@article {pmid40325439,
year = {2025},
author = {Urban, JM and Gerbi, SA and Spradling, AC},
title = {Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {443},
pmid = {40325439},
issn = {1471-2164},
support = {NIH/GM121455/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.

RESULTS: We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.

CONCLUSIONS: The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.},
}

@article {pmid40127991,
year = {2025},
author = {Barretto, LAF and Fowler, CC},
title = {Multifaceted Evolution of the PhoPQ Two-Component System in Salmonella enterica Enhanced the Expression of Horizontally Acquired Virulence Genes.},
journal = {Molecular microbiology},
volume = {123},
number = {5},
pages = {464-478},
doi = {10.1111/mmi.15355},
pmid = {40127991},
issn = {1365-2958},
support = {RGPIN-2020-03964//Natural Sciences and Engineering Research Council of Canada/ ; //NSREC CGS-M Scholarship/ ; //University of Alberta Faculty of Science/ ; },
mesh = {*Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Virulence/genetics ; *Salmonella enterica/genetics/pathogenicity/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; *Virulence Factors/genetics ; Gene Transfer, Horizontal ; },
abstract = {For a bacterium to adapt to a new environmental niche, its regulatory networks must evolve to effectively sense and respond to cues within that niche. For bacterial pathogens, which encounter harsh and dynamic host niches that require efficient coordination between detecting host cues and regulating virulence genes, this process is a key aspect of how virulence properties evolve. Here, we investigate how a widely conserved two-component regulatory system (TCS), PhoP/PhoQ (PhoPQ), evolved in Salmonella enterica to adopt a new role as a master regulator of gene expression within its species-specific intracellular niche: the Salmonella-containing vacuole (SCV). By comparing Salmonella PhoPQ with the closely related Escherichia coli PhoPQ ortholog, we demonstrate that optimizing virulence gene expression in Salmonella required a multifaceted evolution of several PhoPQ functional domains and establish that distinct genetic differences and mechanisms enhance virulence gene expression for different inducing cues. Interestingly, we find that the increased activity of the Salmonella PhoPQ system has a much more profound impact on the expression of H-NS-repressed, horizontally acquired virulence genes than on the ancestral members of the PhoP regulon. We observe that the PhoPQ systems of other related bacteria exhibit activity levels similar to the E. coli system, suggesting that the differences we observe are the result of Salmonella-specific adaptations that produced a more active PhoPQ system when encountering SCV conditions. Collectively, this study offers a window into the evolutionary adaptations of a TCS that enable it to assume an expanded regulatory role in a unique environment.},
}

*Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Virulence/genetics
*Salmonella enterica/genetics/pathogenicity/metabolism
Escherichia coli/genetics/metabolism
Escherichia coli Proteins/genetics/metabolism
Evolution, Molecular
*Virulence Factors/genetics
Gene Transfer, Horizontal

@article {pmid40319560,
year = {2025},
author = {Gross, N and Brodard, I and Overesch, G and Kittl, S},
title = {Genetic basis of β-lactam resistance in Corynebacterium auriscanis and association with otitis externa in dogs and cats.},
journal = {Veterinary microbiology},
volume = {305},
number = {},
pages = {110526},
doi = {10.1016/j.vetmic.2025.110526},
pmid = {40319560},
issn = {1873-2542},
abstract = {Corynebacterium (C.) auriscanis is an opportunistic pathogen regularly isolated from canine otitis externa, an important condition often hard to treat. We found a surprisingly high prevalence of β-lactam resistant isolates of C. auriscanis (47 %), even though β-lactams are not routinely used for otitis externa treatment in Switzerland. To determine the genetic base of this phenotype, a selection of isolates of C. auriscanis with high and low minimal inhibitory concentration values were subjected to whole genome sequencing. Comparative analysis revealed a gene cassette containing three genes (hdfR encoding a LysR-family transcriptional regulator, blaB encoding a β-lactamase related protein and pbp2c encoding a D,D-transpeptidase) as the likely resistance-encoding determinant in the isolates from otitis externa. This locus had previously been described in C. jeikeium as well as C. diphtheriae and was associated with mobile genetic elements. In our six C. auriscanis isolates the pbp2c locus was always associated with the same IS3 family transposase, an association also found on C. diphtheriae plasmid CP091096, indicating horizontal gene transfer between species. To elucidate the function of the three genes in the pbp2c locus, we constructed plasmids with different combinations of these genes, transformed β-lactam sensitive isolates with the plasmids and tested resistance in the mutants phenotypically. By doing so we confirmed Pbp2c to be the primary factor conferring β-lactam resistance and HdfR and BlaB being important for expression and regulation. Interestingly, resistance to all β-lactams including carbapenems was constitutive in one C. auriscanis transformant while an induction effect was visible for the other transformed C. auriscanis strain, C. glutamicum and C. rouxii as previously described for C. jeikeium. Therefore, testing of β-lactam resistance should be done in combination including induction in Corynebacterium spp.},
}

@article {pmid40318462,
year = {2025},
author = {Zhang, T and Fan, L and Zhang, YN},
title = {Antibiotic resistance genes in aquatic systems: Sources, transmission, and risks.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {284},
number = {},
pages = {107392},
doi = {10.1016/j.aquatox.2025.107392},
pmid = {40318462},
issn = {1879-1514},
abstract = {The widespread use of antibiotics has significantly contributed to the spread of antibiotic resistance genes (ARGs), which have become a major challenge to global ecological and public health. Antibiotic resistance not only proliferates in clinical settings but also persists in aquatic systems, where its residues and cross-domain spread pose a dual threat to both ecosystems and human health. ARGs spread rapidly within microbial communities through horizontal gene transfer (HGT) and vertical gene transfer (VGT). Aquatic systems are the key transmission medium. This review summarizes recent studies on the Source-Transport-Sink dynamics of ARGs in aquatic environments, along with their environmental and health risk assessments, with a particular focus on the potential ecotoxicity of ARGs transmission. It also examines the distribution characteristics of ARGs across different regions and the ecological risk assessment methods employed, highlighting the limitations of existing models when addressing the complex behaviors of ARGs. By analyzing the potential hazards of ARGs to aquatic ecosystems and public health, this article aims to provide a scientific foundation for future research and the development of public policies.},
}

@article {pmid40314822,
year = {2025},
author = {Bell I, PJ and Muniyan, R},
title = {Synergistic pathogenesis: exploring biofilms, efflux pumps and secretion systems in Acinetobacter baumannii and Staphylococcus aureus.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {134},
pmid = {40314822},
issn = {1432-072X},
mesh = {*Biofilms/growth & development ; *Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics ; Humans ; *Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial ; Cross Infection/microbiology ; *Membrane Transport Proteins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Acinetobacter Infections/microbiology ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health crisis, particularly among ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. Among them, A. baumannii and S. aureus are major contributors to nosocomial infections, with high prevalence in intensive care units and immunocompromised patients. Their ability to resist multiple antibiotic classes complicates treatment strategies, leading to increased morbidity and mortality. Key resistance mechanisms, including biofilm formation, efflux pump activity, and horizontal gene transfer, enhance their survival and persistence. Furthermore, interactions during polymicrobial infections intensify disease severity through synergistic effects that promote both virulence and resistance. The epidemiological burden of these pathogens highlights the urgent need for novel antimicrobial strategies and targeted interventions. This review explores their virulence factors, resistance mechanisms, pathogenic interactions, and clinical implications, emphasizing the necessity of innovative therapeutic approaches to combat their growing threat.},
}

*Biofilms/growth & development
*Acinetobacter baumannii/pathogenicity/drug effects/physiology/genetics
Humans
*Staphylococcus aureus/pathogenicity/drug effects/physiology/genetics/metabolism
Anti-Bacterial Agents/pharmacology
Virulence Factors/metabolism/genetics
Staphylococcal Infections/microbiology/drug therapy
Drug Resistance, Multiple, Bacterial
Cross Infection/microbiology
*Membrane Transport Proteins/metabolism/genetics
Bacterial Proteins/metabolism/genetics
Acinetobacter Infections/microbiology

@article {pmid40311358,
year = {2025},
author = {Gómez-Brandón, M and Aira, M and Probst, M and Liu, N and Zhang, Z and Zhu, YG and Domínguez, J},
title = {Earthworms attenuate antibiotic resistance genes and mobile genetic elements during vermicomposting of sewage sludge.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125562},
doi = {10.1016/j.jenvman.2025.125562},
pmid = {40311358},
issn = {1095-8630},
abstract = {Sewage sludge is among the richest reservoirs of antibiotic resistance genes (ARGs) that may spread to urban environment. Further investigation is warranted for removal of sludge-borne ARGs in large-scale vermicomposting systems. Under this scenario, there is the necessity to unveil the role of the widely-used earthworm species Eisenia andrei, since the current body of literature mostly focuses on E. fetida. The present study sought to evaluate the changes in sludge-borne ARGs and mobile genetic elements in a pilot-scale vermireactor in the presence of E. andrei in response to both gut- and cast-associated processes (GAPs and CAPs, respectively), by coupling high-throughput quantitative PCR and Illumina sequencing. After gut transit, large decreases in the relative abundances and number of the genes conferring resistance to major antibiotic classes, including some specific genes classified as of potentially high risk to human health, were recorded in the fresh casts. Likewise, genes encoding resistance to heavy metals were about nine-times lower in the egested materials than in the initial sludge. Genes coding for integrases or insertional sequences also exhibited reduced abundance as a result of GAP and CAP processes, suggesting that vermicompost appears to be less prone to horizontal gene transfer than untreated sludge. These findings provide evidence about the capacity of the earthworm E. andrei to diminish the risk of ARG spread during vermicomposting, reinforcing its potential for bioremediation purposes by transforming large quantities of waste into an improved fertiliser. This is crucial to propel vermicomposting technology forward and achieve transition toward net zero-waste process.},
}

@article {pmid40310292,
year = {2025},
author = {Alejandre-Sixtos, JE and Aguirre-Martínez, K and Cruz-López, J and Mares-Rivera, A and Álvarez-Martínez, SM and Zamorano-Sánchez, D},
title = {Insights on the regulation and function of the CRISPR/Cas transposition system located in the pathogenicity island VpaI-7 from Vibrio parahaemolyticus RIMD2210633.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0016925},
doi = {10.1128/iai.00169-25},
pmid = {40310292},
issn = {1098-5522},
abstract = {CRISPR/Cas-mediated transposition is a recently recognized strategy for horizontal gene transfer in a variety of bacterial species. However, our understanding of the factors that control their function in their natural hosts is still limited. In this work, we report our initial genetic characterization of the elements associated with the CRISPR/Cas-transposition machinery (CASTm) from Vibrio parahaemolyticus (VpaCASTm), which are encoded within the pathogenicity island VpaI-7. Our results revealed that the components of the VpaCASTm and their associated CRISPR arrays (VpaCAST system) are transcriptionally active in their native genetic context. Furthermore, we were able to detect the presence of polycistrons and several internal promoters within the loci that compose the VpaCAST system. Our results also suggest that the activity of the promoter of the atypical CRISPR array is not repressed by the baseline activity of its known regulator VPA1391 in V. parahaemolyticus. In addition, we found that the activity of the promoter of tniQ was modulated by a regulatory cascade involving ToxR, LeuO, and H-NS. Since it was previously reported that the activity of the VpaCAST system was less efficient than that of the VchCAST system at promoting transposition of a miniaturized CRISPR-associated transposon (mini-CAST) in Escherichia coli, we analyzed if the transposition efficiency mediated by the VpaCAST system could be enhanced inside its natural host V. parahaemolyticus. We provide evidence that this might be the case, suggesting that there could be host induction factors in V. parahaemolyticus that could enable more efficient transposition of CASTs.IMPORTANCEMobile genetic elements such as transposons play important roles in the evolutionary trajectories of bacterial genomes. The success of transposon dissemination depends on their ability to carry selectable markers that improve the fitness of the host cell or loci with addictive traits such as the toxin-antitoxin systems. Here we aimed to characterize a transposon from Vibrio parahaemolyticus that carries and could disseminate multiple virulence factors. This transposon belongs to a recently discovered family of transposons whose transposition is guided by crRNA. We showed that the transposition machinery of this transposon is transcribed in V. parahaemolyticus and that there are likely host-associated factors that favor transposition in the natural host V. parahaemolyticus over transposition in Escherichia coli.},
}

