than chromosome-borne ARGs. Based on sequence similarities, most plasmids (62%) fell into 32 distinct groups, indicating a potential for horizontal plasmid transfer (HPT) within the frog farm microbiome. HPT was confirmed in inter- and intra-species conjugation experiments. Furthermore, identical mobile ARGs, flanked by mobile genetic elements (MGEs), were found in different locations on the same plasmid, or on different plasmids residing in the same or different hosts. Our results suggest a synergy between MGEs and HPT to facilitate ARGs dissemination in frog farms. Mining public databases retrieved similar plasmids from different bacterial species found in other environmental niches globally. Our findings underscore the importance of HPT in mediating the spread of ARGs in frog farms and other microbiomes of the ecosystem.},
}

Animals
*Plasmids/genetics
China
*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Farms
Drug Resistance, Bacterial/genetics
Rana catesbeiana/microbiology/genetics
Drug Resistance, Microbial/genetics
Microbiota/genetics

@article {pmid39180708,
year = {2024},
author = {Witt, ASA and Carvalho, JVRP and Serafim, MSM and Arias, NEC and Rodrigues, RAL and Abrahão, JS},
title = {The GC% landscape of the Nucleocytoviricota.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39180708},
issn = {1678-4405},
support = {88882.348380/2010-1//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 405249/2022-5//Ministry of Science and Technology/ ; 406441/2022-7//Ministry of Science and Technology/ ; },
abstract = {Genomic studies on sequence composition employ various approaches, such as calculating the proportion of guanine and cytosine within a given sequence (GC% content), which can shed light on various aspects of the organism's biology. In this context, GC% can provide insights into virus-host relationships and evolution. Here, we present a comprehensive gene-by-gene analysis of 61 representatives belonging to the phylum Nucleocytoviricota, which comprises viruses with the largest genomes known in the virosphere. Parameters were evaluated not only based on the average GC% of a given viral species compared to the entire phylum but also considering gene position and phylogenetic history. Our results reveal that while some families exhibit similar GC% among their representatives (e.g., Marseilleviridae), others such as Poxviridae, Phycodnaviridae, and Mimiviridae have members with discrepant GC% values, likely reflecting adaptation to specific biological cycles and hosts. Interestingly, certain genes located at terminal regions or within specific genomic clusters show GC% values distinct from the average, suggesting recent acquisition or unique evolutionary pressures. Horizontal gene transfer and the presence of potential paralogs were also assessed in genes with the most discrepant GC% values, indicating multiple evolutionary histories. Taken together, to the best of our knowledge, this study represents the first global and gene-by-gene analysis of GC% distribution and profiles within genomes of Nucleocytoviricota members, highlighting their diversity and identifying potential new targets for future studies.},
}

@article {pmid39179660,
year = {2024},
author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H},
title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1038},
pmid = {39179660},
issn = {2399-3642},
support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation & purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; },
abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.},
}

*Klebsiella pneumoniae/genetics/isolation & purification
*Metagenomics/methods
Humans
*Disease Outbreaks
*Klebsiella Infections/microbiology/epidemiology/diagnosis
*Phylogeny
China/epidemiology
Nanopore Sequencing/methods
Databases, Genetic
Genome, Bacterial

@article {pmid39176446,
year = {2024},
author = {Ahmed, M and Kayal, E and Lavrov, DV},
title = {Mitochondrial DNA of the demosponge Acanthella acuta: Linear Architecture and Other Unique Features.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae168},
pmid = {39176446},
issn = {1759-6653},
abstract = {While Acanthella acuta (Schmidt 1862), a common demosponge found in the Mediterranean Sea and Atlantic Ocean, is-morphologically-little distinguishable from other sponges, its mitochondrial DNA (mtDNA) is unique within the class. In contrast to all other studied demosponges, mtDNA of A. acuta is inferred to be linear and displays several unusual features: inverted terminal repeats, group II introns in three mt-genes, and two unique ORFs. One of the ORFs (ORF1535) combines a DNA-polymerase domain with a DNA-directed RNA-polymerase domain, while the second bears no discernible similarity to any reported sequences. The group II intron within the cox2 gene is the first such intron reported in an animal. Our phylogenetic analyses indicate that the cox1 intron is related to similar introns found in other demosponges, while the cox2 intron is likely not of animal origin. The two domains found within ORF1535 do not share a common origin and, along with the cox2 intron, were likely acquired by horizontal transfer. The findings of this paper open new avenues of exploration in the understanding of mtDNA linearization within Metazoa.},
}

@article {pmid39174812,
year = {2024},
author = {Döcker, J and Linz, S and Wicke, K},
title = {Bounding the Softwired Parsimony Score of a Phylogenetic Network.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {10},
pages = {121},
pmid = {39174812},
issn = {1522-9602},
support = {XXXX//Marsden Fund/ ; },
mesh = {*Phylogeny ; *Models, Genetic ; *Mathematical Concepts ; Algorithms ; Evolution, Molecular ; Sequence Alignment/statistics & numerical data ; },
abstract = {In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.},
}

*Phylogeny
*Models, Genetic
*Mathematical Concepts
Algorithms
Evolution, Molecular
Sequence Alignment/statistics & numerical data

@article {pmid39173632,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.028},
pmid = {39173632},
issn = {1097-4172},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgos) and the DNA defense module DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}

@article {pmid39173362,
year = {2024},
author = {Zhang, Y and Zuo, S and Zheng, Q and Yu, G and Wang, Y},
title = {Removal of antibiotic resistant bacteria and antibiotic resistance genes by an electrochemically driven UV/chlorine process for decentralized water treatment.},
journal = {Water research},
volume = {265},
number = {},
pages = {122298},
doi = {10.1016/j.watres.2024.122298},
pmid = {39173362},
issn = {1879-2448},
abstract = {The UV/chlorine (UV/Cl2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl2 process (E-UV/Cl2) where Cl2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl[-]) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tetA, sul1, sul2, and ermB) could be effectively degraded (e.g., log(C0/C) > 4 for i-ARGs) within 5 min of the E-UV/Cl2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl2[-]•, and ClO• during the E-UV/Cl2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl2 process, and the energy consumption (EEO) of ARG removal was ∼0.20‒0.27 kWh/m[3]-log, which is generally comparable to that of the UV/Cl2 process (0.18-0.23 kWh/m[3]-log). These results demonstrate that the E-UV/Cl2 process can provide a feasible and attractive alternative to the UV/Cl2 process for ARB and ARG removal in decentralized water treatment system.},
}

@article {pmid39172952,
year = {2024},
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 = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002723},
doi = {10.1371/journal.pbio.3002723},
pmid = {39172952},
issn = {1545-7885},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Fibroblasts/metabolism ; *Brain/metabolism ; Male ; Female ; Cell Nucleus/metabolism ; Middle Aged ; Adult ; Aged ; Longevity/genetics ; Aging/physiology/genetics ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic 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 (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) 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 repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by 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 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 postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.},
}

Humans
*DNA, Mitochondrial/genetics
*Fibroblasts/metabolism
*Brain/metabolism
Male
Female
Cell Nucleus/metabolism
Middle Aged
Adult
Aged
Longevity/genetics
Aging/physiology/genetics

@article {pmid39172793,
year = {2024},
author = {Chen, X and Wang, M and Luo, L and Liu, X and An, L and Nie, Y and Wu, XL},
title = {The evolution of autonomy from two cooperative specialists in fluctuating environments.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {35},
pages = {e2317182121},
doi = {10.1073/pnas.2317182121},
pmid = {39172793},
issn = {1091-6490},
support = {2018YFA0902100//MOST | National Key Research and Development Program of China (NKPs)/ ; 91951204//Data Center of Management Science, National Natural Science Foundation of China - Peking University (DCMS, NSFC-PKU)/ ; },
mesh = {*Naphthalenes/metabolism ; Gene Transfer, Horizontal ; Biological Evolution ; Symbiosis ; Microbial Consortia/genetics/physiology ; Genotype ; },
abstract = {From microbes to humans, organisms perform numerous tasks for their survival, including food acquisition, migration, and reproduction. A complex biological task can be performed by either an autonomous organism or by cooperation among several specialized organisms. However, it remains unclear how autonomy and cooperation evolutionarily switch. Specifically, it remains unclear whether and how cooperative specialists can repair deleted genes through direct genetic exchange, thereby regaining metabolic autonomy. Here, we address this question by experimentally evolving a mutualistic microbial consortium composed of two specialists that cooperatively degrade naphthalene. We observed that autonomous genotypes capable of performing the entire naphthalene degradation pathway evolved from two cooperative specialists and dominated the community. This evolutionary transition was driven by the horizontal gene transfer (HGT) between the two specialists. However, this evolution was exclusively observed in the fluctuating environment alternately supplied with naphthalene and pyruvate, where mutualism and competition between the two specialists alternated. The naphthalene-supplied environment exerted selective pressure that favors the expansion of autonomous genotypes. The pyruvate-supplied environment promoted the coexistence and cell density of the cooperative specialists, thereby increasing the likelihood of HGT. Using a mathematical model, we quantitatively demonstrate that environmental fluctuations facilitate the evolution of autonomy through HGT when the relative growth rate and carrying capacity of the cooperative specialists allow enhanced coexistence and higher cell density in the competitive environment. Together, our results demonstrate that cooperative specialists can repair deleted genes through a direct genetic exchange under specific conditions, thereby regaining metabolic autonomy.},
}

*Naphthalenes/metabolism
Gene Transfer, Horizontal
Biological Evolution
Symbiosis
Microbial Consortia/genetics/physiology
Genotype

@article {pmid39106433,
year = {2024},
author = {Tan, Y and Aravind, L and Zhang, D},
title = {Genomic Underpinnings of Cytoplasmic Incompatibility: CIF Gene-Neighborhood Diversification Through Extensive Lateral Transfers and Recombination in Wolbachia.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
doi = {10.1093/gbe/evae171},
pmid = {39106433},
issn = {1759-6653},
support = {//Saint Louis University/ ; //Intramural Research Program of the NIH/ ; /LM/NLM NIH HHS/United States ; },
mesh = {*Wolbachia/genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; Evolution, Molecular ; Phylogeny ; Genome, Bacterial ; Cytoplasm/genetics ; Animals ; Bacterial Proteins/genetics ; },
abstract = {Cytoplasmic incompatibility (CI), a non-Mendelian genetic phenomenon, involves the manipulation of host reproduction by Wolbachia, a maternally transmitted alphaproteobacterium. The underlying mechanism is centered around the CI Factor (CIF) system governed by two genes, cifA and cifB, where cifB induces embryonic lethality, and cifA counteracts it. Recent investigations have unveiled intriguing facets of this system, including diverse cifB variants, prophage association in specific strains, copy number variation, and rapid component divergence, hinting at a complex evolutionary history. We utilized comparative genomics to systematically classify CIF systems, analyze their locus structure and domain architectures, and reconstruct their diversification and evolutionary trajectories. Our new classification identifies ten distinct CIF types, featuring not just versions present in Wolbachia, but also other intracellular bacteria, and eukaryotic hosts. Significantly, our analysis of CIF loci reveals remarkable variability in gene composition and organization, encompassing an array of diverse endonucleases, variable toxin domains, deubiquitinating peptidases (DUBs), prophages, and transposons. We present compelling evidence that the components within the loci have been diversifying their sequences and domain architectures through extensive, independent lateral transfers and interlocus recombination involving gene conversion. The association with diverse transposons and prophages, coupled with selective pressures from host immunity, likely underpins the emergence of CIF loci as recombination hotspots. Our investigation also posits the origin of CifB-REase domains from mobile elements akin to CR (Crinkler-RHS-type) effectors and Tribolium Medea1 factor, which is linked to another non-Mendelian genetic phenomenon. This comprehensive genomic analysis offers novel insights into the molecular evolution and genomic foundations of Wolbachia-mediated host reproductive control.},
}