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

*Rhizosphere
*Arsenic/metabolism
Oxidation-Reduction
*Oryza/microbiology/virology/metabolism
Soil Microbiology
*Lysogeny/genetics
Microbiota/genetics
Gene Transfer, Horizontal
Metagenome
Plant Roots/microbiology/virology
Oxidoreductases/genetics/metabolism
Metabolic Reprogramming

@article {pmid40306591,
year = {2025},
author = {Sam-On, MFS and Mustafa, S and Mohd Hashim, A and Abdul Malek, AZ},
title = {Probiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.},
journal = {Microbial pathogenesis},
volume = {205},
number = {},
pages = {107645},
doi = {10.1016/j.micpath.2025.107645},
pmid = {40306591},
issn = {1096-1208},
abstract = {Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.},
}

@article {pmid40306109,
year = {2025},
author = {Huang, X and Hou, Y and Zhao, M and Chen, J and Zhu, Z and Liu, H and Wang, M and Hua, L and Chen, H and Wu, B and Peng, Z},
title = {Identification of a broad-spectrum lytic Bordetella phage and assessments of its potential for combating Bordetella infections.},
journal = {Virology},
volume = {608},
number = {},
pages = {110545},
doi = {10.1016/j.virol.2025.110545},
pmid = {40306109},
issn = {1096-0341},
abstract = {Bordetella bronchiseptica (Bb) is a zoonotic respiratory pathogen that frequently causes infections in farming and companion animals, posing threats to agricultural economics and public health. However, Bb strains are intrinsically resistant to several antibiotics commonly used to treat respiratory infections. Phage therapy has been recognized as a promising strategy to combat bacterial infections. In this study, a novel Bordetella phage, designated PY223, was isolated using Bb strains as indicators. Genome network analysis with different phages showed PY223 was related to 15 viral clusters but was not included in any of these clusters. PY223 did not carry any known genes involved in lysogeny and/or horizontal gene transfer. Host range analysis showed that PY223 exhibited the capacity to lyse 70 Bb strains isolated from pigs and/or cats. Measurement of the one-step growth curve showed that PY223 had an incubation period of 10 min and a rapid growth period of 80 min. The burst size was estimated to be approximately 10[9] PFU/cell. In addition, PY223 displayed the capacity to inhibit the growth of Bb for up to 17 h. PY223 was stable under environmental temperatures ranging from 4 °C to 60 °C and/or pH values between 5.0 and 9.0. It remained stable even when exposed to UV light for 30 min. Notably, PY223 effectively eliminated Bb biofilms, inhibited the growth of prophage-harboring Bb strains, and cleared Bb from the environment. In vivo testing in mouse models highlighted its excellent potential for treating respiratory Bordetella infections.},
}

@article {pmid40304893,
year = {2025},
author = {Domingues, S and Lima, T and Escobar, C and Plantade, J and Charpentier, X and da Silva, GJ},
title = {Large DNA fragment ISEc9-mediated transposition during natural transformation allows interspecies dissemination of antimicrobial resistance genes.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40304893},
issn = {1435-4373},
abstract = {PURPOSE: Antimicrobial resistance poses a significant global health challenge, contributing to a lack of effective therapeutic agents, especially against Gram-negative bacteria. Resistance dissemination is accelerated by horizontal gene transfer (HGT) mechanisms. The extended-spectrum beta lactamases CTX-M confer resistance to several beta-lactams, are usually embedded into plasmids and thought to be mainly disseminated by conjugation. However, an increasing number of isolates carry these enzyme-encoding genes in the chromosome, suggesting that they can spread by other means of HGT. In this study, we aimed to test the involvement of natural transformation in the chromosomal acquisition of a blaCTX-M gene.

METHODS: Natural transformation assays were performed during motility on wet surfaces. Acquisition of foreign DNA by transformants was screened by antimicrobial susceptibility testing, polymerase-chain reaction (PCR) and whole genome sequencing (WGS).

RESULTS: Acinetobacter baumannii A118, a naturally competent clinical strain, was transformed with naked DNA from Salmonella enterica serovar Typhimurium Sal25, which was isolated from swine meat. The transformation occurred at low frequency (2.7 × 10[- 8] ± 2.04 × 10[- 8] transformants per recipient) and blaCTX-M was acquired in one transformant, which was named ACI. WGS of the transformant revealed the acquisition of the blaCTX-M-32 as part of a ca. 36 Kb DNA fragment through an ISEc9-mediated transposition event; various mobile genetic elements and other resistance genes were co-transferred. The blaCTX-M-32 gene was subsequently transferred within A. baumannii at a higher frequency (1.8 × 10[- 6] ± 2.49 × 10[- 6] transformants per recipient).

CONCLUSION: Our results highlight the importance of natural transformation events in the dissemination of antimicrobial resistance genes and mobile genetic elements between and within species.},
}

@article {pmid40304813,
year = {2025},
author = {Qin, S and Wang, H and Wang, M and Shao, B and Ma, C and Yang, B and Jin, X},
title = {Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae).},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {96},
pmid = {40304813},
issn = {1438-7948},
support = {2022YFF1301704)//National Key Research and Development Program of China/ ; },
mesh = {*Orchidaceae/genetics/classification ; *Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {In this study, the mitogenomes of nine species in the subfamily Cypripedioideae were newly sequenced and assembled using both short and long reads for evolutionary analyses. Complete multi-chromosomal mitogenomes were obtained for Cypripedium subtropicum, C. henryi, Phragmipedium humboldtii, Phr. kovachii, and Paphiopedilum micranthum, and draft assemblies were obtained for four additional Paphiopedilum species. Thirty-nine protein-coding genes were annotated and shared in nine sampled species. sdh4 was discovered in all species of Cypripedioideae, and rpl10 was detected in four species of Paphiopedilum. These two genes might have been horizontally transferred from non-orchid plants at different times. Approximately 101 to 998 repeat sequences were identified with total lengths of 417,136 to 785,960 bp in the mitogenomes of Cypripedioideae. There were 634 and 662 RNA editing sites in C. subtropicum and Pa. gratrixianum, respectively, and C-to-U editing was dominant. The nad and ccm genes exhibited high frequencies of RNA editing. Our study revealed the complexity of orchid mitogenomes, including evidence for the horizontal transfer of rpl10 and sdh4.},
}

*Orchidaceae/genetics/classification
*Evolution, Molecular
*Genome, Mitochondrial
Phylogeny

@article {pmid40303475,
year = {2025},
author = {Lu, J and Zhang, R and Yu, Y and Lou, H and Li, D and Bao, Q and Feng, C},
title = {Identification of a novel chromosome-encoded fosfomycin resistance gene fosC3 in Aeromonas caviae.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1577167},
pmid = {40303475},
issn = {1664-302X},
abstract = {BACKGROUND: Owing to the rapid emerging of multidrug-, even pandrug-resistant pathogens, and lack of new antibiotics, the older antibiotic, fosfomycin, has been reused in recent years in the clinical practice, especially for treatment of uropathogen infections. With the increased use of fosfomycin, bacterial resistance to it has also increased drastically. Elucidating the resistance mechanism to the antimicrobial has become an urgent task.

METHODS: The putative fosfomycin resistance gene fosC3 was cloned, and minimal inhibitory concentrations were determined by the agar dilution method. Enzyme kinetic parameters were measured by high-performance liquid chromatography. Bioinformatics analysis was applied to understand the evolutionary characteristics of FosC3.

RESULTS: The A. caviae strain DW0021 exhibited high level resistance to several antimicrobials including kanamycin, streptomycin, chloramphenicol, florfenicol, tetracycline, and especially higher to fosfomycin (> 1,024 μg/mL), while genome annotation indicated that no function-characterized resistance gene was associated with fosfomycin resistance. A novel functional gene designated fosC3 responsible for fosfomycin resistance was identified in the chromosome of A. caviae DW0021. Among the function-characterized proteins, FosC3 shared the highest amino acid similarity of 58.65% with FosC2. No mobile genetic element (MGE) was found surrounding the fosC3 gene. The recombinant pMD19-fosC3/DH5α displayed a MIC value of 32 μg/mL to fosfomycin, which revealed a 128-fold increase of MIC value to fosfomycin compared to the control pMD19/E. coli DH5α (0.25 μg/mL). FosC3 was phylogenetically close to FosC2 and exhibited a k cat and K m of 82,442 ± 1,475 s[-1], 70.99 ± 4.31 μM, respectively, and a catalytic efficiency of (1.2 ± 0.3) × 10[3] μM[-1]·s[-1].

CONCLUSION: In this work, a novel functional fosfomycin thiol transferase, FosC3, which shared the highest protein sequence similarity with FosC2, was identified in A. caviae. The fosfomycin inactivation enzyme FosC3 could effectively inactivate fosfomycin by chemical modification. It is implied that such mechanism facilitates A. caviae to respond to fosfomycin exposure, thereby enhancing survival. However, fosC3 was not related with any MGE, which differs from many other fosfomycin thiol transferase genes. As a result, fosC3 is not expected to be transmitted to other species through horizontal gene transfer mechanism. Our findings will contribute to the resistance mechanism of the common pathogenic A. caviae.},
}

@article {pmid40303018,
year = {2024},
author = {Jia, Y and Zheng, Z and Yang, B and Zhang, H and Wang, Z and Liu, Y},
title = {A Broad-Spectrum Horizontal Transfer Inhibitor Prevents Transmission of Plasmids Carrying Multiple Antibiotic Resistance Genes.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {7063673},
pmid = {40303018},
issn = {1865-1682},
mesh = {*Gene Transfer, Horizontal/drug effects ; *Plasmids/genetics/drug effects ; *Zidovudine/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Animals ; *Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of antimicrobial resistance (AMR) severely degrades the performance of antibiotics and constantly paralyzes the global health system. In particular, plasmid-mediated transfer of antibiotic resistance genes (ARGs) across bacteria is recognized as the primary driver. Therefore, antiplasmid transfer approaches are urgently warranted to resolve this intractable problem. Herein, we demonstrated the potential of azidothymidine (AZT), an FDA-approved anti-HIV drug, as a broad-spectrum horizontal transfer inhibitor to effectively prevent the transmission of multiple ARGs, including mcr-1, bla NDM-5, and tet(X4), both in vitro and in vivo. It was also noteworthy that the inhibitory effect of AZT was proved to be valid within and across bacterial genera under different mating conditions. Mechanistic studies revealed that AZT dissipated bacterial proton motive force, which was indispensable for ATP synthesis and flagellar motility. In addition, AZT downregulated bacterial secretion systems involving general and type IV secretion systems (T4SS). Furthermore, the thymidine kinase, which is associated with DNA synthesis, turned out to be the potential target of AZT. Collectively, our work demonstrates the broad inhibitory effect of AZT in preventing ARGs transmission, opening new horizons for controlling AMR.},
}

*Gene Transfer, Horizontal/drug effects
*Plasmids/genetics/drug effects
*Zidovudine/pharmacology
*Anti-Bacterial Agents/pharmacology
Animals
*Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40302206,
year = {2025},
author = {Drebes Dörr, NC and Lemopoulos, A and Blokesch, M},
title = {Exploring Mobile Genetic Elements in Vibrio cholerae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf079},
pmid = {40302206},
issn = {1759-6653},
abstract = {Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and non-pandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/anti-plasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.},
}

@article {pmid40301684,
year = {2025},
author = {Wagner, TM and Torres-Puig, S and Yimthin, T and Irobalieva, RN and Heller, M and Kaessmeyer, S and Démoulins, T and Jores, J},
title = {Extracellular vesicles of minimalistic Mollicutes as mediators of immune modulation and horizontal gene transfer.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {674},
pmid = {40301684},
issn = {2399-3642},
mesh = {*Extracellular Vesicles/immunology/metabolism ; *Gene Transfer, Horizontal ; Animals ; Cattle ; Plasmids/genetics ; *Tenericutes/genetics/immunology ; Mycoplasma/genetics/immunology ; Proteomics ; Mycoplasma mycoides/genetics/immunology ; *Immunomodulation ; },
abstract = {Extracellular vesicles (EVs) are central components of bacterial secretomes, including the small, cell wall-less Mollicutes. Although EV release in Mollicutes has been reported, EV proteomic composition and function have not been explored yet. We developed a protocol for isolating EVs of the pathogens Mycoplasma mycoides subsp. capri (Mmc) and Mycoplasma (Mycoplasmopsis) bovis and examined their functionality. Proteomic analysis demonstrated that EVs mirror the proteome of the EV-producing bacteria. EVs exhibited nuclease activity, effectively digesting both circular and linear DNA. Notably, M. bovis EVs elicited immune responses in bovine primary blood cells, like those induced by live M. bovis. Our findings reveal that EVs can carry plasmids and enable their horizontal transfer, known as vesiduction. Specifically, the natural plasmid pKMK1, with an unknown transmission route, was detected in EVs of Mmc 152/93 and the tetM-containing pIVB08 plasmid was associated with EVs released by an Mmc GM12 strain carrying this plasmid. pIVB08 could be transferred via homo- and heterologous vesiduction to Mmc, M. capricolum subsp. capricolum and M. leachii. Vesiduction was impeded by membrane disruption but resisted DNase and Proteinase K treatment, suggesting that EVs protect their cargo. These findings enhance our understanding of Mollicutes EVs, particularly in host interactions and horizontal gene transfer.},
}