*Wolbachia/genetics
*Gene Transfer, Horizontal
*Recombination, Genetic
Evolution, Molecular
Phylogeny
Genome, Bacterial
Cytoplasm/genetics
Animals
Bacterial Proteins/genetics

@article {pmid39168346,
year = {2024},
author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175639},
doi = {10.1016/j.scitotenv.2024.175639},
pmid = {39168346},
issn = {1879-1026},
abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.},
}

@article {pmid39167960,
year = {2024},
author = {Nasu, T and Maeda, S},
title = {Escherichia coli persisters in biofilm can perform horizontal gene transfer by transformation.},
journal = {Biochemical and biophysical research communications},
volume = {738},
number = {},
pages = {150549},
doi = {10.1016/j.bbrc.2024.150549},
pmid = {39167960},
issn = {1090-2104},
abstract = {Persisters represent a subset of cells that exhibit transient tolerance to antimicrobials. These persisters can withstand sudden exposure to antimicrobials, even as the majority of normal cells perish. In this study, we have demonstrated the capacity of ampicillin-tolerant and alkali-tolerant persisters to execute horizontal gene transfer via in situ transformation within biofilms. Air-solid biofilms, comprising two Escherichia coli populations each with a distinct plasmid, were formed on agar media. They were treated with lethal doses of ampicillin or NaOH for 24 h, followed by a 1-min glass-ball roll. This process led to a high frequency of horizontal plasmid transfer (10[-7]-10[-6] per cell) from dead cells to surviving persisters within the biofilms. Plasmid transfer was DNase-sensitive and also occurred by adding purified plasmid DNA to plasmid-free biofilms, demonstrating a transformation mechanism. This marks the first evidence of persisters' novel ability for horizontal gene transfer, via transformation.},
}

@article {pmid39166873,
year = {2024},
author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L},
title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0043424},
doi = {10.1128/msystems.00434-24},
pmid = {39166873},
issn = {2379-5077},
abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.},
}

@article {pmid39166856,
year = {2024},
author = {Karpenko, A and Shelenkov, A and Manzeniuk, I and Kulikova, N and Gevorgyan, A and Mikhaylova, Y and Akimkin, V},
title = {Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0075124},
doi = {10.1128/spectrum.00751-24},
pmid = {39166856},
issn = {2165-0497},
abstract = {UNLABELLED: The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE: Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.},
}

@article {pmid39166427,
year = {2024},
author = {Wu, JJ and Deng, QW and Qiu, YY and Liu, C and Lin, CF and Ru, YL and Sun, Y and Lai, J and Liu, LX and Shen, XX and Pan, R and Zhao, YP},
title = {Post-transfer adaptation of HGT-acquired genes and contribution to guanine metabolic diversification in land plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20040},
pmid = {39166427},
issn = {1469-8137},
support = {32071484//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; 32371691//National Natural Science Foundation of China/ ; LZ21C030003//Natural Science Foundation of Zhejiang Province/ ; LZ23C020002//Natural Science Foundation of Zhejiang Province/ ; LR23C140001//Natural Science Foundation of Zhejiang Province/ ; 2023000CC0010//Beijing Life Science Academy/ ; 226-2023-00021//Fundamental Research Funds for the Central Universities/ ; 2022YFD1401600//National Key Research and Development Program of China/ ; },
abstract = {Horizontal gene transfer (HGT) is a major driving force in the evolution of prokaryotic and eukaryotic genomes. Despite recent advances in distribution and ecological importance, the extensive pattern, especially in seed plants, and post-transfer adaptation of HGT-acquired genes in land plants remain elusive. We systematically identified 1150 foreign genes in 522 land plant genomes that were likely acquired via at least 322 distinct transfers from nonplant donors and confirmed that recent HGT events were unevenly distributed between seedless and seed plants. HGT-acquired genes evolved to be more similar to native genes in terms of average intron length due to intron gains, and HGT-acquired genes containing introns exhibited higher expression levels than those lacking introns, suggesting that intron gains may be involved in the post-transfer adaptation of HGT in land plants. Functional validation of bacteria-derived gene GuaD in mosses and gymnosperms revealed that the invasion of foreign genes introduced a novel bypass of guanine degradation and resulted in the loss of native pathway genes in some gymnosperms, eventually shaping three major types of guanine metabolism in land plants. We conclude that HGT has played a critical role in land plant evolution.},
}

@article {pmid39165128,
year = {2024},
author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF},
title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae068},
pmid = {39165128},
issn = {1574-6968},
abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here we measure and compare the rate of genome flux for 5 655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30-33% (Alphaproteobacteria, Gammaproteobacteria, Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.},
}

@article {pmid39163267,
year = {2024},
author = {Kloub, L and Gosselin, S and Graf, J and Gogarten, JP and Bansal, MS},
title = {Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae180},
pmid = {39163267},
issn = {1759-6653},
abstract = {Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing non-homologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting 9 method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.},
}

@article {pmid39162532,
year = {2024},
author = {Ito, Y and Hashimoto, Y and Suzuki, M and Kaneko, N and Yoshida, M and Nakayama, H and Tomita, H},
title = {The emergence of metronidazole-resistant Prevotella bivia harboring nimK gene in Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056224},
doi = {10.1128/spectrum.00562-24},
pmid = {39162532},
issn = {2165-0497},
abstract = {UNLABELLED: We present the identification and characterization of the complete genome of metronidazole (MTZ)-resistant Prevotella bivia strain TOH-2715 [minimum inhibitory concentration (MIC): 8 mg/L], isolated from the urine of an elderly Japanese woman, as well as details of its mobile genetic elements (MGEs) containing antimicrobial resistance (AMR) genes and its relationship with other bacterial species determined using whole-genome sequencing (WGS) data. TOH-2715 possessed two chromosomes with putative MGEs containing AMR genes. Two AMR-related MGE regions were present in chromosome 2. MGE-region 1 (7,821 bp) included Tn6456, where nimK was located, and MGE-region 2 (58.8 Kbp) included the integrative and conjugative element (ICE), where tet(Q) and ermF were located. The genetic structure of the ICE of TOH-2715 was similar to that of CTnDOT-family transposons, where ermF and tet(Q) are located. A search of public databases revealed that nimK was present in Prevotella spp., including P. bivia, and was partially composed of a Tn6456-like element lacking the efflux transporter gene qacE and the Crp/Fnr family transcriptional regulator gene in some cases. Core ICE gene analysis showed that ICEs similar to that of TOH-2715 were present in Prevotella spp. and Bacteroides spp., suggesting horizontal gene transfer among anaerobes. This is the report of WGS analysis of an MTZ-resistant clinical strain of P. bivia (TOH-2715) with Tn6456 encoding nimK. Other submitted genomes have described the presence of nimK, but none of them have described MTZ resistance. Additionally, we described putative MGE regions containing the AMR gene within the genus Prevotella and among anaerobes, raising concerns about the future spread of nimK among anaerobes.

IMPORTANCE: Metronidazole (MTZ) is an important antimicrobial agent in anaerobic infections and is widely used in clinical settings. The rate of MTZ resistance in anaerobic bacteria has been increasing in recent years, and the nim gene (nitro-imidazole reductase) is one of the resistance mechanisms. Prevotella bivia is found in humans in the urinary tract and vagina and is known to cause infections in some cases. One of the nim genes, nimK, has recently been discovered in this species of bacteria, but there are no reports of antimicrobial resistance (AMR)-related regions in its whole genome level. In this study, we analyzed the AMR region of nimK-positive P. bivia derived from clinical specimens based on comparisons with other anaerobic genomes. P. bivia was found to be engaged in horizontal gene transfer with other anaerobic bacteria, and the future spread of the nimK gene is a concern.},
}

@article {pmid39162515,
year = {2024},
author = {Wang, Z and Hülpüsch, C and Foesel, B and Traidl-Hoffmann, C and Reiger, M and Schloter, M},
title = {Genomic and functional divergence of Staphylococcus aureus strains from atopic dermatitis patients and healthy individuals: insights from global and local scales.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057124},
doi = {10.1128/spectrum.00571-24},
pmid = {39162515},
issn = {2165-0497},
abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin disease worldwide and is characterized by a complex interplay with skin microbiota, with Staphylococcus aureus often abnormally more abundant in AD patients than in healthy individuals (HE). S. aureus harbors diverse strains with varied genetic compositions and functionalities, which exhibit differential connections with the severity of AD. However, the differences in S. aureus strains between AD and HE remain unclear, with most variations seen at a specific geographic level, implying spontaneous adaptations rather than systematic distinctions. This study presents genomic and functional differences between these S. aureus strains from AD and HE on both global and local levels. We observed reduced gene content diversity but increased functional variation in the global AD-associated strains. Two additional AD-dominant clusters emerged, with Cluster 1 enriched in transposases and Cluster 2 showcasing genes linked to adaptability and antibiotic resistance. Particularly, robust evidence illustrates that the lantibiotic operon of S. aureus, involved in the biosynthesis of lantibiotics, was acquired via horizontal gene transfer from environmental bacteria. Comparisons of the gene abundance profiles in functional categories also indicate limited zoonotic potential between human and animal isolates. Local analysis mirrored global gene diversity but showed distinct functional variations between AD and HE strains. Overall, this research provides foundational insights into the genomic evolution, adaptability, and antibiotic resistance of S. aureus, with significant implications for clinical microbiology.IMPORTANCEOur study uncovers significant genomic variations in Staphylococcus aureus strains associated with atopic dermatitis. We observed adaptive evolution tailored to the disease microenvironment, characterized by a smaller pan-genome than strains from healthy skin both on the global and local levels. Key functional categories driving strain diversification include "replication and repair" and "transporters," with transposases being pivotal. Interestingly, the local strains predominantly featured metal-related genes, whereas global ones emphasized antimicrobial resistances, signifying scale-dependent diversification nuances. We also pinpointed horizontal gene transfer events, indicating interactions between human-associated and environmental bacteria. These insights expand our comprehension of S. aureus's genetic adaptation in atopic dermatitis, yielding valuable implications for clinical approaches.},
}

@article {pmid39159726,
year = {2024},
author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q},
title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131309},
doi = {10.1016/j.biortech.2024.131309},
pmid = {39159726},
issn = {1873-2976},
abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial host in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the "One Health" initiative.},
}

@article {pmid39158272,
year = {2024},
author = {Upreti, C and Kumar, P and Durso, LM and Palmer, KL},
title = {CRISPR-Cas inhibits plasmid transfer and immunizes bacteria against antibiotic resistance acquisition in manure.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0087624},
doi = {10.1128/aem.00876-24},
pmid = {39158272},
issn = {1098-5336},
abstract = {The horizontal transfer of antibiotic resistance genes among bacteria is a pressing global issue. The bacterial defense system clustered regularly interspaced short palindromic repeats (CRISPR)-Cas acts as a barrier to the spread of antibiotic resistance plasmids, and CRISPR-Cas-based antimicrobials can be effective to selectively deplete antibiotic-resistant bacteria. While significant surveillance efforts monitor the spread of antibiotic-resistant bacteria in the clinical context, a major, often overlooked aspect of the issue is resistance emergence in agriculture. Farm animals are commonly treated with antibiotics, and antibiotic resistance in agriculture is on the rise. Yet, CRISPR-Cas efficacy has not been investigated in this setting. Here, we evaluate the prevalence of CRISPR-Cas in agricultural Enterococcus faecalis strains and its antiplasmid efficacy in an agricultural niche: manure. Analyzing 1,986 E. faecalis genomes from human and animal hosts, we show that the prevalence of CRISPR-Cas subtypes is similar between clinical and agricultural E. faecalis strains. Using plasmid conjugation assays, we found that CRISPR-Cas is a significant barrier against resistance plasmid transfer in manure. Finally, we used a CRISPR-based antimicrobial approach to cure resistant E. faecalis of erythromycin resistance, but this was limited by delivery efficiency of the CRISPR antimicrobial in manure. However, immunization of bacteria against resistance gene acquisition in manure was highly effective. Together, our results show that E. faecalis CRISPR-Cas is prevalent and effective in an agricultural setting and has the potential to be utilized for depleting antibiotic-resistant populations. Our work has broad implications for tackling antibiotic resistance in the increasingly relevant agricultural setting, in line with a One Health approach.IMPORTANCEAntibiotic resistance is a growing global health crisis in human and veterinary medicine. Previous work has shown technologies based on CRISPR-Cas-a bacterial defense system-to be effective in tackling antibiotic resistance. Here we test if CRISPR-Cas is present and effective in agricultural niches, specifically in the ubiquitously present bacterium, Enterococcus faecalis. We show that CRISPR-Cas is both prevalent and functional in manure and has the potential to be used to specifically kill bacteria carrying antibiotic resistance genes. This study demonstrates the utility of CRISPR-Cas-based strategies for control of antibiotic resistance in agricultural settings.},
}