*Extracellular Vesicles/immunology/metabolism
*Gene Transfer, Horizontal
Animals
Cattle
Plasmids/genetics
*Tenericutes/genetics/immunology
Mycoplasma/genetics/immunology
Proteomics
Mycoplasma mycoides/genetics/immunology
*Immunomodulation

@article {pmid40301564,
year = {2025},
author = {Xue, W and Hong, J and Zhao, R and Yao, H and Zhang, Y and Dai, Z and Wang, T},
title = {Spatial entropy drives the maintenance and dissemination of transferable plasmids.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40301564},
issn = {1744-4292},
support = {2024YFA0920200//MOST | National Key Research and Development Program of China (NKPs)/ ; 32470701//MOST | National Natural Science Foundation of China (NSFC)/ ; HSE499011086//Shenzhen Institute of Synthetic Biology (iSynBio)/ ; },
abstract = {The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.},
}

@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}

*Geologic Sediments/microbiology
*Vibrionaceae/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
Japan
*Seawater/microbiology
Genetic Variation

@article {pmid40300599,
year = {2025},
author = {Ba, F and Zhang, Y and Wang, L and Ji, X and Liu, WQ and Ling, S and Li, J},
title = {Integrase enables synthetic intercellular logic via bacterial conjugation.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101268},
doi = {10.1016/j.cels.2025.101268},
pmid = {40300599},
issn = {2405-4720},
abstract = {Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.},
}

@article {pmid40298586,
year = {2025},
author = {Niño-Vega, GA and Ortiz-Ramírez, JA and López-Romero, E},
title = {Novel Antibacterial Approaches and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298586},
issn = {2079-6382},
abstract = {The increase in multidrug-resistant organisms worldwide is a major public health threat driven by antibiotic overuse, horizontal gene transfer (HGT), environmental drivers, and deficient infection control in hospitals. In this article, we discuss these factors and summarize the new drugs and treatment strategies suggested to combat the increasing challenges of multidrug-resistant (MDR) bacteria. New treatments recently developed involve targeting key processes involved in bacterial growth, such as riboswitches and proteolysis, and combination therapies to improve efficacy and minimize adverse effects. It also tackles the challenges of the Gram-negative bacterial outer membrane, stressing that novel strategies are needed to evade permeability barriers, efflux pumps, and resistance mechanisms. Other approaches, including phage therapy, AMPs, and AI in drug discovery, are also discussed as potential alternatives. Finally, this review points out the urgency for continued research and development (R&D), industry-academic partnerships, and financial engines to ensure that MDR microbes do not exceed the value of antibacterial therapies.},
}

@article {pmid40298491,
year = {2025},
author = {Karampatakis, T and Tsergouli, K and Behzadi, P},
title = {Carbapenem-Resistant Pseudomonas aeruginosa's Resistome: Pan-Genomic Plasticity, the Impact of Transposable Elements and Jumping Genes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298491},
issn = {2079-6382},
abstract = {Pseudomonas aeruginosa, a Gram-negative, motile bacterium, may cause significant infections in both community and hospital settings, leading to substantial morbidity and mortality. This opportunistic pathogen can thrive in various environments, making it a public health concern worldwide. P. aeruginosa's genomic pool is highly dynamic and diverse, with a pan-genome size ranging from 5.5 to 7.76 Mbp. This versatility arises from its ability to acquire genes through horizontal gene transfer (HGT) via different genetic elements (GEs), such as mobile genetic elements (MGEs). These MGEs, collectively known as the mobilome, facilitate the spread of genes encoding resistance to antimicrobials (ARGs), resistance to heavy metals (HMRGs), virulence (VGs), and metabolic functions (MGs). Of particular concern are the acquired carbapenemase genes (ACGs) and other β-lactamase genes, such as classes A, B [metallo-β-lactamases (MBLs)], and D carbapenemases, which can lead to increased antimicrobial resistance. This review emphasizes the importance of the mobilome in understanding antimicrobial resistance in P. aeruginosa.},
}

@article {pmid40298490,
year = {2025},
author = {Garcia-Torné, M and Falcó, I and Borrell, X and Bautista, A and Mazigh, R and Aznar, R and Sánchez, G and Farré, M and Llorca, M},
title = {Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298490},
issn = {2079-6382},
support = {869178-Aquatic Pollutants//Water JPI/ ; ON-HEALTH 2021 SGR 01150//Government of Catalonia/ ; CEX2021-001189-S//Spanish Ministry of Science and Innovation/ ; PRE2021-099409//Spanish Ministry of Science and Innovation/ ; MS21-006//Ministry of Universities of the Government of Spain, financed by the European Union (NextGeneration EU)/ ; },
abstract = {Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.},
}

@article {pmid40294085,
year = {2025},
author = {Bellotti, G and Cortimiglia, C and Antinori, ME and Cocconcelli, PS and Puglisi, E},
title = {Comprehensive genome-wide analysis for the safety assessment of microbial biostimulants in agricultural applications.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
pmid = {40294085},
issn = {2057-5858},
mesh = {*Agriculture/methods ; Whole Genome Sequencing ; *Genome, Bacterial ; *Bacteria/genetics/drug effects ; Virulence Factors/genetics ; *Fertilizers/microbiology ; Interspersed Repetitive Sequences ; },
abstract = {Microbial biostimulants (MBs) offer a sustainable approach to agriculture by helping to reduce reliance on synthetic fertilizers. However, as MBs are intentionally released into the environment, their safety should be rigorously assessed. While taxa with qualified presumption of safety (QPS) benefit from established safety indications, non-QPS taxa lack such guidance. To address this gap, we propose a pipeline combining whole genome sequencing (WGS) and extensive literature search (ELS) data to evaluate microbial safety. We analysed public genomes of three QPS species (Rhodopseudomonas palustris, Bacillus velezensis, Priestia megaterium) and four non-QPS genera (Arthrobacter, Azotobacter, Azospirillum, Herbaspirillum), screening them for virulence factors (VFs), antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). Results confirmed the safety of QPS taxa, revealing no VFs and only a few intrinsic and non-clinically relevant AMRs. Among non-QPS taxa, VF hits were more prevalent in Azotobacter and Azospirillum spp., though they were mostly related to beneficial plant interactions rather than pathogenicity. AMR genes in non-QPS taxa were primarily associated with efflux pumps or were sporadically distributed. Notably, the only genus-wide pattern observed was that most Azospirillum and Herbaspirillum genomes harboured chromosomally encoded β-lactamases sharing similar genetic structures; however, the detected β-lactamase (bla) genes were distantly related to clinically relevant bla variants, and the absence of MGEs suggests a low risk of horizontal gene transfer, indicating the overall safety of these genera. In general, this WGS-ELS framework provides a robust tool for assessing the safety of non-QPS MBs, supporting regulatory decision-making and ensuring their safe use in sustainable agriculture while safeguarding public health.},
}

*Agriculture/methods
Whole Genome Sequencing
*Genome, Bacterial
*Bacteria/genetics/drug effects
Virulence Factors/genetics
*Fertilizers/microbiology
Interspersed Repetitive Sequences

@article {pmid40289079,
year = {2025},
author = {Tsiklauri, R and Kobakhidze, S and Tsereteli, M and Jimsherishvili, L and Kakabadze, N and Koulouris, S and Kotetishvili, M},
title = {Genome data cross-contamination versus interdomain recombination: Equus caballus and Mus musculus genetic loci in the insertion sequence-rich genomes of two clonally related methicillin-resistant Staphylococcus aureus strains from China.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {251},
pmid = {40289079},
issn = {1471-2180},
mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation & purification ; China ; *Genome, Bacterial ; Animals ; *Recombination, Genetic ; Staphylococcal Infections/microbiology/veterinary ; Horses/microbiology ; *DNA Transposable Elements ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) represents a significant global health threat, responsible for infections in both humans and animals. Determining genetic patterns associated with the genome plasticity of MRSA is critical for predicting the evolutionary trajectories of its emerging pathogenic clones.

RESULTS: The specific genetic loci of the MRSA strains WH3018 and WH9628 from Wuhan, China, ranging in size from 399 to 3,622 base pairs, were determined to be highly homologous (DNA identity: 90.95-100%) to corresponding chromosomal regions from Equus caballus and Mus musculus in the GenBank database. These eukaryotic-associated loci included the microsatellite DNAs or Y chromosome-specific regions from E. caballus, or 45 S-28 S ribosomal RNA/H19 loci from M. musculus, all exhibiting recurrent patterns across the genomes of both MRSA strains. The SplitsTree and RDP4 analyses did not reveal significant recombination signals for the eukaryotic-associated loci that had mimicked interdomain recombination events in the MRSA strains WH3018 and WH9628. The G + C content of these loci (47.6-65.0%) was notably higher than that of the S. aureus reference genome (32.5%). Furthermore, the MRSA genomes showed a significantly larger number and greater diversity of insertion sequences (ISs) (38 ISs per genome) compared to the S. aureus reference genome (16 ISs). Additionally, these genomes also exhibited an extensive decay of prophages and the accumulation of pseudo-transposases.

CONCLUSIONS: The recurring patterns of the eukaryotic-associated loci strongly suggested genome data contamination across the genomes of the MRSA strains WH3018 and WH9628. These MRSA genomes likely underwent extensive prophage decay and an increased proliferation of pseudo-transposases.},
}

*Methicillin-Resistant Staphylococcus aureus/genetics/classification/isolation & purification
China
*Genome, Bacterial
Animals
*Recombination, Genetic
Staphylococcal Infections/microbiology/veterinary
Horses/microbiology
*DNA Transposable Elements
DNA, Bacterial/genetics

@article {pmid40288735,
year = {2025},
author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J},
title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121693},
doi = {10.1016/j.envres.2025.121693},
pmid = {40288735},
issn = {1096-0953},
abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.},
}

@article {pmid40288673,
year = {2025},
author = {Kabeya, N and Ramos-Llorens, M and Nakano, Y and Gomes-Dos-Santos, A and Teixeira, A and Fujibayashi, M and Haro, JG and Navarro, JC and Castro, LFC and Haga, Y and Monroig, Ó},
title = {Methyl-end desaturases determine the capability for de novo biosynthesis of polyunsaturated fatty acids in bivalves.},
journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids},
volume = {1870},
number = {5},
pages = {159617},
doi = {10.1016/j.bbalip.2025.159617},
pmid = {40288673},
issn = {1879-2618},
abstract = {Recent studies have shown that many invertebrate species possess methyl-end desaturases (herein referred to as 'ωx'), enabling biosynthesis of polyunsaturated fatty acids (PUFA). However, the phylogenetic distribution of these enzymes across the animal kingdom remains puzzling, possibly due to horizontal gene transfer (HGT) and/or independent large-scale gene loss in certain invertebrate lineages. In molluscs, ωx genes have been identified in various cephalopods and gastropods but remain barely explored in bivalves. The increasing availability of genomic and transcriptomic resources enables a comprehensive exploration of the ωx gene repertoire in bivalves. To elucidate the distribution of ωx in bivalves, we conducted a broad homology search across existing genome and transcriptome assemblies, followed by functional characterisation of ωx in lineage representative species. Our results revealed no ωx-like sequences in any of the 65 Pteriomorphia species, suggesting gene loss in this clade. However, ωx-like sequences were found in Protobranchia, Palaeoheterodonta and Imparidentia. We analysed ωx from Solemya pusilla (Protobranchia), Lanceolaria oxyrhyncha and Margaritifera margaritifera (Palaeoheterodonta), and Ruditapes philippinarum and Tridacna crocea (Imparidentia). Except for M. margaritifera, which had two ωx genes, each species had a single ωx gene. Functional analysis showed Δ15Δ17Δ19 desaturase activity in the R. philippinarum and T. crocea ωx, while the L. oxyrhyncha ωx exhibited Δ15Δ17 activity but not Δ19. Both ωx from M. margaritifera showed no detectable activity in yeast. Interestingly, the S. pusilla ωx exhibited Δ12 desaturase activity. These findings highlight the diversity of ωx desaturation capabilities in bivalves, with significant gene loss in Pteriomorphia.},
}

@article {pmid40284824,
year = {2025},
author = {Silva, V and Caniça, M and de la Rivière, R and Barros, P and Cabral, JA and Poeta, P and Igrejas, G},
title = {Bats as Hosts of Antimicrobial-Resistant Mammaliicoccus lentus and Staphylococcus epidermidis with Zoonotic Relevance.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
pmid = {40284824},
issn = {2306-7381},
abstract = {Bats are increasingly recognized as reservoirs for antimicrobial-resistant bacteria, playing a potential role in the dissemination of resistance genes across species and regions. In this study, 105 bats from 19 species in Portugal were sampled to investigate the presence, antimicrobial resistance, and genetic characteristics of Mammaliicoccus and Staphylococcus isolates. Thirteen Mammaliicoccus lentus and Staphylococcus epidermidis were recovered. Antimicrobial susceptibility testing revealed multidrug resistance in three isolates, with S. epidermidis carrying mph(C), msr(A), and dfrC genes, and M. lentus harboring salB, tet(K), and str. Notably, qacA was detected in S. epidermidis, highlighting its plasmid-associated potential for horizontal gene transfer to more pathogenic bacteria. Heavy metal resistance genes (arsB and cadD) were also identified, suggesting the role of environmental factors in co-selecting antimicrobial resistance. Molecular typing revealed the S. epidermidis strain as ST297, a clone associated with both healthy humans and invasive infections. These findings emphasize the need for monitoring bats as reservoirs of resistance determinants, particularly in the context of zoonotic and environmental health. The presence of mobile genetic elements and plasmids further underscores the potential for the dissemination of resistance. This study reinforces the importance of adopting a One Health approach to mitigate the risks associated with antimicrobial resistance.},
}

@article {pmid40284646,
year = {2025},
author = {Alglave, L and Faure, K and Mullié, C},
title = {Plasmid Dissemination in Multispecies Carbapenemase-Producing Enterobacterales Outbreaks Involving Clinical and Environmental Strains: A Narrative Review.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284646},
issn = {2076-2607},
abstract = {Outbreaks involving carbapenemase-producing enterobacteria (CPE) have become a common occurrence in healthcare settings. While clonal dissemination is firmly established as a cause for these outbreaks, horizontal gene transfers (HGTs) between different species of Enterobacterales found in clinical and environmental isolates are less so. To gather evidence backing up this hypothesis, a review covering the 2013-2024 period was performed. HGTs between different species of clinical and environmental Enterobacterales were identified in thirteen papers, half of those published within the last three years. A combination of short- and long-read whole genome sequencing (WGS) was predominantly used to identify mobile genetic elements and plasmids. The more frequently reported carbapenemases were KPCs, followed by NDMs and IMPs. Predictably, broad-host-range plasmids were responsible for over 50% of HGTs, with the IncA/C group being in the lead. Klebsiella pneumoniae and Enterobacter cloacae complexes were the most frequent species identified in clinical samples, while Citrobacter freundii dominated environmental ones. Drains and pipework frequently constituted CPE reservoirs in protracted outbreaks, alternating epidemic outbursts with silent phases. Including WGS in a systematic environmental surveillance would help in swiftly identifying those CPE reservoirs and possibly help better control plasmid outbursts by allowing the implementation of adequate infection prevention and control measures.},
}

@article {pmid40284645,
year = {2025},
author = {González-Sánchez, A and Lozano-Aguirre, L and Jiménez-Flores, G and López-Sámano, M and García-de Los Santos, A and Cevallos, MA and Le Borgne, S},
title = {Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico).},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
pmid = {40284645},
issn = {2076-2607},
abstract = {Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401[T], NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved.},
}

@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}

@article {pmid40280885,
year = {2025},
author = {Kaur, A and Sunny, A and Jones, JB and Goss, EM},
title = {Investigating Plasmids Diversity in X. euvesicatoria pv. perforans Population.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0042-FI},
pmid = {40280885},
issn = {0031-949X},
abstract = {Plasmids are key drivers of horizontal gene transfer. These genetic elements promote diversification and rapid adaptation of bacterial populations to changing environments by transferring beneficial traits within and between bacterial species. Xanthomonas euvesicatoria pv. perforans is a devastating plant pathogen that causes bacterial spot disease in tomato and pepper. The pathogen population in Florida contains several distinct genetic lineages that differ in relative frequency. The objective of this study was to characterize plasmid diversity and gene content, and plasmid distribution in relation to chromosomal phylogeny. Our in silico-based plasmid prediction revealed the presence of diverse plasmids ranging from ~16 kb to ~235 kb. A network approach based on shared k-mer content uncovered ten distinct plasmid groups with high genetic similarity (cliques). Interestingly, these plasmid cliques were confined to specific phylogenetic clusters suggesting potential incompatibility or restricted plasmid movement between clusters. Some of the predicted plasmids carry virulence genes coding for type III secretion effectors (T3SEs), including transcriptional activator-like effectors (TALEs) and genes related to biocide resistance, such as copper. We also identified gene reshuffling between the plasmids, likely carried out by transposons present within them. Overall, these results provide foundational insights into plasmid diversity in Xanthomonas euvesicatoria pv. perforans with implications for the role of these mobile genetic elements in genome dynamics and pathogen adaptation.},
}

@article {pmid40279390,
year = {2025},
author = {Djermoun, S and Rode, DKH and Jiménez-Siebert, E and Netter, N and Lesterlin, C and Drescher, K and Bigot, S},
title = {Biofilm architecture determines the dissemination of conjugative plasmids.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {17},
pages = {e2417452122},
doi = {10.1073/pnas.2417452122},
pmid = {40279390},
issn = {1091-6490},
support = {ANR-19-ARMB-0006-01//Agence Nationale de la Recherche (ANR)/ ; 16GW0245//Bundesministerium für Bildung und Forschung (BMBF)/ ; RF20200502684//Association Vaincre la Mucoviscidose (French CF Association)/ ; 955910//EC | H2020 | PRIORITY 'Excellent science' | H2020 Marie Skłodowska-Curie Actions (MSCA)/ ; TMCG-3 _ 213801/SNSF_/Swiss National Science Foundation/Switzerland ; DR 982/6-1 part of SPP 2389//Deutsche Forschungsgemeinschaft (DFG)/ ; 57552336//Deutscher Akademischer Austauschdienst France (DAAD France)/ ; 47902YJ//Germaine de Stael swiss Academy of Engineering Sciences/ ; },
mesh = {*Biofilms/growth & development ; *Plasmids/genetics ; *Escherichia coli/genetics/physiology ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Microscopy, Fluorescence ; },
abstract = {Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic resistance among bacteria. While the molecular mechanisms of conjugation have been extensively studied, our understanding of plasmid transfer dynamics within spatially structured bacterial communities and the influence of community architecture on plasmid dissemination remains limited. In this study, we use live-cell fluorescence microscopy to investigate the propagation of the broad host range RP4 conjugative plasmid in Escherichia coli populations exhibiting varying levels of spatial organization. In high-density, two-dimensional cell monolayers, direct and tight contact between donors and recipients is not only necessary but also sufficient to trigger RP4 plasmid transfer, ensuring optimal plasmid propagation. In three-dimensional mature biofilms, the emergent community architecture limits the ability of donor cells to enter regions with high cell density, which hinders the establishment of direct contacts with recipients and impedes plasmid transfer in biofilms. In contrast, microcolonies, early-stage biofilms, and biofilms with a lower surface coverage leave open access points for donor cells in regions that later emerge as high-cell-density regions in mature biofilms, which facilitates plasmid transfer. These findings reveal the crucial role of bacterial community architecture in determining the efficiency of plasmid dissemination.},
}

*Biofilms/growth & development
*Plasmids/genetics
*Escherichia coli/genetics/physiology
*Conjugation, Genetic
Gene Transfer, Horizontal
Microscopy, Fluorescence

@article {pmid40278619,
year = {2025},
author = {Pei, Y and Hamar, P and Pei, DS},
title = {Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278619},
issn = {2305-6304},
support = {CSTB2024TIAD-CYKJCXX0017//Sichuan-Chongqing Special Key Project/ ; },
abstract = {The rise of multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) presents a significant challenge to clinical treatment and environmental risks. This review delves into the complex mechanisms underlying MDR development in P. aeruginosa, such as genetic mutations, horizontal gene transfer (HGT), and the interaction between virulence factors and resistance genes. It evaluates current detection methods, from traditional bacteriology to advanced molecular techniques, emphasizing the need for rapid and accurate diagnostics. This review also examines therapeutic strategies, including broad-spectrum antibiotics, novel drug candidates, combination therapies, and innovative approaches like RNA interference, CRISPR-Cas9 gene editing, and bridge RNA-guided gene editing. Importantly, this review highlights the distribution, migration, and environmental risks of MDR P. aeruginosa, underscoring its adaptability to diverse environments. It concludes by stressing the necessity for continued research and development in antimicrobial resistance, advocating for an integrated approach that combines genomics, clinical practice, and environmental considerations to devise innovative solutions and preserve antibiotic efficacy.},
}

@article {pmid40278556,
year = {2025},
author = {Zeng, Y and Feng, R and Huang, C and Liu, J and Yang, F},
title = {Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278556},
issn = {2305-6304},
support = {42277033//the National Natural Science Foundation of China/ ; 202401AT070304//Basic Research Foundation of Yunnan Province of China/ ; Y2024QC28//Central Public-interest Scientific Institution Basal Research Fund/ ; 23JCYBJC00250//Tianjin Municipal Natural Science Foundation/ ; },
abstract = {This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.},
}

@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}

@article {pmid40275130,
year = {2025},
author = {Medina-Chávez, NO and Rodriguez-Cruz, UE and Souza, V and De la Torre-Zavala, S and Travisano, M},
title = {Salty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {399},
pmid = {40275130},
issn = {1471-2164},
support = {IG200319,IN204822//PAPIIT-DGAPA, UNAM/ ; NASA IDEAS16002//NASA IDEAS/ ; },
mesh = {*Halobacterium salinarum/genetics/isolation & purification/classification/metabolism ; Phylogeny ; Genome, Archaeal ; Mexico ; Genomics ; },
abstract = {The Cuatro Cienegas Basin (CCB) in Mexico, represents a unique ecological habitat, characterized by extreme and fluctuating conditions, providing a window into ancient evolutionary processes. This basin, characterized by hypersalinity and phosphorus scarcity, harbors diverse microbial communities that exhibit remarkable adaptations to oligotrophic conditions. Among these, Halobacterium salinarum, a halophilic archaeon known for its polyploid genome and metabolic versatility, has been extensively studied as a model for extremophile survival. However, only a limited number of H. salinarum strains have been successfully cultured and characterized to date. Here, we report the isolation and genomic analysis of a novel Halobacterium salinarum strain, AD88, from microbial mats at the Archaean Domes site in the CCB. This strain displays unique genomic features, including smaller plasmid sizes and distinctive metabolic pathways for phosphorus and sulfur utilization. Comparative analyses with other Halobacterium strains revealed genetic innovations, such as genes involved in sulfolipid biosynthesis, enabling membrane stability in phosphorus-depleted environments, and adaptations for horizontal gene transfer, which facilitate genomic flexibility in response to environmental pressures. This study reveals that H. salinarum AD88 is the first recorded diploid strain of Halobacterium, a feature previously undocumented in this genus. Phylogenomic reconstruction positioned AD88 tightly within the Halobacterium clade, reflecting its evolutionary history within the genus. Pangenome analysis further highlighted the open nature of the Halobacterium genus, with AD88 contributing novel accessory genes linked to ecological specialization. These findings emphasize the evolutionary significance of the CCB as a natural laboratory for studying microbial adaptation and expand our understanding of archaeal genomic diversity and functional innovation under extreme conditions.},
}