@article {pmid39158107,
year = {2024},
author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q},
title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17507},
doi = {10.1111/mec.17507},
pmid = {39158107},
issn = {1365-294X},
support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.},
}

@article {pmid39153565,
year = {2024},
author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J},
title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119808},
doi = {10.1016/j.envres.2024.119808},
pmid = {39153565},
issn = {1096-0953},
abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.},
}

@article {pmid39153075,
year = {2024},
author = {Panickar, A and Manoharan, A and Anbarasu, A and Ramaiah, S},
title = {Respiratory tract infections: an update on the complexity of bacterial diversity, therapeutic interventions and breakthroughs.},
journal = {Archives of microbiology},
volume = {206},
number = {9},
pages = {382},
pmid = {39153075},
issn = {1432-072X},
support = {IRIS ID: 2021-11889//Indian Council of Medical Research/ ; },
mesh = {*Respiratory Tract Infections/microbiology/drug therapy ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial ; Bacterial Infections/microbiology/drug therapy ; Virulence ; },
abstract = {Respiratory tract infections (RTIs) have a significant impact on global health, especially among children and the elderly. The key bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Staphylococcus aureus and non-fermenting Gram Negative bacteria such as Acinetobacter baumannii and Pseudomonas aeruginosa are most commonly associated with RTIs. These bacterial pathogens have evolved a diverse array of resistance mechanisms through horizontal gene transfer, often mediated by mobile genetic elements and environmental acquisition. Treatment failures are primarily due to antimicrobial resistance and inadequate bacterial engagement, which necessitates the development of alternative treatment strategies. To overcome this, our review mainly focuses on different virulence mechanisms and their resulting pathogenicity, highlighting different therapeutic interventions to combat resistance. To prevent the antimicrobial resistance crisis, we also focused on leveraging the application of artificial intelligence and machine learning to manage RTIs. Integrative approaches combining mechanistic insights are crucial for addressing the global challenge of antimicrobial resistance in respiratory infections.},
}

*Respiratory Tract Infections/microbiology/drug therapy
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Bacteria/genetics/drug effects/classification
Drug Resistance, Bacterial
Bacterial Infections/microbiology/drug therapy
Virulence

@article {pmid39149034,
year = {2024},
author = {Kadkhoda, H and Gholizadeh, P and Samadi Kafil, H and Ghotaslou, R and Pirzadeh, T and Ahangarzadeh Rezaee, M and Nabizadeh, E and Feizi, H and Aghazadeh, M},
title = {Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34692},
pmid = {39149034},
issn = {2405-8440},
abstract = {The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.},
}

@article {pmid39148687,
year = {2024},
author = {Santos, AJDC and Dias, RS and da Silva, CHM and Vidigal, PMP and de Sousa, MP and da Silva, CC and de Paula, SO},
title = {Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39148687},
issn = {2516-8290},
abstract = {Bacteria of the species Oceanotoga teriensis belong to the family Petrotogaceae, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant O. teriensis UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.},
}

@article {pmid39147525,
year = {2024},
author = {Wu, Q and Li, W and Kwok, LY and Lv, H and Sun, J and Sun, Z},
title = {Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut.},
journal = {Food research international (Ottawa, Ont.)},
volume = {192},
number = {},
pages = {114840},
doi = {10.1016/j.foodres.2024.114840},
pmid = {39147525},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Phylogeny ; *Genome, Bacterial ; *Bifidobacterium pseudocatenulatum/genetics/metabolism ; Genetic Variation ; Genomics ; Diet ; },
abstract = {Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Phylogeny
*Genome, Bacterial
*Bifidobacterium pseudocatenulatum/genetics/metabolism
Genetic Variation
Genomics
Diet

@article {pmid39144201,
year = {2024},
author = {Pramanik, S and Sil, AK},
title = {Anti-foam cell activity of metabolites of a bacterium isolated from yogurt.},
journal = {Food science and biotechnology},
volume = {33},
number = {11},
pages = {2597-2610},
pmid = {39144201},
issn = {2092-6456},
abstract = {UNLABELLED: Existing literature documents the beneficial effects of probiotics against atherosclerosis, a major cause of human death. However, it suffers from a serious limitation due to horizontal gene transfer. Therefore, currently, efforts are targeted to examine the beneficial effects of metabolites obtained from probiotics. In this context, the current study isolated a bacterium from yogurt and investigated the effect of its metabolites on foam cell formation, a key event for developing atherosclerosis. Results showed that the cell-free conditioned medium (CM) of this isolate and di-chloro methane extract of CM (CME) not only prevented the formation but also reduced the level of preformed foam cells. To understand the mechanism, the GC-MS study revealed the presence of compounds known to exert anti-atherogenic activities like anti-oxidant, anti-NF-κB, and lipolytic activities. Consistently, CME exhibited substantial anti-oxidant and anti-NF-κB activity. In conclusion, metabolites of this bacterium have anti-atherogenic activities and thus have therapeutic potential.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01515-7.},
}

@article {pmid39141729,
year = {2024},
author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM},
title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn3316},
doi = {10.1126/sciadv.adn3316},
pmid = {39141729},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.},
}

*Bacteriophages/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/virology/genetics
*Gene Transfer, Horizontal
Metagenomics/methods
Genetic Variation
Virome/genetics
Genome, Viral
High-Throughput Nucleotide Sequencing

@article {pmid39141562,
year = {2024},
author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L},
title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {209},
pages = {},
doi = {10.3791/66899},
pmid = {39141562},
issn = {1940-087X},
mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation & purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.},
}

*Wastewater/microbiology/chemistry
Polyethylene Glycols/chemistry
Molecular Weight
DNA, Bacterial/genetics/isolation & purification
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics

@article {pmid39096644,
year = {2024},
author = {Wu, Q and Wu, GG and Pan, KN and Wang, XP and Li, HY and Tian, Z and Jin, RC and Fan, NS},
title = {Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135403},
doi = {10.1016/j.jhazmat.2024.135403},
pmid = {39096644},
issn = {1873-3336},
mesh = {*Metoprolol ; *Plasmids/genetics ; *Conjugation, Genetic/drug effects ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Adrenergic beta-Antagonists/pharmacology ; Gene Transfer, Horizontal ; Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, MDR/genetics ; Microbiota/drug effects ; },
abstract = {Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.},
}

*Metoprolol
*Plasmids/genetics
*Conjugation, Genetic/drug effects
Drug Resistance, Multiple, Bacterial/genetics/drug effects
Adrenergic beta-Antagonists/pharmacology
Gene Transfer, Horizontal
Bacteria/genetics/drug effects/metabolism
Anti-Bacterial Agents/pharmacology
Genes, MDR/genetics
Microbiota/drug effects

@article {pmid39139006,
year = {2024},
author = {Rao, Y and Wang, Y and Zhang, H and Wang, Y and He, Q and Yuan, X and Guo, J and Chen, H},
title = {A Strategy of Killing Two Birds With One Stone for Blocking Drug Resistance Spread With Engineered Bdellovibrio bacteriovorus.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2406910},
doi = {10.1002/adma.202406910},
pmid = {39139006},
issn = {1521-4095},
support = {21935008//National Natural Science Foundation of China/ ; SKJY2021042//Livelihood Technology Project of Suzhou/ ; 23KJA150008//Jiangsu Province Higher Education Natural Science Research Major Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Drug-resistant pathogens significantly threaten human health and life. Simply killing drug-resistant pathogens cannot effectively eliminate their threat since the drug-resistant genes (DRGs) released from dead drug-resistant pathogens are difficult to eliminate and can further spread via horizontal gene transfer, leading to the spread of drug resistance. The development of antibacterial materials with sterilization and DRGs cleavage activities is highly crucial. Herein, a living system, Ce-PEA@Bdello, is fabricated with bacterial killing and DRGs cleavage activities for blocking bacterial drug resistance dissemination by engineered Bdellovibrio bacteriovorus (Bdello). Ce-PEA@Bdello is obtained by engineering Bdello with dopamine and a multinuclear cerium (IV) complex. Ce-PEA@Bdello can penetrate and eliminate kanamycin-resistant P. aeruginosa (Kan[R]) biofilms via the synergistic effect of predatory Bdello and photothermal polydopamine under near-infrared light. Additionally, the DNase-mimicking ability of Ce-PEA@Bdello endows it with genome and plasmid DNA cleavage ability. An in vivo study reveals that Ce-PEA@Bdello can eliminate P. aeruginosa (Kan[R]) and cleave DRGs in scald/burn infected wounds to block the spread of drug resistance and accelerate wound healing. This bioactive system constructed from natural living materials offers a promising means for blocking the spread of drug resistance.},
}

@article {pmid39135654,
year = {2024},
author = {Winter, M and Vos, M and Buckling, A and Johnsen, PJ and Harms, K},
title = {Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi.},
journal = {Access microbiology},
volume = {6},
number = {7},
pages = {},
pmid = {39135654},
issn = {2516-8290},
abstract = {Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.},
}

@article {pmid39132438,
year = {2024},
author = {Liu, H and Fan, S and Zhang, X and Yuan, Y and Zhong, W and Wang, L and Wang, C and Zhou, Z and Zhang, S and Geng, Y and Peng, G and Wang, Y and Zhang, K and Yan, Q and Luo, Y and Shi, K and Zhong, Z},
title = {Antibiotic-resistant characteristics and horizontal gene transfer ability analysis of extended-spectrum β-lactamase-producing Escherichia coli isolated from giant pandas.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1394814},
pmid = {39132438},
issn = {2297-1769},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2, VAGs of papA, fimC and ompT, MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M. Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment.},
}

@article {pmid39128935,
year = {2024},
author = {Wang, W and Ge, Q and Wen, J and Zhang, H and Guo, Y and Li, Z and Xu, Y and Ji, D and Chen, C and Guo, L and Xu, M and Shi, C and Fan, G and Xie, C},
title = {Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {976},
pmid = {39128935},
issn = {2399-3642},
support = {42176117//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20265//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100514//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Symbiosis/genetics ; *Porphyra/microbiology/genetics ; Adaptation, Physiological/genetics ; Phylogeny ; Biological Evolution ; },
abstract = {Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.},
}

*Gene Transfer, Horizontal
*Symbiosis/genetics
*Porphyra/microbiology/genetics
Adaptation, Physiological/genetics
Phylogeny
Biological Evolution

@article {pmid39127705,
year = {2024},
author = {Park, H and Bulzu, PA and Shabarova, T and Kavagutti, VS and Ghai, R and Kasalický, V and Jezberová, J},
title = {Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {150},
pmid = {39127705},
issn = {2049-2618},
support = {20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 23-05081S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 20‑12496X//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; 19-23261S//Grantová Agentura Ceské Republiky (GAČR)/ ; },
mesh = {*Symbiosis ; *Fresh Water/microbiology ; *Genome, Bacterial ; *Phylogeny ; *Cyanobacteria/genetics/classification ; Adaptation, Physiological/genetics ; Europe ; Ecosystem ; Gene Transfer, Horizontal ; Genomics ; },
abstract = {BACKGROUND: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies.

RESULTS: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.

CONCLUSIONS: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. Video Abstract.},
}

*Symbiosis
*Fresh Water/microbiology
*Genome, Bacterial
*Phylogeny
*Cyanobacteria/genetics/classification
Adaptation, Physiological/genetics
Europe
Ecosystem
Gene Transfer, Horizontal
Genomics

@article {pmid39125965,
year = {2024},
author = {Sadowska-Bartosz, I and Bartosz, G},
title = {Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125965},
issn = {1422-0067},
mesh = {Animals ; *Tardigrada/metabolism/genetics ; *Antioxidants/metabolism ; Oxidative Stress ; Earth, Planet ; Trehalose/metabolism ; },
abstract = {Tardigrades are unique among animals in their resistance to dehydration, mainly due to anhydrobiosis and tun formation. They are also very resistant to high-energy radiation, low and high temperatures, low and high pressure, and various chemical agents, Interestingly, they are resistant to ionizing radiation both in the hydrated and dehydrated states to a similar extent. They are able to survive in the cosmic space. Apparently, many mechanisms contribute to the resistance of tardigrades to harmful factors, including the presence of trehalose (though not common to all tardigrades), heat shock proteins, late embryogenesis-abundant proteins, tardigrade-unique proteins, DNA repair proteins, proteins directly protecting DNA (Dsup and TDR1), and efficient antioxidant system. Antioxidant enzymes and small-molecular-weight antioxidants are an important element in the tardigrade resistance. The levels and activities of many antioxidant proteins is elevated by anhydrobiosis and UV radiation; one explanation for their induction during dehydration is provided by the theory of "preparation for oxidative stress", which occurs during rehydration. Genes coding for some antioxidant proteins are expanded in tardigrades; some genes (especially those coding for catalases) were hypothesized to be of bacterial origin, acquired by horizontal gene transfer. An interesting antioxidant protein found in tardigrades is the new Mn-dependent peroxidase.},
}

Animals
*Tardigrada/metabolism/genetics
*Antioxidants/metabolism
Oxidative Stress
Earth, Planet
Trehalose/metabolism

@article {pmid39125866,
year = {2024},
author = {Cheng, X and Liu, X and Jordan, KW and Yu, J and Whitworth, RJ and Park, Y and Chen, MS},
title = {Frequent Acquisition of Glycoside Hydrolase Family 32 (GH32) Genes from Bacteria via Horizontal Gene Transfer Drives Adaptation of Invertebrates to Diverse Sources of Food and Living Habitats.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125866},
issn = {1422-0067},
mesh = {*Gene Transfer, Horizontal ; *Glycoside Hydrolases/genetics/metabolism ; Animals ; *Bacteria/genetics/enzymology ; *Phylogeny ; Invertebrates/genetics ; Adaptation, Physiological/genetics ; Ecosystem ; Evolution, Molecular ; },
abstract = {Glycoside hydrolases (GHs, also called glycosidases) catalyze the hydrolysis of glycosidic bonds in polysaccharides. Numerous GH genes have been identified from various organisms and are classified into 188 families, abbreviated GH1 to GH188. Enzymes in the GH32 family hydrolyze fructans, which are present in approximately 15% of flowering plants and are widespread across microorganisms. GH32 genes are rarely found in animals, as fructans are not a typical carbohydrate source utilized in animals. Here, we report the discovery of 242 GH32 genes identified in 84 animal species, ranging from nematodes to crabs. Genetic analyses of these genes indicated that the GH32 genes in various animals were derived from different bacteria via multiple, independent horizontal gene transfer events. The GH32 genes in animals appear functional based on the highly conserved catalytic blades and triads in the active center despite the overall low (35-60%) sequence similarities among the predicted proteins. The acquisition of GH32 genes by animals may have a profound impact on sugar metabolism for the recipient organisms. Our results together with previous reports suggest that the acquired GH32 enzymes may not only serve as digestive enzymes, but also may serve as effectors for manipulating host plants, and as metabolic enzymes in the non-digestive tissues of certain animals. Our results provide a foundation for future studies on the significance of horizontally transferred GH32 genes in animals. The information reported here enriches our knowledge of horizontal gene transfer, GH32 functions, and animal-plant interactions, which may result in practical applications. For example, developing crops via targeted engineering that inhibits GH32 enzymes could aid in the plant's resistance to animal pests.},
}

*Gene Transfer, Horizontal
*Glycoside Hydrolases/genetics/metabolism
Animals
*Bacteria/genetics/enzymology
*Phylogeny
Invertebrates/genetics
Adaptation, Physiological/genetics
Ecosystem
Evolution, Molecular

@article {pmid39125715,
year = {2024},
author = {Bucka-Kolendo, J and Kiousi, DE and Dekowska, A and Mikołajczuk-Szczyrba, A and Karadedos, DM and Michael, P and Galanis, A and Sokołowska, B},
title = {Exploration of Alicyclobacillus spp. Genome in Search of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125715},
issn = {1422-0067},
mesh = {*Alicyclobacillus/genetics/drug effects ; *Genome, Bacterial ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Guaiacol/pharmacology/analogs & derivatives ; },
abstract = {The study investigates the antibiotic resistance (AR) profiles and genetic determinants in three strains of guaiacol-producing Alicyclobacillus spp. isolated from orchard soil and pears. Their phenotypic characteristics, such as spore formation; resistance to different factors, including drugs or disinfectants; or production of off-flavor compounds, can affect the taste and aroma of spoiled products. Food and beverages are potential vectors for the transfer of antibiotic resistance genes, which is a growing health concern; thus, microorganisms in food and beverages should not be a potential source of drug resistance to consumers. Whole-genome sequencing (WGS) was utilized to identify antibiotic resistance genes, metabolic pathways, and elements associated with guaiacol and halophenol production. Minimum inhibitory concentration (MIC) testing revealed that all strains were susceptible to eight out of nine tested antibiotics (ampicillin, gentamycin, kanamycin, streptomycin, clindamycin, tetracycline, chloramphenicol, and vancomycin) but exhibited high resistance to erythromycin. Analysis indicated that the erythromycin resistance gene, ribosomal RNA small subunit methyltransferase A (RsmA), was intrinsic and likely acquired through horizontal gene transfer (HGT). The comprehensive genomic analysis provides insights into the molecular mechanisms of antibiotic resistance in Alicyclobacillus spp., highlighting the potential risk of these bacteria as vectors for antibiotic resistance genes in the food chain. This study expands the understanding of the genetic makeup of these spoilage bacteria and their role in antimicrobial resistance dissemination.},
}

*Alicyclobacillus/genetics/drug effects
*Genome, Bacterial
*Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Guaiacol/pharmacology/analogs & derivatives

@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}

*Mitochondria/metabolism/genetics
*Phylogeny
*Proteome/metabolism/genetics
Transcriptome
Eukaryota/genetics/metabolism/classification
Gene Transfer, Horizontal
Iron-Sulfur Proteins/metabolism/genetics

@article {pmid37754684,
year = {2023},
author = {Zhang, Y and Kitazumi, A and Liao, Y-T and de Los Reyes, BG and Wu, VCH},
title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.},
journal = {Microbiology spectrum},
volume = {11},
number = {5},
pages = {e0022623},
pmid = {37754684},
issn = {2165-0497},
support = {2030-42000-0055-000-D//USDA | Agricultural Research Service (ARS)/ ; },
mesh = {*Bacteriophages/genetics ; *Gene Transfer, Horizontal ; *Metagenomics ; *Agriculture ; *Bacteria/genetics/virology/drug effects ; *Microbiota/genetics ; Metagenome ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.},
}

*Bacteriophages/genetics
*Gene Transfer, Horizontal
*Metagenomics
*Agriculture
*Bacteria/genetics/virology/drug effects
*Microbiota/genetics
Metagenome
Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Ecosystem
Drug Resistance, Bacterial/genetics
Soil Microbiology

@article {pmid39121985,
year = {2024},
author = {Yan, Y and Lu, H and Liang, X and Xu, T and Yan, S and Yu, Y and Wang, Y},
title = {The virulence plasmid associated with AHPND in shrimp appears to have originated from Vibrio owensii through a process of homologous recombination of parental plasmids and the transposable insertion of two large fragments.},
journal = {Journal of invertebrate pathology},
volume = {206},
number = {},
pages = {108173},
doi = {10.1016/j.jip.2024.108173},
pmid = {39121985},
issn = {1096-0805},
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is a highly contagious and lethal disease of shrimp caused by Vibrio strains carrying the virulence plasmid (pAHPND) containing the pirAB virulence genes. Through analysis of plasmid sequence similarity, clustering, and phylogeny, a horizontal transfer element similar to IS91 was discovered within the pAHPND plasmid. Additionally, two distinct clades of plasmids related to pAHPND (designated as pAHPND-r1 and pAHPND-r2) were identified, which may serve as potential parental plasmids for pAHPND. The available evidence, including the difference in G+C content between the plasmid and its host, codon usage preference, and plasmid recombination event prediction, suggests that the formation of the pAHPND plasmid in the Vibrio owensii strain was likely due to the synergistic effect of the recombinase RecA and the associated proteins RecBCD on the pAHPND-r1 and pAHPND-r2, resulting in the recombination and formation of the precursor plasmid for pAHPND (pre-pAHPND). The emergence of pAHPND was found to be a result of successive insertions of the horizontal transfer elements of pirAB-Tn903 and IS91-like segment, which led to the deletion of one third of the pre-pAHPND. This plasmid was then able to spread horizontally to other Vibrio strains, contributing to the epidemics of AHPND. These findings shed light on previously unknown mechanisms involved in the emergence of pAHPND and improve our understanding of the disease's spread.},
}

@article {pmid39119206,
year = {2024},
author = {Zaer-Anaqz, Z and Khakvar, R and Mohammadi, SA and Bannazadeh Baghi, H and Koolivand, D},
title = {Physicochemical Characterization of Novel Bacteriophages of Pseudomonas syringe from Northwest Iran.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {99-106},
pmid = {39119206},
issn = {2641-6549},
abstract = {Bacterial canker, caused by Pseudomonas syringae, is a devastating disease of stone fruit trees worldwide. The bacterium has a broad host range and a high capacity for adaptation and dissemination, owing to its high mutation rate and horizontal gene transfer. Traditional control methods based on copper compounds and antibiotics have resulted in the development of resistance in the bacterial population. Thus, alternative approaches are needed, such as phage therapy. This study aimed to characterize the physicochemical and biological properties of novel Pseudomonas syringae pv. syringae (Pss)-specific phages isolated from the soils of northwestern Iran. Seventy-five phage isolates were obtained, and their host range was determined against various bacterial pathogens. Five phages exhibiting the highest lytic activity against Pss and a narrow host range were selected for subsequent analysis. The stability of the selected phages was assessed under different conditions such as ultraviolet irradiation, temperature, pH, NaCl concentration, and chloroform exposure. The selected phages demonstrated significant effectiveness in vivo, exerting substantial suppression on the population of Pss. This reduction was observed for both individual phages and when the phages were utilized as a mixture. The findings indicate that phages have the potential to be used as biocontrol agents in agriculture.},
}

@article {pmid39119203,
year = {2024},
author = {Delesalle, VA and Ankeriasniemi, RE and Lewis, CM and Mody, JM and Roy, AM and Sarvis, WA and Vo, DD and Walsh, AE and Zappia, RJ},
title = {Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {84-90},
pmid = {39119203},
issn = {2641-6549},
abstract = {BACKGROUND: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc[2]155 continue to be discovered.