*Halobacterium salinarum/genetics/isolation & purification/classification/metabolism
Phylogeny
Genome, Archaeal
Mexico
Genomics

@article {pmid40274494,
year = {2025},
author = {Good, BH and Bhatt, AS and McDonald, MJ},
title = {Unraveling the tempo and mode of horizontal gene transfer in bacteria.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.009},
pmid = {40274494},
issn = {1878-4380},
abstract = {Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facilitating adaptive innovations, and shaping pangenomes. Recent experimental and theoretical results have shown how HGT shapes the flow of genetic information within and between populations, expanding the range of possibilities for microbial evolution. These advances set the stage for a new wave of research seeking to predict how HGT shapes microbial evolution within natural communities, especially during rapid ecological shifts. In this article, we highlight these developments and outline promising research directions, emphasizing the necessity of quantifying the rates of HGT within diverse ecological contexts.},
}

@article {pmid40273693,
year = {2025},
author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH},
title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123627},
doi = {10.1016/j.watres.2025.123627},
pmid = {40273693},
issn = {1879-2448},
abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.},
}

@article {pmid40273218,
year = {2025},
author = {Urriza, M and Dimaria, G and de Oliveira, LO and Catara, V and Murillo, J},
title = {Comparative genomics of native plasmids from plant pathogenic Gammaproteobacteria.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf009},
pmid = {40273218},
issn = {1756-1663},
abstract = {Plasmids are key in the evolution and adaptation of plant pathogenic Gammaproteobacteria (PPG), yet their diversity and functional contributions remain underexplored. Here, comparative genomics revealed extensive variation in plasmid size, replicon types, mobility, and genetic content across PPG. Most plasmids are small (<200 kb), except in Pantoea, exhibiting high coding densities (76-78%). Five ancestral replicon types were identified across multiple orders, indicating vertical descent yet efficient horizontal transfer across taxa, although with limited genetic conservation. Virulence plasmids are widespread (56-68%) but differ in virulence gene content across orders: type III effector (T3E) genes are common in Pseudomonas and Xanthomonas, but rare in Enterobacterales and Xylella, aligning with their smaller effector repertoires. Plasmids frequently carry regulatory genes, highlighting their role in bacterial phenotype modulation. Distinct patterns were observed among orders: Enterobacterales plasmids often harbor thiamine biosynthesis operons and transcriptional regulators but lack post-transcriptional regulators, while Pseudomonas and Xanthomonas plasmids are highly mobile, enriched in T3E genes, and exhibit high insertion sequence densities, fostering DNA mobility. Resistance to ultraviolet light is common, but not to antimicrobial compounds. These findings highlight the dynamic role of plasmids in spreading adaptive traits, shaping virulence, and driving the evolution of plant pathogenic bacteria.},
}

@article {pmid40269132,
year = {2025},
author = {Kumar, T and Rekhi, A and Lee, Y and Tran, J and Nagtalon, AGD and Rohatgi, S and Cyphert, EL},
title = {Leveraging the microbiome to combat antibiotic resistant gynecological infections.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {32},
pmid = {40269132},
issn = {2731-8745},
abstract = {The vaginal resistome can be considered a collection of the resistant determinants in the vaginal microbiome. Here we review the vaginal resistome including the microbes and resistant genes harbored in common gynecological infections, vaginal microbes that participate in horizontal gene transfer, host factors that contribute to the resistome, and common therapies. Finally, we provide perspective on technologies that can be leveraged to study the vaginal resistome and remaining challenges.},
}

@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}

*Biodiversity
*Microbiota
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Genetic Variation
Ecosystem
Biological Evolution

@article {pmid40267282,
year = {2025},
author = {Yang, Z and Chen, H and Zhong, GH and Liu, J},
title = {cAMP-Mediated Biofilm eDNA Transfer Facilitates the Resilience of Soil Microbiome to Agrochemical Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00961},
pmid = {40267282},
issn = {1520-5118},
abstract = {Soil microorganisms utilize extracellular DNA (eDNA)-based biofilms as a defense against xenobiotics. However, the specific effects and transfer pathways of eDNA under persistent agrochemical exposure remain unclear. This study examined the transfer dynamics of carbofuran-hydrolase gene pchA from Pseudomonas stutzeri PS21. During biofilm formation, pchA was released from eDNA, leading to an enrichment of beneficial microorganisms such as Acidobacteria and Elusimicrobia, which enhanced organic compound metabolism and improved soil microbiome resilience. An increase in the pchA-associated mobile genetic elements and the colocalization of pchA with other bacterial species indicated the potential horizontal gene transfer (HGT) under carbofuran exposure. Additionally, carbofuran triggered a cAMP-dependent apoptotic pathway, leading to a 59.6% increase in pchA copy number, which suggested that cAMP played a role in initiating HGT. In conclusion, the cAMP-mediated interspecific transfer of pchA could enhance microbial coadaptation to carbofuran contamination, thereby strengthening the collective defense of soil microbiome against agrochemical stress.},
}

@article {pmid40262895,
year = {2025},
author = {Lind, AL and McDonald, NA and Gerrick, ER and Bhatt, AS and Pollard, K},
title = {Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279080.124},
pmid = {40262895},
issn = {1549-5469},
abstract = {Blastocystis, an obligate host-associated protist, is the most common microbial eukaryote in the human gut and is widely distributed across vertebrate hosts. The evolutionary transition of Blastocystis from its free-living stramenopile ancestors to a radiation of host-associated organisms is poorly understood. To explore this, we cultured and sequenced eight strains representing the significant phylogenetic diversity of the genus using long-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses revealed significant variation in gene content and genome structure across Blastocystis Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly larger genomes with longer introns and intergenic regions, and retain canonical stop codons absent in the human-associated strains. Despite these genetic differences, all eight isolates exhibit gene losses linked to the reduced cellular complexity of Blastocystis, including losses of cilia and flagella genes, microtubule motor genes, and signal transduction genes. Isolates from herbivorous tortoises contained higher numbers of plant carbohydrate-metabolizing enzymes, suggesting that like gut bacteria, these protists ferment plant material in the host gut. We find evidence that some of these carbohydrate-metabolizing enzymes were horizontally acquired from bacteria, indicating that horizontal gene transfer is an ongoing process in Blastocystis that has contributed to host-related adaptation. Together, these results highlight substantial genetic and metabolic diversity within the Blastocystis genus, indicating different lineages of Blastocystis have varied ecological roles in the host gut.},
}

@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}

@article {pmid40261943,
year = {2025},
author = {Gori, K and Baez-Ortega, A and Strakova, A and Stammnitz, MR and Wang, J and Chan, J and Hughes, K and Belkhir, S and Hammel, M and Moralli, D and Bancroft, J and Drydale, E and Allum, KM and Brignone, MV and Corrigan, AM and de Castro, KF and Donelan, EM and Faramade, IA and Hayes, A and Ignatenko, N and Karmacharya, R and Koenig, D and Lanza-Perea, M and Lopez Quintana, AM and Meyer, M and Neunzig, W and Pedraza-Ordoñez, F and Phuentshok, Y and Phuntsho, K and Ramirez-Ante, JC and Reece, JF and Schmeling, SK and Singh, S and Tapia Martinez, LJ and Taulescu, M and Thapa, S and Thapa, S and van der Wel, MG and Wehrle-Martinez, AS and Stratton, MR and Murchison, EP},
title = {Horizontal transfer of nuclear DNA in transmissible cancer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2424634122},
doi = {10.1073/pnas.2424634122},
pmid = {40261943},
issn = {1091-6490},
support = {102942/Z/13/A 222551/Z/21/Z//Wellcome Trust (WT)/ ; BB/Y514299/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Dogs ; *Dog Diseases/genetics ; *Venereal Tumors, Veterinary/genetics ; *Cell Nucleus/genetics ; Marsupialia/genetics ; *DNA/genetics ; },
abstract = {Horizontal transfer of nuclear DNA between cells of host and cancer is a potential source of adaptive variation in cancer cells. An understanding of the frequency and significance of this process in naturally occurring tumors is, however, lacking. We screened for this phenomenon in the transmissible cancers of dogs and Tasmanian devils and found an instance in the canine transmissible venereal tumor (CTVT). This involved introduction of a 15-megabase dicentric genetic element, composed of 11 fragments of six chromosomes, to a CTVT sublineage occurring in Asia around 2,000 y ago. The element forms the short arm of a small submetacentric chromosome and derives from a dog with ancestry associated with the ancient Middle East. The introduced DNA fragment is transcriptionally active and has adopted the expression profile of CTVT. Its features suggest that it may derive from an engulfed apoptotic body. Our findings indicate that nuclear horizontal gene transfer, although likely a rare event in tumor evolution, provides a viable mechanism for the acquisition of genetic material in naturally occurring cancer genomes.},
}

Animals
*Gene Transfer, Horizontal
Dogs
*Dog Diseases/genetics
*Venereal Tumors, Veterinary/genetics
*Cell Nucleus/genetics
Marsupialia/genetics
*DNA/genetics

@article {pmid40261018,
year = {2025},
author = {Chi, W and Zhang, H and Li, X and Zhou, Y and Meng, Q and He, L and Yang, Y and Liu, S and Shi, K},
title = {Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326524},
doi = {10.1128/spectrum.03265-24},
pmid = {40261018},
issn = {2165-0497},
abstract = {Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.},
}

@article {pmid40259521,
year = {2025},
author = {Gatica-Soria, LM and Roulet, ME and Tulle, WD and Sato, HA and Barrandeguy, ME and Sanchez-Puerta, MV},
title = {Highly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.},
journal = {Physiologia plantarum},
volume = {177},
number = {2},
pages = {e70231},
doi = {10.1111/ppl.70231},
pmid = {40259521},
issn = {1399-3054},
support = {06/A092-T1//Secretaría de Investigación, Internacionales y Posgrado, Universidad Nacional de Cuyo/ ; PICT2020-01018//Fondo para la Investigación Científica y Tecnológica/ ; PICT2021 -GTR_TI-00435//Fondo para la Investigación Científica y Tecnológica/ ; },
mesh = {Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; *Chromosomes, Plant/genetics ; *DNA, Circular/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.},
}

Gene Transfer, Horizontal/genetics
DNA, Mitochondrial/genetics
*Chromosomes, Plant/genetics
*DNA, Circular/genetics
*Genome, Mitochondrial/genetics
Evolution, Molecular
Phylogeny

@article {pmid40258067,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in a representative Gram-positive and Gram-negative species.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013128},
pmid = {40258067},
issn = {1553-7374},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; },
mesh = {*Streptococcus pneumoniae/genetics/metabolism ; *Fimbriae, Bacterial/metabolism/genetics ; *DNA, Bacterial/metabolism/genetics ; *Fimbriae Proteins/metabolism/genetics ; *DNA-Binding Proteins/metabolism/genetics ; *Gram-Negative Bacteria/metabolism/genetics ; *DNA Transformation Competence ; Bacterial Proteins/metabolism/genetics ; *Gram-Positive Bacteria/metabolism/genetics ; Protein Binding ; },
abstract = {Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.},
}

*Streptococcus pneumoniae/genetics/metabolism
*Fimbriae, Bacterial/metabolism/genetics
*DNA, Bacterial/metabolism/genetics
*Fimbriae Proteins/metabolism/genetics
*DNA-Binding Proteins/metabolism/genetics
*Gram-Negative Bacteria/metabolism/genetics
*DNA Transformation Competence
Bacterial Proteins/metabolism/genetics
*Gram-Positive Bacteria/metabolism/genetics
Protein Binding

@article {pmid40253436,
year = {2025},
author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y},
title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {39},
pmid = {40253436},
issn = {2524-6372},
support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; },
abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.},
}

@article {pmid40251489,
year = {2025},
author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E},
title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {382},
pmid = {40251489},
issn = {1471-2164},
support = {INV-004891/GATES/Gates Foundation/United States ; },
mesh = {*Bacillus/genetics/isolation & purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.

RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.

CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.},
}

*Bacillus/genetics/isolation & purification/drug effects/classification/pathogenicity
*Probiotics
*Whole Genome Sequencing
*Genome, Bacterial
Polymorphism, Single Nucleotide
*Sanitation
Humans
*Drug Resistance, Bacterial/genetics

@article {pmid40250499,
year = {2025},
author = {Yang, Y and Sun, Y and Zhou, Z and Song, Y and Zhu, Y and Zhou, W and Yue, M and Zhao, G and Jiang, H and Tang, B},
title = {Surveillance of Escherichia coli antimicrobial resistance in pig farms in Zhejiang province, China: high prevalence of multidrug resistance and risk-associated genes.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107598},
doi = {10.1016/j.micpath.2025.107598},
pmid = {40250499},
issn = {1096-1208},
abstract = {OBJECTIVES: The global rise in antimicrobial resistance (AMR) poses a critical threat to public health, with the overuse of antibiotics in livestock being a key driver of this escalating problem. However, research on livestock-associated AMR remains limited, with few systematic monitoring efforts. This study addresses this gap by presenting findings from our surveillance of Escherichia coli resistance in pig farms in Zhejiang Province, China.

METHODS: The minimum inhibitory concentrations were determined via broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence was acquired using both Illumina NovaSeq 6000 platforms. In the plasmid conjugation experiment, sodium azide-resistant E. coli strain J53 served as the recipient. The E. coli genomes were analyzed for AMR genes, multi-locus sequence typing (MLST) types, plasmid types, and virulence genes using the ABRicate.

RESULTS: A total of 51 E. coli strains from 90 fecal samples collected across six farms. Resistance rates for amoxicillin/clavulanic acid and sulfamethoxazole exceeded 90%, while resistance to ampicillin, florfenicol, tetracycline, and trimethoprim/sulfamethoxazole was above 80%. The prevalence of multidrug-resistant strains was 89.24%. Whole-genome sequencing revealed 58 acquired AMR genes and 17 virulence-associated genes, notably including the astA gene. Two strains exhibited meropenem resistance and carried blaNDM-5, located on IncI1-I plasmids. These strains shared an identical genetic context, characterized by an "IS26-IS30-blaNDM-5-bleMBL-dsdD-IS91" structure, which may promote horizontal gene transfer of blaNDM-5. Additionally, six strains harbored the tet(X4) gene.

CONCLUSIONS: Despite ongoing antibiotic reduction efforts, the high prevalence of resistant E. coli in pigs underscores the urgent need for sustained surveillance of AMR in animal populations to mitigate the threat of resistance.},
}

@article {pmid40250277,
year = {2025},
author = {Han, Q and Yang, ML and Liu, ZS and Zhao, YH and Liu, XH and Ai, GM and Qin, WH and Liu, XY and Li, DF},
title = {Simultaneous high molecular weight PAHs degradation and chromate and arsenite detoxification by Altererythrobacter sp. H2.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138314},
doi = {10.1016/j.jhazmat.2025.138314},
pmid = {40250277},
issn = {1873-3336},
abstract = {The cooccurrence of high molecular weight PAHs and heavy metals Cr and As is frequently observed in soil and water and challenges public health and environmental management. Yet the limited microbial resources were reported to simultaneously detoxify PAHs, Cr(VI) and As(III), which restricts the bioremediation of co-contaminated soil by PAHs, Cr and As. Here, we isolated Altererythrobacter sp. H2 and found it could degrade various PAHs, including phenanthrene, fluoranthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene, and tolerate and detoxify high concentrations of Cr(VI) and As(III). Genomic, transcriptomic, and biochemical assays reveal strain H2 degrades PAHs, reduces Cr(VI), and oxidize As(III) via a horizontally transferred RHO gene cluster, a chromate reductase ChrR, and a arsenite resistance gene cluster arsRBC. The horizontally transferred PAHs-degrading gene cluster encodes the Rieske dioxygenase three-component system and other enzymes required for PAHs degradation, which suggested those heavy metal-detoxifying bacteria could be excellent PAHs-degrading and heavy metal-detoxifying agents after accommodating a PAHs degradation gene cluster like strain H2 did. To our knowledge, strain H2 is the only reported Altererythrobacter member that uses a classical Rieske dioxygenase three-component system to initial PAHs degradation and the only one could simultaneously detoxify PAHs, Cr(VI), and As(III). Our study provides insights into the PAHs degradation mechanism of Altererythrobacter members and demonstrates the excellent potential of H2 in the bioremediation of both PAHs and heavy metal pollutants.},
}

@article {pmid40249581,
year = {2025},
author = {Deslauriers, N and Boulianne, M},
title = {Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks.},
journal = {Avian diseases},
volume = {68},
number = {S1},
pages = {421-426},
doi = {10.1637/aviandiseases-D-24-00081},
pmid = {40249581},
issn = {1938-4351},
mesh = {Animals ; *Chickens ; *Osteomyelitis/veterinary/microbiology/epidemiology ; *Poultry Diseases/microbiology/epidemiology ; *Enterococcus/genetics/isolation & purification/classification ; *Gram-Positive Bacterial Infections/veterinary/microbiology/epidemiology ; Quebec/epidemiology ; *Housing, Animal ; Virulence ; },
abstract = {Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.},
}

Animals
*Chickens
*Osteomyelitis/veterinary/microbiology/epidemiology
*Poultry Diseases/microbiology/epidemiology
*Enterococcus/genetics/isolation & purification/classification
*Gram-Positive Bacterial Infections/veterinary/microbiology/epidemiology
Quebec/epidemiology
*Housing, Animal
Virulence

@article {pmid40249005,
year = {2025},
author = {Kerek, Á and Román, I and Szabó, Á and Kovács, D and Kardos, G and Kovács, L and Jerzsele, Á},
title = {Antibiotic resistance genes in Escherichia coli - literature review.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/1040841X.2025.2492156},
pmid = {40249005},
issn = {1549-7828},
abstract = {Antimicrobial resistance threatens humans and animals worldwide and is recognized as one of the leading global public health issues. Escherichia coli (E. coli) has an unquestionable role in carrying and transmitting antibiotic resistance genes (ARGs), which in many cases are encoded on plasmids or phage, thus creating the potential for horizontal gene transfer. In this literature review, the authors summarize the major antibiotic resistance genes occurring in E. coli bacteria, through the major antibiotic classes. The aim was not only listing the resistance genes against the clinically relevant antibiotics, used in the treatment of E. coli infections, but also to cover the entire resistance gene carriage in E. coli, providing a more complete picture. We started with the long-standing antibiotic groups (beta-lactams, aminoglycosides, tetracyclines, sulfonamides and diaminopyrimidines), then moved toward the newer groups (phenicols, peptides, fluoroquinolones, nitrofurans and nitroimidazoles), and in every group we summarized the resistance genes grouped by the mechanism of their action (enzymatic inactivation, antibiotic efflux, reduced permeability, etc.). We observed that the frequency of antibiotic resistance mechanisms changes in the different groups.},
}

@article {pmid40248430,
year = {2025},
author = {Chen, S and Liao, L and Wang, M},
title = {Editorial: Opportunistic pathogens: pathogenesis and multi-drug resistance mechanisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597769},
doi = {10.3389/fmicb.2025.1597769},
pmid = {40248430},
issn = {1664-302X},
}

@article {pmid40246490,
year = {2025},
author = {Huang, L and Yang, Y and Xue, Y and Hu, S and Liang, T and Ye, J and Xue, X},
title = {A gene island from plasmid pkk5 of Burkholderia sp. KK1 confers arsenic resistance to Caballeronia jiangsuensis.},
journal = {Journal of environmental sciences (China)},
volume = {155},
number = {},
pages = {562-572},
doi = {10.1016/j.jes.2024.09.011},
pmid = {40246490},
issn = {1001-0742},
mesh = {*Arsenic/toxicity/metabolism ; *Burkholderia/genetics/metabolism ; *Plasmids/genetics ; Biodegradation, Environmental ; *Hypocreales/metabolism ; },
abstract = {Microorganisms play a critical role in the biotransformation of arsenic and the form which it exists in the environment. In this study, a methyl parathion-degrading bacterium Caballeronia jiangsuensis, isolated from an abandoned pesticide manufacturing plant, was used to analyze arsenic accumulation and transformation. The accumulation of trivalent organoarsenic compounds in C. jiangsuensis occurred to a greater extent than that of their pentavalent counterparts. The chromosome of C. jiangsuensis contains an arsenic gene island whose GC content is significantly lower than that of the genome, suggesting that the island was acquired via horizontal gene transfer. There was approximately 90 %-99 % similarity between the proteins encoded by the gene island and the corresponding sequence of the plasmid pkk5 from Burkholderia sp. KK1. The biotransformation of different arsenic species by C. jiangsuensis was subsequently analyzed. The results revealed that monomethylarsenic acid (MAs(V)) was rapidly demethylated to arsenate with very small amounts of intermediate monomethylarsonous acid (MAs(III)), whereas MAs(III) was largely oxidized to MAs(V) despite the occurrence of the gene arsI probably responsible for aerobic demethylation of MAs(III) in C. jiangsuensis. In addition, dimethylarsenic acid was partly demethylated to arsenate. Horizontal gene transfer of ars operon from a plasmid to other bacteria represents an adaptation to a specific environment. This study provides a new perspective for understanding arsenic biogeochemical cycling.},
}

*Arsenic/toxicity/metabolism
*Burkholderia/genetics/metabolism
*Plasmids/genetics
Biodegradation, Environmental
*Hypocreales/metabolism

@article {pmid40245502,
year = {2025},
author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT},
title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179353},
doi = {10.1016/j.scitotenv.2025.179353},
pmid = {40245502},
issn = {1879-1026},
mesh = {*beta-Lactamases/genetics ; *Gram-Negative Bacteria/genetics ; *Interspersed Repetitive Sequences ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; Singapore ; },
abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.},
}

*beta-Lactamases/genetics
*Gram-Negative Bacteria/genetics
*Interspersed Repetitive Sequences
*Water Microbiology
*Drug Resistance, Bacterial/genetics
Singapore

@article {pmid40243369,
year = {2025},
author = {Li, J and Chang, J and Ma, J and Zhou, W and Yang, Y and Wu, J and Guan, C and Yuan, X and Xu, L and Yu, B and Su, F and Ye, S and Chen, Y and Zhao, G and Tang, B},
title = {Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period.},
journal = {mBio},
volume = {},
number = {},
pages = {e0065125},
doi = {10.1128/mbio.00651-25},
pmid = {40243369},
issn = {2150-7511},
abstract = {The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.},
}

@article {pmid40240954,
year = {2025},
author = {Feng, Y and Liu, Y and Han, J and Huang, Y and Lee, J and Kokubugata, G and Qi, Z and Yan, X},
title = {Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {488},
pmid = {40240954},
issn = {1471-2229},
support = {G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau/ ; G242412, G252409//Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; LY21C030008//Natural Science Foundation of Zhejiang Province/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; *Salvia/genetics ; RNA Editing ; *Genome, Plant ; Genetic Engineering ; },
abstract = {BACKGROUND: Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to the Mediterranean region, thriving in rocky or arid soils. Widely used in food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding and germplasm innovation. While mitogenome engineering holds promise for introducing heritable mutations, incomplete mitogenome information for rosemary has hindered such efforts. This study addresses this gap by assembling and analyzing the complete mitogenome of S. rosmarinus, focusing on its structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), and phylogenetic relationships.

RESULTS: The S. rosmarinus mitogenome spans 384,113 bp with a GC content of 44.8%, containing 34 unique protein-coding genes and 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between the mitogenome and plastome, totaling 18,675 bp in length. Furthermore, homologous fragments between nuclear and organellar genomes were identified, including 1,069,255 bp of organelle-derived sequences in the nuclear genome, with 194,689 bp from nuclear plastid DNA transfers (NUPTs) and 15,192 bp from nuclear mitochondrial DNA transfers (NUMTs). NUPTs were more abundant and contributed more significantly to the total length. Synteny analysis of eight Lamiales species revealed extensive mitogenomic recombination and structural rearrangements. These findings highlight the dynamic nature of mitogenomes, offering insights into genome evolution and supporting future breeding programs to enhance the genetic diversity and adaptability of S. rosmarinus.