MATERIALS AND METHODS: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared.

RESULTS: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence.

CONCLUSIONS: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.},
}

@article {pmid39117207,
year = {2024},
author = {Erler, T and Droop, F and Lübbert, C and Knobloch, JK and Carlsen, L and Papan, C and Schwanz, T and Zweigner, J and Dengler, J and Hoffmann, M and Mutters, NT and Savin, M},
title = {Analysing carbapenemases in hospital wastewater: Insights from intracellular and extracellular DNA using qPCR and digital PCR.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175344},
doi = {10.1016/j.scitotenv.2024.175344},
pmid = {39117207},
issn = {1879-1026},
abstract = {The widespread dissemination of carbapenem-resistant bacteria in wastewater systems, particularly from clinical sources, poses a significant public health risk. This study assessed the concentrations and distributions of extracellular DNA (exDNA) and intracellular DNA (iDNA) harboring carbapenemase genes in wastewater from six tertiary care hospitals in Germany. We collected a total of 36 samples, comprising six biological replicates from each hospital, and analysed them using quantitative real-time PCR (qPCR) and digital PCR (dPCR). The analysis targeted seven carbapenemase genes: blaNDM, blaKPC, blaIMP, blaVIM, blaOXA-23-like, blaOXA-48-like, and blaOXA-58-like across both DNA fractions. Our results revealed significant variability in the concentrations of exDNA and iDNA across the sampling sites, with iDNA typically present at higher concentrations. Using NanoDrop One spectrophotometry and the Qubit dsDNA kit, exDNA concentrations ranged from 2.7 to 7.7 ng/mL, while Qubit recorded lower values between 1.1 and 4.0 ng/mL. Conversely, iDNA concentrations were markedly higher, spanning from 42.3 to 191.7 ng/mL with NanoDrop and 12.0 to 46.5 ng/mL with Qubit, highlighting the variability between DNA types and quantification methods. Despite its lower concentrations, exDNA comprised up to 18.2 % of total DNA, highlighting its potential role in the horizontal transfer of antimicrobial resistance genes (ARGs). The study detected target ARGs in both DNA fractions at all sites, with notable differences in their concentrations; iDNA consistently exhibited higher levels of ARGs, with the highest concentrations reaching 10.57 ± 0.20 log gene copies per liter (GC/L) for blaVIM in iDNA and 6.96 ± 0.72 log GC/L for blaIMP in exDNA. dPCR demonstrated greater sensitivity than qPCR, especially effective for detecting low-abundance targets like blaOXA-23-like in the exDNA fraction. Additionally, qPCR's susceptibility to inhibition and contamination emphasizes the superior robustness of dPCR. This research highlights the need for improved monitoring and the implementation of advanced treatment technologies to mitigate ARG dissemination in wastewater.},
}

@article {pmid39113256,
year = {2024},
author = {Hossain, AKMZ and Chowdhury, AMMA},
title = {Understanding the Evolution and Transmission Dynamics of Antibiotic Resistance Genes: A Comprehensive Review.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e2400259},
doi = {10.1002/jobm.202400259},
pmid = {39113256},
issn = {1521-4028},
abstract = {Antibiotic resistance poses a formidable challenge to global public health, necessitating comprehensive understanding and strategic interventions. This review explores the evolution and transmission dynamics of antibiotic resistance genes, with a focus on Bangladesh. The indiscriminate use of antibiotics, compounded by substandard formulations and clinical misdiagnosis, fuels the emergence and spread of resistance in the country. Studies reveal high resistance rates among common pathogens, emphasizing the urgent need for targeted interventions and rational antibiotic use. Molecular assessments uncover a diverse array of antibiotic resistance genes in environmental reservoirs, highlighting the complex interplay between human activities and resistance dissemination. Horizontal gene transfer mechanisms, particularly plasmid-mediated conjugation, facilitate the exchange of resistance determinants among bacterial populations, driving the evolution of multidrug-resistant strains. The review discusses clinical implications, emphasizing the interconnectedness of environmental and clinical settings in resistance dynamics. Furthermore, bioinformatic and experimental evidence elucidates novel mechanisms of resistance gene transfer, underscoring the dynamic nature of resistance evolution. In conclusion, combating antibiotic resistance requires a multifaceted approach, integrating surveillance, stewardship, and innovative research to preserve the efficacy of antimicrobial agents and safeguard public health.},
}

@article {pmid39103341,
year = {2024},
author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ},
title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6653},
pmid = {39103341},
issn = {2041-1723},
support = {R01 GM124141/GM/NIGMS NIH HHS/United States ; R01GM088344//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM088344/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/ ; R01GM124141//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*DNA Transposable Elements/genetics ; *Escherichia coli/genetics/metabolism ; *CRISPR-Cas Systems ; *Clustered Regularly Interspaced Short Palindromic Repeats ; *Gene Transfer, Horizontal ; *CRISPR-Associated Proteins/metabolism/genetics ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.},
}

*DNA Transposable Elements/genetics
*Escherichia coli/genetics/metabolism
*CRISPR-Cas Systems
*Clustered Regularly Interspaced Short Palindromic Repeats
*Gene Transfer, Horizontal
*CRISPR-Associated Proteins/metabolism/genetics
Escherichia coli Proteins/genetics/metabolism

@article {pmid39102038,
year = {2024},
author = {Olanrewaju, OS and Molale-Tom, LG and Bezuidenhout, CC},
title = {Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {289},
pmid = {39102038},
issn = {1573-0972},
mesh = {South Africa ; *Genome, Bacterial ; *Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation & purification ; Virulence/genetics ; *Genetic Variation ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors/genetics ; Humans ; Drug Resistance, Bacterial/genetics ; Genomic Islands/genetics ; Gram-Positive Bacterial Infections/microbiology ; Enterococcus/genetics/drug effects/pathogenicity/isolation & purification/classification ; Phylogeny ; Gene Transfer, Horizontal ; Genomics ; Microbial Sensitivity Tests ; },
abstract = {This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.},
}

South Africa
*Genome, Bacterial
*Enterococcus faecalis/genetics/drug effects/pathogenicity/isolation & purification
Virulence/genetics
*Genetic Variation
*Anti-Bacterial Agents/pharmacology
*Virulence Factors/genetics
Humans
Drug Resistance, Bacterial/genetics
Genomic Islands/genetics
Gram-Positive Bacterial Infections/microbiology
Enterococcus/genetics/drug effects/pathogenicity/isolation & purification/classification
Phylogeny
Gene Transfer, Horizontal
Genomics
Microbial Sensitivity Tests

@article {pmid39101807,
year = {2024},
author = {Dhurve, G and Behera, SR and Kodetham, G and Siddavattam, D},
title = {Outer membrane vesicles of Acinetobacter baumannii DS002 carry circular DNA similar to bovine meat and milk factors (BMMFs) and SPHINX 2.36 and probably play a role in interdomain lateral gene transfer.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0081724},
doi = {10.1128/spectrum.00817-24},
pmid = {39101807},
issn = {2165-0497},
abstract = {UNLABELLED: The discovery of Replication Competent Circular DNA molecules in mammalian cells and tissues is being linked to debilitating diseases, such as multiple sclerosis (MS), bovine spongiform encephalopathy (BSE), and colorectal cancer (CRC). These circular DNA molecules, otherwise known as bovine meat and milk factors (BMMFs) and Slow Progressive Hidden INfections of variable (X) latency (SPHINX), bear significant (80%) sequence similarity with the plasmids of Acinetobacter baumannii strains. Nanostructures, such as bacterial outer membrane vesicles (OMVs) serve as vehicles for transporting biomolecular cargo and have the potential to facilitate interkingdom lateral mobility of DNA. Strengthening the proposed hypothesis, this study demonstrates that OMVs derived from A. baumannii DS002 carrying four plasmids and genome (pTS236) of phage, AbDs1, successfully reached different parts of the body, including the central nervous system, following the injection of fluorescein isothiocyanate (FITC)-labeled OMVs into experimental mice. Out of the four OMV-associated plasmids, three (pTS4586, pTS9900, and pTS134338) were identified within the lumen, and the fourth one (pTS11291) was found on the surface of OMVs. In addition to the indigenous plasmids, the phage-encoded protein, Orf96, anchored on the surface of the OMVs by establishing a strong interaction with the OMV-associated porin, OmpA. Intriguingly, a subset of labeled OMVs, when incubated with Neuro2A cells, translocated across the membrane and reached to the cytoplasmic space of the cells. Collectively, the experimental evidence presented herein underscores the promising potential of OMVs as vehicles for delivering molecular cargo containing plasmids and phage genomes to diverse mammalian tissues and cells.

IMPORTANCE: Several independent studies have demonstrated the existence of replication competent circular DNA molecules of bacterial and viral origin in mammalian cells and tissues. However, studies about their origin and lateral mobility to mammalian cells are scarce. Our work describes the existence of circular DNA, similar to that of DNA molecules identified in mammalian cells, OMVs derived from soil isolate of A. baumannii DS002. Furthermore, the work also provides visual evidence that demonstrates the passage of labeled OMVs to different organs of experimental mice within hours after intravenously administering OMVs into experimental mice. Some of the labeled OMVs have even crossed the membrane of Neuro2A, suggesting the existence of interkingdom horizontal mobility between bacteria and mammals.},
}

@article {pmid39101574,
year = {2024},
author = {Rappaport, HB and Oliverio, AM},
title = {Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life.},
journal = {Genome biology and evolution},
volume = {16},
number = {8},
pages = {},
pmid = {39101574},
issn = {1759-6653},
mesh = {*Eukaryota/genetics ; *Extremophiles/genetics ; Adaptation, Physiological/genetics ; Genomics ; Genome ; Evolution, Molecular ; Phylogeny ; },
abstract = {From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.},
}

*Eukaryota/genetics
*Extremophiles/genetics
Adaptation, Physiological/genetics
Genomics
Genome
Evolution, Molecular
Phylogeny

@article {pmid39100236,
year = {2024},
author = {Bhattacharya, A and Aluquin, A and Kennedy, DA},
title = {Exceptions to the rule: When does resistance evolution not undermine antibiotic therapy in human bacterial infections?.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {478-493},
pmid = {39100236},
issn = {2056-3744},
abstract = {The use of antibiotics to treat bacterial infections often imposes strong selection for antibiotic resistance. However, the prevalence of antibiotic resistance varies greatly across different combinations of pathogens and drugs. What underlies this variation? Systematic reviews, meta-analyses, and literature surveys capable of integrating data across many studies have tried to answer this question, but the vast majority of these studies have focused only on cases where resistance is common or problematic. Yet much could presumably be learned from the cases where resistance is infrequent or absent. Here we conducted a literature survey and a systematic review to study the evolution of antibiotic resistance across a wide range of pathogen-by-drug combinations (57 pathogens and 53 antibiotics from 15 drug classes). Using Akaike information criterion-based model selection and model-averaged parameter estimation we explored 14 different factors posited to be associated with resistance evolution. We find that the most robust predictors of high resistance are nosocomial transmission (i.e., hospital-acquired pathogens) and indirect transmission (e.g., vector-, water-, air-, or vehicle-borne pathogens). While the former was to be expected based on prior studies, the positive correlation between high resistance frequencies and indirect transmission is, to our knowledge, a novel insight. The most robust predictor of low resistance is zoonosis from wild animal reservoirs. We also found partial support that resistance was associated with pathogen type, horizontal gene transfer, commensalism, and human-to-human transmission. We did not find support for correlations between resistance and environmental reservoirs, mechanisms of drug action, and global drug use. This work explores the relative explanatory power of various pathogen and drug factors on resistance evolution, which is necessary to identify priority targets of stewardship efforts to slow the spread of drug-resistant pathogens.},
}