CONCLUSIONS: This study provides the first complete mitogenome of S. rosmarinus, revealing dispersed repeats, RNA editing, and horizontal gene transfer between the nuclear and organelle genomes. The mitogenome exhibits a typical circular structure with evidence of frequent recombination, providing valuable insights into Salvia mitochondrial genetics, genome evolution, and molecular biology.},
}

*Genome, Mitochondrial/genetics
*Evolution, Molecular
Phylogeny
*Salvia/genetics
RNA Editing
*Genome, Plant
Genetic Engineering

@article {pmid40238219,
year = {2025},
author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G},
title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40238219},
issn = {2304-8158},
abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.},
}

@article {pmid40236771,
year = {2025},
author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J},
title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70008},
pmid = {40236771},
issn = {2770-596X},
abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.},
}

@article {pmid40234663,
year = {2025},
author = {Luk-In, S and Phopin, K and Bangmuangngam, S and Chatsuwan, T and Wannigama, DL and Shein, AMS and Plongla, R and Lawung, R and Yainoy, S and Eiamphungporn, W and Chatupheeraphat, C and Tantimongcolwat, T},
title = {Inhibitory effects of benzyl isothiocyanate on widespread mcr-1-harbouring IncX4 plasmid transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12892},
pmid = {40234663},
issn = {2045-2322},
mesh = {*Plasmids/genetics ; *Klebsiella pneumoniae/genetics/drug effects ; *Escherichia coli/genetics/drug effects ; Colistin/pharmacology ; *Isothiocyanates/pharmacology ; *Escherichia coli Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Humans ; Gene Transfer, Horizontal/drug effects ; Thailand ; },
abstract = {The global dissemination of mobile colistin resistance (mcr) genes represents a significant public health threat due to colistin's critical role in treating multidrug-resistant (MDR) bacterial infections. We identified high rates of carbapenem resistance in Escherichia coli (27.82%) and Klebsiella pneumoniae (57.98%) and colistin resistance in E. coli (7.52%) and K. pneumoniae (19.68%) among MDR clinical isolates in Thailand. We reported sequences of self-transferable IncX4 plasmids (~ 34 kb) that facilitated the spread of the mcr-1.1 gene among six diverse MDR strains, often co-transferring blaCTX-M-55. Additionally, E. coli ST101 was found to co-transfer mcr-1.1, mcr-3.5, blaCTX-M-55, and tet(X4) via three plasmids (~ 34-kb IncX4, ~ 84-kb IncFII, ~ 278-kb IncHI2), resulting in increases in MICs for colistin, ceftriaxone, and tigecycline. Core SNP analysis revealed that closely related IncX4 plasmids harbouring mcr-1 (< 35 SNP differences) were reported from at least 12 countries. We first demonstrated the inhibitory effects of benzyl isothiocyanate (BITC) on the conjugation of mcr-1-bearing IncX4 plasmids to 1.57 ± 1.00% to 48.86 ± 12.31% relative to control (100%), targeting VirB4 and VirB11 proteins, reducing ATPase activity by over 30%. This study highlights the widespread mcr-1-harbouring IncX4 plasmids and proposes BITC as a potential inhibitor to control the dissemination of colistin resistance.},
}

*Plasmids/genetics
*Klebsiella pneumoniae/genetics/drug effects
*Escherichia coli/genetics/drug effects
Colistin/pharmacology
*Isothiocyanates/pharmacology
*Escherichia coli Proteins/genetics
Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Drug Resistance, Multiple, Bacterial/genetics/drug effects
Humans
Gene Transfer, Horizontal/drug effects
Thailand

@article {pmid40230384,
year = {2025},
author = {Sousa, M and Machado, I and Simões, LC and Simões, M},
title = {Biocides as drivers of antibiotic resistance: A critical review of environmental implications and public health risks.},
journal = {Environmental science and ecotechnology},
volume = {25},
number = {},
pages = {100557},
pmid = {40230384},
issn = {2666-4984},
abstract = {The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, and environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex and influenced significantly by environmental factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, and hospitals produces persistent chemical residues that pollute soil and aquatic environments. Such contaminants contribute to the selection and proliferation of resistant bacteria and antimicrobial resistance genes (ARGs), facilitating their dissemination among humans, animals, and ecosystems. In this review, we conduct a critical assessment of four significant issues pertaining to this topic. Specifically, (i) the role of biocides in exerting selective pressure within the environmental resistome, thereby promoting the proliferation of resistant microbial populations and contributing to the global spread of antimicrobial resistance genes (ARGs); (ii) the role of biocides in triggering transient phenotypic adaptations in bacteria, including efflux pump overexpression, membrane alterations, and reduced porin expression, which often result in cross-resistance to multiple antibiotics; (iii) the capacity of biocides to disrupt bacteria and make the genetic content accessible, releasing DNA into the environment that remains intact under certain conditions, facilitating horizontal gene transfer and the spread of resistance determinants; (iv) the capacity of biocides to disrupt bacterial cells, releasing intact DNA into the environment and enhancing horizontal gene transfer of resistance determinants; and (iv) the selective interactions between biocides and bacterial biofilms in the environment, strengthening biofilm cohesion, inducing resistance mechanisms, and creating reservoirs for resistant microorganisms and ARG dissemination. Collectively, this review highlights the critical environmental and public health implications of biocide use, emphasizing an urgent need for strategic interventions to mitigate their role in antibiotic resistance proliferation.},
}

@article {pmid40228732,
year = {2025},
author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH},
title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126245},
doi = {10.1016/j.envpol.2025.126245},
pmid = {40228732},
issn = {1873-6424},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5 %-65.8 %, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12 %-100 % compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.},
}

*Soil Microbiology
*Soil/chemistry
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Genes, Bacterial

@article {pmid40226105,
year = {2025},
author = {Wen, Y and Wu, J and You, L and Wei, X and Wang, J and Li, S},
title = {Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532036},
pmid = {40226105},
issn = {1664-302X},
abstract = {BACKGROUND: The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.

METHODS: A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.

RESULTS: Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.

CONCLUSION: The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.},
}

@article {pmid40223056,
year = {2025},
author = {Colp, MJ and Blais, C and Curtis, BA and Archibald, JM},
title = {The fate of artificial transgenes in Acanthamoeba castellanii.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {368},
pmid = {40223056},
issn = {1471-2164},
support = {GBMF5782//Gordon and Betty Moore Foundation/ ; },
mesh = {*Acanthamoeba castellanii/genetics ; *Transgenes/genetics ; Plasmids/genetics ; Transformation, Genetic ; },
abstract = {BACKGROUND: The soil amoeba Acanthamoeba castellanii is an emerging model organism with which to study a wide range of biomedical, microbiological, and evolutionary phenomena. While transformation systems were established for this organism more than two decades ago, the fate of artificial transgenes has not been well characterized. In this study, artificial transformation experiments were performed to investigate how the A. castellanii genome responds to foreign DNA presented in both circular and linear plasmid form.

RESULTS: Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance in A. castellanii is proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends.

CONCLUSIONS: Our results suggest that transformation of A. castellanii with foreign DNA leads to linear molecules that are maintained as telomere-containing, transgene-bearing minichromosomes, which may facilitate chromosomal integration. This process may allow lateral gene transfer by expanding the window of opportunity for exogenous DNA to be taken up and integrated into the A. castellanii genome. Similar mechanisms exist in other eukaryote groups, suggesting this may be a widespread feature of eukaryote genome biology.},
}

*Acanthamoeba castellanii/genetics
*Transgenes/genetics
Plasmids/genetics
Transformation, Genetic

@article {pmid40220390,
year = {2025},
author = {Xiao, B and Pu, Q and Ding, G and Wang, Z and Li, Y and Hou, J},
title = {Synergistic effect of horizontal transfer of antibiotic resistance genes between bacteria exposed to microplastics and per/polyfluoroalkyl substances: An explanation from theoretical methods.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138208},
doi = {10.1016/j.jhazmat.2025.138208},
pmid = {40220390},
issn = {1873-3336},
abstract = {Microplastics (MPs) and per/polyfluoroalkyl substances (PFASs), as emerging pollutants widely present in aquatic environments, pose a significant threat to human health through the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Molecular dynamics simulations and machine learning can accurately capture the complex interactions between molecules. This study utilized them to identify the HGT risk between bacteria under MPs and PFASs stress. This study found that MPs and PFASs significantly increase the HGT risk between bacteria, up to 1.57 and 1.59 times, respectively. Notably, long-chain PFASs and perfluoroalkyl carboxylic acids increased the HGT risk by 1.38 and 1.40 times, respectively. Additionally, MPs primarily increase the HGT risk by enhancing hydrogen bonding interaction between key proteins in the HGT pathway and "active codons". The electronegativity and polarizability of PFASs critically influence the HGT risk, acting inversely and directly proportional, respectively. The HGT risk between bacteria under the combined stress from PP-MPs and PFASs exhibits a significant synergistic effect (synergistic effect value of 27.6), which markedly increases the HGT risk. Further analysis revealed that a smaller minimum distance and sharper RDF curve peaks between key proteins and "active codons" indicate higher HGT risk. This indicates that stronger interactions lead to higher HGT risk. This study identifies the characteristics of HGT risks between bacteria in aquatic environments under the individual and combined stresses from MPs and PFASs at the molecular level. It provides a theoretical basis for mitigating ARG transfer and comprehensively assessing the health risks posed by these emerging pollutants.},
}

@article {pmid40217451,
year = {2025},
author = {Hotor, P and Kotey, FCN and Donkor, ES},
title = {Antibiotic resistance in hospital wastewater in West Africa: a systematic review and meta-analysis.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {1364},
pmid = {40217451},
issn = {1471-2458},
support = {D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; D43TW012487/TW/FIC NIH HHS/United States ; },
mesh = {Africa, Western ; *Wastewater/microbiology ; *Hospitals ; Humans ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents ; },
abstract = {BACKGROUND: The occurrence of antibiotic-resistant bacteria (ARB) has become a global menace and therefore increases morbidity, mortality and healthcare costs. Globally, hospital wastewater (HWW) has been identified as a significant source of antibiotic-resistant elements.

OBJECTIVES: This review aims to systematically review and to perform meta-analyses from evidence on antibiotic resistance studies in HWW in West Africa.

METHODS: The review was conducted in compliance with PRISMA and included studies published between 1990 and 2024 in West Africa from the Scopus, PubMed, and Web of Science databases. Eligible studies that characterized resistant bacteria, genes, or antibiotic residues in HWW were included. Meta-analyses for resistant bacteria and genes as well risk of bias using the Newcastle-Ottawa scale were conducted.

RESULTS: Out of 23 studies reviewed, resistant bacteria were reported in 39% (E. coli), 26% (K. pneumoniae), and 17% (P. aeruginosa), while 17 studies reported ARGs, with blaTEM (29%), blaOXA- 48 (18%), blaSHV (18%), and mecA (18%) being the most common. Only 4% and 9% of studies focused on toxin genes and antibiotic residues, respectively. Meta-analysis showed pooled prevalence rates for resistant bacteria: E. coli 42.6% (95% CI: 26.7%-60.3%) and K. pneumoniae 32.1% (95% Cl: 28.8%- 36.5%), and ARGs: blaTEM 76.0% (95% CI = 64.6%-84.6%) and blaSHV 59.3% (95% CI = 19.5%-89.8%).