@article {pmid39100235,
year = {2024},
author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A},
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {526-538},
pmid = {39100235},
issn = {2056-3744},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.},
}

@article {pmid39098155,
year = {2024},
author = {Wang, H and Gao, J and Ren, H and Zhao, Y and Wang, Y and An, J and Chen, H and Wang, Q},
title = {Whatever does not kill them makes them stronger: Using quaternary ammonia antimicrobials to alleviate the inhibition of ammonia oxidation under perfluorooctanoic acid stress.},
journal = {Water research},
volume = {263},
number = {},
pages = {122171},
doi = {10.1016/j.watres.2024.122171},
pmid = {39098155},
issn = {1879-2448},
abstract = {Perfluorooctanoic acid (PFOA), benzalkyl dimethylammonium compounds (BAC) and antibiotic resistance genes (ARGs) have negative effects on biological sewage treatment. The performance of nitrification systems under stress of PFOA (0.1-5 mg/L) or/and BAC (0.2-10 mg/L) was explored during 84-day experiments using four sequencing batch reactors, in this study. Low (0.1 mg/L) concentration PFOA had a positive influence on ammonia removal, while medium and high (2 and 5 mg/L) concentrations PFOA caused severe inhibition. Meanwhile, PFOA stress resulted in the enrichment of ARGs in water (w-ARGs). BAC (0-10 mg/L) had no obvious influence on ammonia removal. However, BAC promoted the reduction of ARGs and the bacterial community was the main participator (48.07%) for the spread of ARGs. Interestingly, the joint stress of PFOA and BAC increased the ammonia-oxidizing bacteria (AOB) activity from 5.81 ± 0.19 and 6.05 ± 0.79 mg N/(g MLSS·h) to 7.09 ± 0.87 and 7.23 ± 0.29 mg N/(g MLSS·h) in medium and high concentrations, compared to single stress of PFOA, which was observed for the first time. BAC could reduce bioavailability of PFOA through competitive adsorption and decreasing sludge hydrophobicity by the lower β-Sheet and α-Helix in tightly bound protein. Furthermore, the joint stress of PFOA and BAC was able to intensify the proliferation of w-ARGs and extracellular ARGs in sludge, and developed the most active horizontal gene transfer mediated by intl1 compared to single stress of PFOA or BAC. The batch tests verified the detoxification capacity of BAC on nitrification under 2.5 mg/L PFOA (48 h exposing), and the maximum alleviation of AOB activity was achieved at BAC and PFOA mass ratio of 2:1. In summary, BAC could be used to alleviate the inhibition of PFOA on ammonia oxidation, providing an efficient and sustainable approach in wastewater treatment.},
}

@article {pmid39096995,
year = {2024},
author = {Tian, J and Xu, L and Sun, JQ},
title = {Taxonomic characterization and comparative genomic analysis of a novel Devosia species revealed that phenolic acid-degrading traits are ubiquitous in the Devosia genus.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119724},
doi = {10.1016/j.envres.2024.119724},
pmid = {39096995},
issn = {1096-0953},
abstract = {Phenolic acids (PAs) are widely distributed allelochemicals in various environments. To better understand the fate of PAs in environments, a halotolerant PAs-degrading bacterium (named strain RR2S18[T]) isolated from rhizosphere soil was identified as a novel species of Devosia, named Devosia rhizosphaerae sp. nov. The strain initially degraded PAs into central ring-fission intermediates (protocatechuic acid) using the CoA-dependent non-β-oxidation pathway. The produced ring-fission intermediates were then consecutively degraded by an ortho-cleavage reaction and the β-ketoadipic acid pathway. A comparative genomics analysis of 62 Devosia strains revealed that PAs-degrading genes were ubiquitous in their genomes, indicating that PAs degradation is universal among members of this genus. The analysis also suggested that the genes involved in CoA-dependent non-β-oxidation are inherent to Devosia strains, while those involved in ring-fission and β-ketoadipic acid pathways were obtained by horizontal gene transfer.},
}

@article {pmid39095425,
year = {2024},
author = {Landa, CR and Ariza-Mateos, A and Briones, C and Perales, C and Wagner, A and Domingo, E and Gómez, J},
title = {Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17914},
pmid = {39095425},
issn = {2045-2322},
mesh = {*Rhizome/virology ; *Evolution, Molecular ; *Quasispecies/genetics ; *Phylogeny ; RNA Viruses/genetics/classification ; Gene Transfer, Horizontal ; Mutation ; Genome, Viral ; },
abstract = {The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.},
}

*Rhizome/virology
*Evolution, Molecular
*Quasispecies/genetics
*Phylogeny
RNA Viruses/genetics/classification
Gene Transfer, Horizontal
Mutation
Genome, Viral

@article {pmid39095161,
year = {2025},
author = {Guo, Z and Tang, X and Wang, W and Luo, Z and Zeng, Y and Zhou, N and Yu, Z and Wang, D and Song, B and Zhou, C and Xiong, W},
title = {The photo-based treatment technology simultaneously removes resistant bacteria and resistant genes from wastewater.},
journal = {Journal of environmental sciences (China)},
volume = {148},
number = {},
pages = {243-262},
doi = {10.1016/j.jes.2024.01.005},
pmid = {39095161},
issn = {1001-0742},
mesh = {*Wastewater/chemistry ; *Waste Disposal, Fluid/methods ; Bacteria ; Disinfection/methods ; Drug Resistance, Bacterial/genetics ; Ultraviolet Rays ; Water Purification/methods ; },
abstract = {Because of the recent widespread usage of antibiotics, the acquisition and dissemination of antibiotic-resistance genes (ARGs) were prevalent in the majority of habitats. Generally, the biological wastewater treatment processes used in wastewater treatment plants have a limited efficiencies of antibiotics resistant bacteria (ARB) disinfection and ARGs degradation and even promote the proliferation of ARGs. Problematically, ARB and ARGs in effluent pose potential risks if they are not further treated. Photocatalytic oxidation is considered a promising disinfection technology, where the photocatalytic process generates many free radicals that enhance the interaction between light and deoxyribonucleic acid (DNA) for ARB elimination and subsequent degradation of ARGs. This review aims to illustrate the progress of photocatalytic oxidation technology for removing antibiotics resistant (AR) from wastewater in recent years. We discuss the sources and transfer of ARGs in wastewater. The overall removal efficiencies of ultraviolet radiation (UV)/chlorination, UV/ozone, UV/H2O2, and UV/sulfate-radical based system for ARB and ARGs, as well as the experimental parameters and removal mechanisms, are systematically discussed. The contribution of photocatalytic materials based on TiO2 and g-C3N4 to the inactivation of ARB and degradation of ARGs is highlighted, producing many free radicals to attack ARB and ARGs while effectively limiting the horizontal gene transfer (HGT) in wastewater. Finally, based on the reviewed studies, future research directions are proposed to realize specific photocatalytic oxidation technology applications and overcome current challenges.},
}

*Wastewater/chemistry
*Waste Disposal, Fluid/methods
Bacteria
Disinfection/methods
Drug Resistance, Bacterial/genetics
Ultraviolet Rays
Water Purification/methods

@article {pmid39093595,
year = {2024},
author = {Wu, J and Meng, L and Gaïa, M and Hikida, H and Okazaki, Y and Endo, H and Ogata, H},
title = {Gene transfer among viruses substantially contributes to gene gain of giant viruses.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae161},
pmid = {39093595},
issn = {1537-1719},
abstract = {The phylum Nucleocytoviricota comprises a diverse group of double-stranded DNA viruses that display a wide range of gene repertoires. Although these gene repertoires determine the characteristics of individual viruses, the evolutionary processes that have shaped the gene repertoires of extant viruses since their common ancestor are poorly characterized. In this study, we aimed to address this gap in knowledge by using amalgamated likelihood estimation (ALE), a probabilistic tree reconciliation method that infers evolutionary scenarios by distinguishing origination, gene duplications, virus-to-virus horizontal gene transfer (vHGT), and gene losses. We analyzed over 4,700 gene families from 195 genomes spanning all known viral orders. The evolutionary reconstruction suggests a history of extensive gene gains and losses during the evolution of these viruses, notably with vHGT contributing to gene gains at a comparable level to duplications and originations. The vHGT frequently occurred between phylogenetically closely related viruses, as well as between distantly related viruses with an overlapping host range. We observed a pattern of massive gene duplications that followed vHGTs for gene families that was potentially related to host range control and virus-host arms race. These results suggest that vHGT represents a previously overlooked, yet important, evolutionary force that integrates the evolutionary paths of multiple viruses and affects shaping of Nucleocytoviricota virus gene repertoires.},
}

@article {pmid39082809,
year = {2024},
author = {Kanno, K and Kuriki, R and Yasuno, Y and Shinada, T and Ito, T and Hemmi, H},
title = {Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0110624},
doi = {10.1128/aem.01106-24},
pmid = {39082809},
issn = {1098-5336},
abstract = {The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do.},
}

@article {pmid38823494,
year = {2024},
author = {Tang, C and Shen, S and Yang, W and Shi, Q and Ding, L and Han, R and Hu, F},
title = {Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation.},
journal = {International journal of antimicrobial agents},
volume = {64},
number = {2},
pages = {107228},
doi = {10.1016/j.ijantimicag.2024.107228},
pmid = {38823494},
issn = {1872-7913},
mesh = {*Ceftazidime/pharmacology ; *Azabicyclo Compounds/pharmacology ; *Drug Combinations ; *Plasmids/genetics ; Humans ; *Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Enterobacter cloacae/genetics/drug effects ; *Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/genetics/drug effects ; Klebsiella Infections/microbiology/drug therapy ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects ; },
abstract = {The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10[-3]-10[-5], while the mutation frequency of K. pneumoniae 5298 was 10[-6]-10[-8] at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.},
}

*Ceftazidime/pharmacology
*Azabicyclo Compounds/pharmacology
*Drug Combinations
*Plasmids/genetics
Humans
*Klebsiella pneumoniae/genetics/drug effects
*beta-Lactamases/genetics
*Anti-Bacterial Agents/pharmacology
*Microbial Sensitivity Tests
*Enterobacter cloacae/genetics/drug effects
*Mutation
*Drug Resistance, Multiple, Bacterial/genetics
Escherichia coli/genetics/drug effects
Klebsiella Infections/microbiology/drug therapy
Bacterial Proteins/genetics
Gene Transfer, Horizontal
Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects

@article {pmid39080678,
year = {2024},
author = {Rajput, M and Pandey, M and Dixit, R and Shukla, VK},
title = {Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis.},
journal = {World journal of surgical oncology},
volume = {22},
number = {1},
pages = {201},
pmid = {39080678},
issn = {1477-7819},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Gallbladder Neoplasms/genetics/pathology/virology ; Carcinogenesis/genetics ; RNA, Antisense/genetics ; Gene Expression Regulation, Neoplastic ; Transcriptome ; },
abstract = {BACKGROUND: Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.

METHODS: Transcriptomic data obtained from patients with gallbladder cancer (GBC) was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.

RESULTS: A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15 asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.

CONCLUSION: The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.},
}

Humans
*Gene Transfer, Horizontal
*Gallbladder Neoplasms/genetics/pathology/virology
Carcinogenesis/genetics
RNA, Antisense/genetics
Gene Expression Regulation, Neoplastic
Transcriptome

@article {pmid39079455,
year = {2024},
author = {Russell, SL and Penunuri, G and Condon, C},
title = {Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them.},
journal = {Seminars in cell & developmental biology},
volume = {165},
number = {},
pages = {1-12},
doi = {10.1016/j.semcdb.2024.07.001},
pmid = {39079455},
issn = {1096-3634},
abstract = {In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.},
}

@article {pmid39078126,
year = {2024},
author = {Ai, C and Cui, P and Liu, C and Wu, J and Xu, Y and Liang, X and Yang, Q and Tang, X and Zhou, S and Liao, H and Friman, V-P},
title = {Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0069524},
doi = {10.1128/aem.00695-24},
pmid = {39078126},
issn = {1098-5336},
abstract = {UNLABELLED: While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA.

IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.},
}

@article {pmid38598855,
year = {2024},
author = {Hsieh, SC and Peters, JE},
title = {Natural and Engineered Guide RNA-Directed Transposition with CRISPR-Associated Tn7-Like Transposons.},
journal = {Annual review of biochemistry},
volume = {93},
number = {1},
pages = {139-161},
doi = {10.1146/annurev-biochem-030122-041908},
pmid = {38598855},
issn = {1545-4509},
mesh = {*DNA Transposable Elements/genetics ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Transposases/metabolism/genetics ; Gene Editing/methods ; Bacteria/genetics ; Plasmids/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA-directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR-Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA-directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.},
}

*DNA Transposable Elements/genetics
*CRISPR-Cas Systems
*RNA, Guide, CRISPR-Cas Systems/genetics/metabolism
*Transposases/metabolism/genetics
Gene Editing/methods
Bacteria/genetics
Plasmids/metabolism/genetics
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid39073917,
year = {2024},
author = {Gao, L and Liu, L and Lv, AP and Fu, L and Lian, ZH and Nunoura, T and Hedlund, BP and Xu, QY and Wu, D and Yang, J and Ali, M and Li, MM and Liu, YH and Antunes, A and Jiang, HC and Cheng, L and Jiao, JY and Li, WJ and Fang, BZ},
title = {Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae147},
pmid = {39073917},
issn = {1751-7370},
abstract = {Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes (MAGs) from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.},
}

@article {pmid39071422,
year = {2024},
author = {Robinson, LR and Mcdevitt, CJ and Regan, MR and Quail, SL and Wadsworth, CB},
title = {In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39071422},
issn = {2692-8205},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; },
abstract = {Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. Small clusters of gonococcal isolates had commensal-like alleles at parC and parE, indicating recent cross-species recombination events.},
}

@article {pmid39071318,
year = {2024},
author = {Sloan, DB and Broz, AK and Kuster, SA and Muthye, V and Peñafiel-Ayala, A and Marron, JR and Lavrov, DV and Brieba, LG},
title = {Expansion of the MutS Gene Family in Plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.17.603841},
pmid = {39071318},
issn = {2692-8205},
abstract = {UNLABELLED: The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1 " is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6 / MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.

ONE-SENTENCE SUMMARY: Plants are distinguished from other eukaryotes by a functionally diverse complement of MutS proteins gained via a combination of gene duplication, endosymbiotic gene transfer, and horizontal gene transfer.},
}

@article {pmid38964386,
year = {2024},
author = {Shi, J and Sun, C and An, T and Jiang, C and Mei, S and Lv, B},
title = {Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects.},
journal = {The Science of the total environment},
volume = {947},
number = {},
pages = {174466},
doi = {10.1016/j.scitotenv.2024.174466},
pmid = {38964386},
issn = {1879-1026},
mesh = {*Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microplastics ; Anti-Bacterial Agents ; Bacteria/drug effects ; Genes, Bacterial ; },
abstract = {Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.},
}

*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Microplastics
Anti-Bacterial Agents
Bacteria/drug effects
Genes, Bacterial

@article {pmid39071313,
year = {2024},
author = {Yang, XY and Shen, Z and Wang, C and Nakanishi, K and Fu, TM},
title = {DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.20.604412},
pmid = {39071313},
issn = {2692-8205},
abstract = {Horizontal gene transfer is a key driver of bacterial evolution, but it also presents severe risks to bacteria by introducing invasive mobile genetic elements. To counter these threats, bacteria have developed various defense systems, including prokaryotic Argonautes (pAgo) and the D NA D efense M odule DdmDE system. Through biochemical analysis, structural determination, and in vivo plasmid clearance assays, we elucidate the assembly and activation mechanisms of DdmDE, which eliminates small, multicopy plasmids. We demonstrate that DdmE, a pAgo-like protein, acts as a catalytically inactive, DNA-guided, DNA-targeting defense module. In the presence of guide DNA, DdmE targets plasmids and recruits a dimeric DdmD, which contains nuclease and helicase domains. Upon binding to DNA substrates, DdmD transitions from an autoinhibited dimer to an active monomer, which then translocates along and cleaves the plasmids. Together, our findings reveal the intricate mechanisms underlying DdmDE-mediated plasmid clearance, offering fundamental insights into bacterial defense systems against plasmid invasions.},
}

@article {pmid39067739,
year = {2024},
author = {Chen, X and Song, X and Liang, Y and Wang, F and Pan, C and Wei, Z},
title = {Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124621},
doi = {10.1016/j.envpol.2024.124621},
pmid = {39067739},
issn = {1873-6424},
abstract = {Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.},
}

@article {pmid38920383,
year = {2024},
author = {Rakibova, Y and Dunham, DT and Seed, KD and Freddolino, L},
title = {Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae.},
journal = {mSphere},
volume = {9},
number = {7},
pages = {e0001124},
doi = {10.1128/msphere.00011-24},
pmid = {38920383},
issn = {2379-5042},
support = {R35 GM128637/GM/NIGMS NIH HHS/United States ; R01AI127652//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2018257700//National Science Foundation (NSF)/ ; AI134678//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; *Vibrio cholerae/genetics/pathogenicity/metabolism ; *Gene Expression Regulation, Bacterial ; *Cholera/microbiology ; DNA-Binding Proteins/genetics/metabolism ; Humans ; Transcription, Genetic ; Virulence ; Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.

IMPORTANCE: New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.},
}

*Bacterial Proteins/genetics/metabolism
*Vibrio cholerae/genetics/pathogenicity/metabolism
*Gene Expression Regulation, Bacterial
*Cholera/microbiology
DNA-Binding Proteins/genetics/metabolism
Humans
Transcription, Genetic
Virulence
Virulence Factors/genetics
Gene Transfer, Horizontal

@article {pmid39067603,
year = {2024},
author = {Miaomiao, L and Ikuro, K},
title = {Impact of chlorine disinfection on intracellular and extracellular antimicrobial resistance genes in wastewater treatment and water reclamation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175046},
doi = {10.1016/j.scitotenv.2024.175046},
pmid = {39067603},
issn = {1879-1026},
abstract = {Wastewater treatment plants and water reclamation facilities are reservoirs of antimicrobial resistance genes (ARGs). These ARGs are not limited solely to intracellular DNA (inARGs) but include extracellular DNA (exARGs) present in wastewater. The release of exARGs from cells can be exacerbated by treatment processes, including chlorine disinfection, which disrupts bacterial cells. Given the potential for exARGs to drive horizontal gene transfer and contribute to the proliferation of antimicrobial resistance, it is imperative to recognize these fractions as emerging environmental pollutants. In this study, we conducted a comprehensive year-long assessment of both inARGs and exARGs, further differentiating between dissolved exARGs (Dis_exARGs) and exARGs adsorbed onto particulate matter (Ads_exARGs), within a full-scale wastewater treatment and water reclamation facility. The results revealed that Ads_exARGs comprised up to 30 % of the total ARGs in raw sewage with high biomass content. Generally, treatments at low and high doses of chlorine increased the abundance of Dis_exARGs and Ads_exARGs. The fate of ARG levels that varied depending on the type of ARGs suggested variations in the susceptibility of the host bacteria to chlorination. Moreover, co-occurrence of several potential opportunistic pathogenic bacteria and ARGs were observed. Therefore, we propose higher doses of chlorination as a prerequisite for the effective removal of inARGs and exARGs.},
}

@article {pmid39066295,
year = {2024},
author = {Li, W and Tahiri, N},
title = {Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
pmid = {39066295},
issn = {1999-4915},
support = {326911//Fonds de recherche du Québec/ ; RGPIN-2022-04322//Natural Sciences and Engineering Research Council/ ; },
mesh = {*Chiroptera/virology ; Animals ; *Phylogeny ; *Coronavirus/genetics/classification/physiology ; Evolution, Molecular ; Host-Pathogen Interactions/genetics ; Spike Glycoprotein, Coronavirus/genetics/metabolism ; Host Specificity ; Coronavirus Infections/virology ; },
abstract = {Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.},
}

*Chiroptera/virology
Animals
*Phylogeny
*Coronavirus/genetics/classification/physiology
Evolution, Molecular
Host-Pathogen Interactions/genetics
Spike Glycoprotein, Coronavirus/genetics/metabolism
Host Specificity
Coronavirus Infections/virology

@article {pmid39061350,
year = {2024},
author = {Drane, K and Sheehan, M and Whelan, A and Ariel, E and Kinobe, R},
title = {The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061350},
issn = {2079-6382},
support = {2256.95982.2331//Townsville City Council, Townsville Australia/ ; },
abstract = {Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.},
}

@article {pmid39061343,
year = {2024},
author = {Fahy, S and O'Connor, JA and Sleator, RD and Lucey, B},
title = {From Species to Genes: A New Diagnostic Paradigm.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39061343},
issn = {2079-6382},
abstract = {Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.},
}

@article {pmid38032214,
year = {2023},
author = {Kubori, T},
title = {A two-component system serves as a central hub for connecting energy metabolism and plasmid dissemination in bacteria.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0247423},
pmid = {38032214},
issn = {2150-7511},
support = {//Takeda Science Foundation (TSF)/ ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/metabolism ; *Energy Metabolism/genetics ; *Conjugation, Genetic ; Bacterial Proteins/genetics/metabolism ; Type IV Secretion Systems/genetics/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Gene Expression Regulation, Bacterial ; },
abstract = {Mobile genetic elements such as conjugative plasmids play a key role in the acquisition of antibiotic resistance by pathogenic bacteria. Resistance genes on plasmids can be transferred between bacteria using specialized conjugation machinery. Acinetobacter baumannii, the most common bacterium associated with nosocomial infections, harbors a large conjugative plasmid that encodes a type IV secretion system (T4SS). Feng et al. recently found that the A. baumannii T4SS is specialized for plasmid transfer, suggesting that it may be involved in multidrug resistance (Z. Feng, L. Wang, Q. Guan, X. Chu, and Z.-Q. Luo, mBio e02276-23, 2023, https://doi.org/10.1128/mbio.02276-23), T4SS-encoding genes are shown to be controlled by a versatile GacA/S two-component regulatory system. GacA/S is also found to regulate genes involved in central metabolism. The coordinated regulation of metabolism and plasmid conjugation may be a bacterial strategy for adapting to selective pressure from antibiotics.},
}

*Plasmids/genetics
*Acinetobacter baumannii/genetics/metabolism
*Energy Metabolism/genetics
*Conjugation, Genetic
Bacterial Proteins/genetics/metabolism
Type IV Secretion Systems/genetics/metabolism
Drug Resistance, Multiple, Bacterial/genetics
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Gene Expression Regulation, Bacterial

@article {pmid39061274,
year = {2024},
author = {Ghazawi, A and Anes, F and Mouftah, S and Elbediwi, M and Baig, A and Alketbi, M and Almazrouei, F and Alhashmi, M and Alzarooni, N and Manzoor, A and Habib, I and Strepis, N and Nabi, A and Khan, M},
title = {Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/antibiotics13070592},
pmid = {39061274},
issn = {2079-6382},
support = {G00004620 and G00004164//United Arab Emirates University/ ; },
abstract = {Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.},
}

@article {pmid39060998,
year = {2024},
author = {Seth-Smith, H and Bommana, S and Dean, D and Read, TD and Marti, H},
title = {Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {724},
pmid = {39060998},
issn = {1471-2164},
support = {323530_177579//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {BACKGROUND: The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63).

RESULTS: We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream.

CONCLUSIONS: Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.},
}

@article {pmid39058093,
year = {2024},
author = {Peñil-Celis, A and Tagg, KA and Webb, HE and Redondo-Salvo, S and Francois Watkins, L and Vielva, L and Griffin, C and Kim, JY and Folster, JP and Garcillan-Barcia, MP and de la Cruz, F},
title = {Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0036524},
doi = {10.1128/msystems.00365-24},
pmid = {39058093},
issn = {2379-5077},
abstract = {Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.},
}

@article {pmid39056664,
year = {2024},
author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V},
title = {Database Bias in the Detection of Interdomain Horizontal Gene Transfer Events in Pezizomycotina.},
journal = {Biology},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/biology13070469},
pmid = {39056664},
issn = {2079-7737},
support = {PRG.BIO.23.14.01//Universidad de Las Américas/ ; },
abstract = {Horizontal gene transfer (HGT) is a widely acknowledged phenomenon in prokaryotes for generating genetic diversity. However, the impact of this process in eukaryotes, particularly interdomain HGT, is a topic of debate. Although there have been observed biases in interdomain HGT detection, little exploration has been conducted on the effects of imbalanced databases. In our study, we conducted experiments to assess how different databases affect the detection of interdomain HGT using proteomes from the Pezizomycotina fungal subphylum as our focus group. Our objective was to simulate the database imbalance commonly found in public biological databases, where bacterial and eukaryotic sequences are unevenly represented, and demonstrate that an increase in uploaded eukaryotic sequences leads to a decrease in predicted HGTs. For our experiments, four databases with varying proportions of eukaryotic sequences but consistent proportions of bacterial sequences were utilized. We observed a significant reduction in detected interdomain HGT candidates as the proportion of eukaryotes increased within the database. Our data suggest that the imbalance in databases bias the interdomain HGT detection and highlights challenges associated with confirming the presence of interdomain HGT among Pezizomycotina fungi and potentially other groups within Eukarya.},
}

@article {pmid39053184,
year = {2024},
author = {Checcucci, A and Buscaroli, E and Modesto, M and Luise, D and Blasioli, S and Scarafile, D and Di Vito, M and Bugli, F and Trevisi, P and Braschi, I and Mattarelli, P},
title = {The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116774},
doi = {10.1016/j.ecoenv.2024.116774},
pmid = {39053184},
issn = {1090-2414},
abstract = {The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.},
}

@article {pmid39052705,
year = {2024},
author = {Wan, Y and Myall, AC and Boonyasiri, A and Bolt, F and Ledda, A and Mookerjee, S and Weiße, AY and Getino, M and Turton, JF and Abbas, H and Prakapaite, R and Sabnis, A and Abdolrasouli, A and Malpartida-Cardenas, K and Miglietta, L and Donaldson, H and Gilchrist, M and Hopkins, KL and Ellington, MJ and Otter, JA and Larrouy-Maumus, G and Edwards, AM and Rodriguez-Manzano, J and Didelot, X and Barahona, M and Holmes, AH and Jauneikaite, E and Davies, F},
title = {Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {1},
pages = {e159-e170},
doi = {10.1093/infdis/jiae019},
pmid = {39052705},
issn = {1537-6613},
support = {//Faculty of Medicine, Siriraj Hospital, Mahidol University/ ; MR/T005254/1/MRC_/Medical Research Council/United Kingdom ; MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; EP/N014529///EPSRC Centre for Mathematics of Precision Healthcare/ ; //National Institute for Health Research/ ; //Imperial Biomedical Research Centre/ ; //Rosetrees Trust/ ; M683//Stoneygate Trust/ ; /WT_/Wellcome Trust/United Kingdom ; PSN109//Imperial College London/ ; //Imperial Health Charity/ ; //NIHR Health Protection Research Unit in Genomics and Enabling Data/ ; //NIHR Health Protection Research Unit/ ; NIHR200915//University of Oxford/ ; //UK Health Security Agency/ ; },
mesh = {Humans ; *Plasmids/genetics ; *beta-Lactamases/genetics ; *Enterobacteriaceae Infections/epidemiology/microbiology/transmission ; *Disease Outbreaks ; *Bacterial Proteins/genetics ; London/epidemiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Male ; Female ; Middle Aged ; Microbial Sensitivity Tests ; Adult ; Enterobacteriaceae/genetics/drug effects ; Aged ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; Colistin/pharmacology ; },
abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.

METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.

RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.

CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.},
}

Humans
*Plasmids/genetics
*beta-Lactamases/genetics
*Enterobacteriaceae Infections/epidemiology/microbiology/transmission
*Disease Outbreaks
*Bacterial Proteins/genetics
London/epidemiology
Anti-Bacterial Agents/pharmacology
Phylogeny
Genome, Bacterial
Male
Female
Middle Aged
Microbial Sensitivity Tests
Adult
Enterobacteriaceae/genetics/drug effects
Aged
Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification
Colistin/pharmacology

@article {pmid39052112,
year = {2024},
author = {Li, H and Liu, B and Li, M and Shen, M},
title = {Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39052112},
issn = {1614-7499},
abstract = {The excessive use of antibiotics, disinfectants, and drugs in livestock and poultry breeding has resulted in a rise in the presence of antibiotic resistance genes (ARGs). Antibiotic-resistant bacteria (ARB) and ARGs have been widely found in animal feces, farm wastewater, and farm air. ARGs can not only spread across media through adsorption and migration, but also transfer resistance across bacterial genera through horizontal gene transfer. Livestock breeding has become a fixed and unavoidable source of ARGs in the environment. Existing technologies for controlling ARGs, such as composting, disinfection, and sewage treatment, are not efficient in removing ARB and ARGs from waste. Furthermore, the remaining ARGs still possess a strong capacity for dissemination. At present, antibiotics used in animal husbandry are difficult to replace in a short period of time. The growth and potential risks of resistance genes in livestock and poultry breeding sources in the receiving environment are not yet clear. In this paper, we summarize the current situation of ARGs in the livestock and poultry breeding environment. We also explain the key environmental processes, main influencing factors, and corresponding ecological risks associated with ARGs in this environment. The advantages and disadvantages of current technologies for the removal of ARGs are primarily discussed. There is a particular emphasis on clarifying the spatiotemporal evolution patterns and environmental process mechanisms of ARGs, as well as highlighting the importance and urgency of developing efficient pollution control technologies.},
}

@article {pmid39052074,
year = {2024},
author = {Allman, ES and Baños, H and Garrote-Lopez, M and Rhodes, JA},
title = {Identifiability of Level-1 Species Networks from Gene Tree Quartets.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {9},
pages = {110},
pmid = {39052074},
issn = {1522-9602},
support = {DMS-2051760//National Science Foundation/ ; DMS-2331660//National Science Foundation/ ; P20GM103395//Foundation for the National Institutes of Health/ ; },
mesh = {*Phylogeny ; *Mathematical Concepts ; *Models, Genetic ; *Gene Transfer, Horizontal ; Evolution, Molecular ; Genetic Speciation ; Gene Regulatory Networks ; Computer Simulation ; Hybridization, Genetic ; },
abstract = {When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several recently proposed methods are based on quartet concordance factors-the probabilities that a tree relating a gene sampled from the species displays the possible 4-taxon relationships. Building on earlier results, we investigate what level-1 network features are identifiable from concordance factors under the network multispecies coalescent model. We obtain results on both topological features of the network, and numerical parameters, uncovering a number of failures of identifiability related to 3-cycles in the network. Addressing these identifiability issues is essential for designing statistically consistent inference methods.},
}

*Phylogeny
*Mathematical Concepts
*Models, Genetic
*Gene Transfer, Horizontal
Evolution, Molecular
Genetic Speciation
Gene Regulatory Networks
Computer Simulation
Hybridization, Genetic

@article {pmid39044460,
year = {2024},
author = {Roulet, ME and Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV},
title = {Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19984},
pmid = {39044460},
issn = {1469-8137},
support = {PICT2020-01018//Fondo para la Investigación Científica y Tecnológica/ ; 06/A092-T1//Secretaría de Investigación, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; },
abstract = {The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.},
}

@article {pmid39042422,
year = {2024},
author = {Alves, J and Dry, I and White, JH and Dryden, DTF and Lynskey, NN},
title = {Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {7},
pages = {},
doi = {10.1099/mic.0.001465},
pmid = {39042422},
issn = {1465-2080},
mesh = {*Recombinant Proteins/genetics/metabolism/isolation & purification ; Viral Proteins/genetics/metabolism ; Bacteriophages/genetics/enzymology ; Streptococcus pyogenes/genetics/enzymology/metabolism ; Transformation, Bacterial ; Deoxyribonucleases, Type I Site-Specific/metabolism/genetics ; Gene Expression ; Escherichia coli/genetics/metabolism ; },
abstract = {DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.},
}

*Recombinant Proteins/genetics/metabolism/isolation & purification
Viral Proteins/genetics/metabolism
Bacteriophages/genetics/enzymology
Streptococcus pyogenes/genetics/enzymology/metabolism
Transformation, Bacterial
Deoxyribonucleases, Type I Site-Specific/metabolism/genetics
Gene Expression
Escherichia coli/genetics/metabolism

@article {pmid39039821,
year = {2024},
author = {Bohl, V and Mogk, A},
title = {When the going gets tough, the tough get going-Novel bacterial AAA+ disaggregases provide extreme heat resistance.},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16677},
doi = {10.1111/1462-2920.16677},
pmid = {39039821},
issn = {1462-2920},
support = {MO970/7-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacterial Proteins/metabolism/genetics ; HSP70 Heat-Shock Proteins/metabolism/genetics ; Thermotolerance ; Hot Temperature ; Bacteria/genetics/metabolism ; Endopeptidase Clp/metabolism/genetics ; Heat-Shock Proteins/metabolism/genetics ; Heat-Shock Response ; },
abstract = {Heat stress can lead to protein misfolding and aggregation, potentially causing cell death due to the loss of essential proteins. Bacteria, being particularly exposed to environmental stress, are equipped with disaggregases that rescue these aggregated proteins. The bacterial Hsp70 chaperone DnaK and the ATPase associated with diverse cellular activities protein ClpB form the canonical disaggregase in bacteria. While this combination operates effectively during physiological heat stress, it is ineffective against massive aggregation caused by temperature-based sterilization protocols used in the food industry and clinics. This leaves bacteria unprotected against these thermal processes. However, bacteria that can withstand extreme, man-made stress conditions have emerged. These bacteria possess novel ATPase associated with diverse cellular activities disaggregases, ClpG and ClpL, which are key players in extreme heat resistance. These disaggregases, present in selected Gram-negative or Gram-positive bacteria, respectively, function superiorly by exhibiting increased thermal stability and enhanced threading power compared to DnaK/ClpB. This enables ClpG and ClpL to operate at extreme temperatures and process large and tight protein aggregates, thereby contributing to heat resistance. The genes for ClpG and ClpL are often encoded on mobile genomic islands or conjugative plasmids, allowing for their rapid spread among bacteria via horizontal gene transfer. This threatens the efficiency of sterilization protocols. In this review, we describe the various bacterial disaggregases identified to date, characterizing their commonalities and the specific features that enable these novel disaggregases to provide stress protection against extreme stress conditions.},
}

*Bacterial Proteins/metabolism/genetics
HSP70 Heat-Shock Proteins/metabolism/genetics
Thermotolerance
Hot Temperature
Bacteria/genetics/metabolism
Endopeptidase Clp/metabolism/genetics
Heat-Shock Proteins/metabolism/genetics
Heat-Shock Response

@article {pmid39039101,
year = {2024},
author = {Brown, CL and Maile-Moskowitz, A and Lopatkin, AJ and Xia, K and Logan, LK and Davis, BC and Zhang, L and Vikesland, PJ and Pruden, A},
title = {Author Correction: Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6166},
doi = {10.1038/s41467-024-50577-6},
pmid = {39039101},
issn = {2041-1723},
}