CONCLUSION: This systematic review highlights significant findings of high levels of ARGs and ARBs of public health concern in HWW in West Africa. This highlights the need to improve upon the monitoring of antibiotic resistance and treatment of HWW in West Africa.},
}

Africa, Western
*Wastewater/microbiology
*Hospitals
Humans
*Drug Resistance, Microbial
*Drug Resistance, Bacterial
Anti-Bacterial Agents

@article {pmid40216901,
year = {2025},
author = {Robinson, LR and McDevitt, CJ and Regan, MR and Quail, SL and Swartz, M and Wadsworth, CB},
title = {Revisiting the potential impact of doxycycline post-exposure prophylaxis on the selection of doxycycline resistance in Neisseria commensals.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12400},
pmid = {40216901},
issn = {2045-2322},
support = {R15 AI174182/AI/NIAID NIH HHS/United States ; R15AI174182/NH/NIH HHS/United States ; },
mesh = {*Doxycycline/pharmacology/therapeutic use ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics/drug effects ; *Post-Exposure Prophylaxis/methods ; *Neisseria/drug effects/genetics ; Gonorrhea/prevention & control/microbiology ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Female ; Male ; },
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) is a strategy to reduce bacterial sexually transmitted infections. However, the impact of doxy-PEP on resistance emergence is as of yet unclear. Commensal Neisseria are known reservoirs of resistance for gonococci through horizontal gene transfer (HGT), and are more likely to experience bystander selection from doxy-PEP as they are universally carried. The consequences of doxycycline selection on commensal Neisseria will be critical to investigate to understand possible resistance mechanisms that may be transferred to an important human pathogen. Here, collection of commensals from human hosts demonstrated 46% of isolates carry doxycycline resistance; and doxycycline resistance was significantly greater in participants self-reporting doxycycline use in the past 6 months. High-level doxycycline resistance (> 8 µg/mL) was always associated with the ribosomal protection protein (tetM) and pConj. In vitro selection of Neisseria commensals (N. cinerea, N. canis, N. elongata, and N. subflava) resulted in 12 of 16 lineages evolving doxycycline resistance (> 1 µg/mL). An A46T substitution in the repressor of the Mtr efflux pump (MtrR) and a V57M substitution in the 30 ribosomal protein S10 were associated with elevated MICs. Mutations in ribosomal components also emerged (i.e., 16 S rRNA G1057C, RplX A14T). We find the MtrR 46T, RpsJ 57M, and RplX 14T in natural commensal populations. In vitro co-evolution of N. gonorrhoeae with Neisseria commensals demonstrated rapid transfer of the pConj plasmid to N. subflava and N. cinerea, and pbla to N. cinerea. This work underscores the importance of commensal Neisseria as reservoirs of doxycycline resistance, and demonstrates a link between doxycycline use and the emergence of resistance. Though novel chromosomal resistance mutations are nominated herein, resistance emergence in natural commensal populations appears to be mainly associated with acquisition of the tetM gene. A secondary danger to pConj acquisition, is spread of pbla and β-lactam resistance, which we demonstrate here in vitro. Ultimately, characterizing the contemporary prevalence of doxycycline resistance, and underlying resistance mechanisms, in commensal communities may help us to predict the long-term impact of doxy-PEP on Neisseria, and the likelihood of transferring resistance across species' boundaries.},
}

*Doxycycline/pharmacology/therapeutic use
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Drug Resistance, Bacterial/genetics/drug effects
*Post-Exposure Prophylaxis/methods
*Neisseria/drug effects/genetics
Gonorrhea/prevention & control/microbiology
Bacterial Proteins/genetics
Gene Transfer, Horizontal
Microbial Sensitivity Tests
Female
Male

@article {pmid40216324,
year = {2025},
author = {Muteeb, G and Kazi, RNA and Aatif, M and Azhar, A and Oirdi, ME and Farhan, M},
title = {Antimicrobial resistance: Linking molecular mechanisms to public health impact.},
journal = {SLAS discovery : advancing life sciences R & D},
volume = {33},
number = {},
pages = {100232},
doi = {10.1016/j.slasd.2025.100232},
pmid = {40216324},
issn = {2472-5560},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) develops into a worldwide health emergency through genetic and biochemical adaptations which enable microorganisms to resist antimicrobial treatment. β-lactamases (blaNDM, blaKPC) and efflux pumps (MexAB-OprM) working with mobile genetic elements facilitate fast proliferation of multidrug-resistant (MDR) and exttreme drug-resistant (XDR) phenotypes thus creating major concerns for healthcare systems and community health as well as the agricultural sector.

OBJECTIVES: The review dissimilarly unifies molecular resistance pathways with public health implications through the study of epidemiological data and monitoring approaches and innovative therapeutic solutions. Previous studies separating their attention between molecular genetics and clinical outcomes have been combined into our approach which delivers an all-encompassing analysis of AMR.

KEY INSIGHTS: The report investigates the resistance mechanisms which feature enzymatic degradation and efflux pump overexpression together with target modification and horizontal gene transfer because these factors represent important contributors to present-day AMR developments. This review investigates AMR effects on hospital and community environments where it affects pathogens including MRSA, carbapenem-resistant Klebsiella pneumoniae, and drug-resistant Pseudomonas aeruginosa. This document explores modern AMR management methods that comprise WHO GLASS molecular surveillance systems and three innovative strategies such as CRISPR-modified genome editing and bacteriophage treatments along with antimicrobial peptides and artificial intelligence diagnostic tools.

CONCLUSION: The resolution of AMR needs complete scientific and global operational methods alongside state-of-the-art therapeutic approaches. Worldwide management of drug-resistant infection burden requires both enhanced infection prevention procedures with next-generation antimicrobial strategies to reduce cases effectively.},
}

@article {pmid40215939,
year = {2025},
author = {Chen, Y and Yan, Z and Su, P and Liu, S and Chen, X and Jiang, R and Lu, G and Yuan, S},
title = {Remediation strategy of biochar with different addition approaches on antibiotic resistance genes in riparian zones under dry wet alternation.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138207},
doi = {10.1016/j.jhazmat.2025.138207},
pmid = {40215939},
issn = {1873-3336},
abstract = {The global prevalence of antibiotic resistance genes (ARGs) has aroused increasing concern due to its threat to ecological security and human health. Although biochar has been widely used for pollution remediation including ARGs, little is known its regulation on antibiotics and ARGs propagation under riparian zones, where undergo frequent occurrence of dry and wet alternations (DWA) caused by water-level fluctuation. Therefore, this study investigated the regulative effects of biochar through different addition approaches on ARGs spread in riparian zone sediments. Under DWA, the presence of biochar (2 % w/w) inhibited microbial diversity and function expression, especially for tiled biochar. In addition, compared with DWA, the tiled biochar decreased ARGs abundance by 45.36 %, while the well-mixed increased that by 269.02 %. The ARGs abundance in sediments was positively correlated with mobile genetic element abundance (R[2]=0.996, p < 0.05), indicative of high horizontal gene transfer potential of ARGs. Metabolomics revealed that both DWA and biochar significantly altered microbial metabolism pathways in sediments, involving sulfur metabolism and histidine metabolism. Furthermore, ARGs propagation in riparian zones may be dominantly driven by MGEs, especially by transposases and integrase. These findings highlight the tiled biochar remediation effects on ARGs in riparian zones under DWA caused by global warming.},
}

@article {pmid40215278,
year = {2025},
author = {Dalia, TN and Machouri, M and Lacrouts, C and Fauconnet, Y and Guerois, R and Andreani, J and Radicella, JP and Dalia, AB},
title = {DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {15},
pages = {e2421764122},
pmid = {40215278},
issn = {1091-6490},
support = {R35 GM128674/GM/NIGMS NIH HHS/United States ; ANR-22-CE44-0044//Agence Nationale de la Recherche (ANR)/ ; R35GM128674//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Bacterial Proteins/metabolism/genetics/chemistry ; *Vibrio cholerae/genetics/metabolism ; *Helicobacter pylori/genetics/metabolism ; *Recombination, Genetic ; *Transformation, Bacterial ; *DNA Helicases/metabolism/genetics/chemistry ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria/genetics/metabolism ; Membrane Proteins ; },
abstract = {Natural transformation (NT) represents one of the major modes of horizontal gene transfer in bacterial species. During NT, cells can take up free DNA from the environment and integrate it into their genome by homologous recombination. While NT has been studied for >90 y, the molecular details underlying this recombination remain poorly understood. Recent work has demonstrated that ComM is an NT-specific hexameric helicase that promotes recombinational branch migration in Gram-negative bacteria. How ComM is loaded onto the postsynaptic recombination intermediate during NT, however, remains unclear. Another NT-specific recombination mediator protein that is ubiquitously conserved in both Gram-positive and Gram-negative bacteria is DprA. Here, we uncover that DprA homologs in Gram-negative species contain a C-terminal winged helix domain that is predicted to interact with ComM by AlphaFold. Using Helicobacter pylori and Vibrio cholerae as model systems, we demonstrate that ComM directly interacts with the DprA winged-helix domain, and that this interaction is critical for DprA to recruit ComM to the recombination site to promote branch migration during NT. These results advance our molecular understanding of recombination during this conserved mode of horizontal gene transfer. Furthermore, they demonstrate how structural modeling can help uncover unexpected interactions between well-studied proteins to provide deep mechanistic insight into the molecular coordination required for their activity.},
}

*Bacterial Proteins/metabolism/genetics/chemistry
*Vibrio cholerae/genetics/metabolism
*Helicobacter pylori/genetics/metabolism
*Recombination, Genetic
*Transformation, Bacterial
*DNA Helicases/metabolism/genetics/chemistry
Gene Transfer, Horizontal
*Gram-Negative Bacteria/genetics/metabolism
Membrane Proteins

@article {pmid40215220,
year = {2025},
author = {Zhong, W and Zhou, Y and Che, M and Wang, L and Tian, X and Wang, C and Cheng, Y and Liu, H and Zhou, Z and Peng, G and Zhang, K and Luo, Y and Shi, K and Zhong, Z},
title = {Extended-spectrum β-lactamase-producing Escherichia coli isolated from captive primates: characteristics and horizontal gene transfer ability analysis.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321514},
pmid = {40215220},
issn = {1932-6203},
mesh = {Animals ; *beta-Lactamases/genetics/metabolism ; *Gene Transfer, Horizontal ; *Escherichia coli/genetics/isolation & purification/enzymology/drug effects ; *Escherichia coli Infections/microbiology/veterinary ; China ; Phylogeny ; *Primates/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Animals, Zoo/microbiology ; Microbial Sensitivity Tests ; },
abstract = {The rapid spread of extended-spectrum β-lactamases (ESBLs)-producing Escherichia coli (ESBL-EC) around the world has become a significant challenge for humans and animals. In this study, we aimed to examine the characteristics and horizontal gene transfer (HGT) capacity of ESBL-EC derived from captive primates. We screened for ESBL-EC among a total of 444 multidrug-resistant (MDR) E. coli strains isolated from 13 zoos in China using double-disk test. ESBL genes, mobile genetic elements (MGEs), and virulence-associated genes (VAGs) in ESBL-EC were detected through polymerase chain reaction (PCR). Furthermore, conjugation experiments were conducted to examine the HGT capacity of ESBL-EC, and the population structure (phylogenetic groups and MLST) was determined. Our results showed that a total of 69 (15.54%, 69/444) ESBL-EC strains were identified, and 5 variants of blaCTX and 3 variants of blaTEM were detected. The highest detection rate was blaCTX-M-55 (49.28%, 34/69), followed by blaCTX-M-15 (39.13%, 27/69). Ten MGEs were detected and the most prevalent was IS26 (78.26%, 54/69), followed by ISEcp1 (60.87%, 42/69). Eighteen combinations of MGEs were detected, in which ISEcp1 + IS26 was predominant (18.84%, n = 13). A total of 15 VAGs were detected and the most prevalent was fimC (84.06%, 58/69), followed by sitA (78.26%, 54/69). Furthermore, HGT ability analysis results showed that 40.58% (28/69) of ESBL-EC strains exhibited the ability to engage in conjugative transfer. Plasmid typing revealed that IncFIB (78.57%, 22/28) had the highest detection rates. Furthermore, antibiotic resistance genes (ARGs) of blaTEM-135, tetA and qnrS; MGEs of IS26, trbC and ISCR3/14 showed high rates of conjugative transfer. The population structure analysis showed that the phylogroup B1 and ST2161 were the most prevalent. ESBL-EC poses a potential threat to captive primates and may spread to other animals, humans, and the environment. It is imperative to implement measures to prevent the transmission of ESBL-EC among captive primates.},
}

Animals
*beta-Lactamases/genetics/metabolism
*Gene Transfer, Horizontal
*Escherichia coli/genetics/isolation & purification/enzymology/drug effects
*Escherichia coli Infections/microbiology/veterinary
China
Phylogeny
*Primates/microbiology
Drug Resistance, Multiple, Bacterial/genetics
Animals, Zoo/microbiology
Microbial Sensitivity Tests

@article {pmid40214801,
year = {2025},
author = {Sun, J and Wang, X and He, Y and Han, M and Li, M and Wang, S and Chen, J and Zhang, Q and Yang, B},
title = {Environmental fate of antibiotic resistance genes in livestock farming.},
journal = {Archives of microbiology},
volume = {207},
number = {5},
pages = {120},
pmid = {40214801},
issn = {1432-072X},
support = {32272444//National Natural Science Foundation of China/ ; },
mesh = {*Livestock/microbiology ; Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Animal Husbandry ; Farms ; Manure/microbiology ; Genes, Bacterial ; },
abstract = {As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.},
}

*Livestock/microbiology
Animals
Humans
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
Animal Husbandry
Farms
Manure/microbiology
Genes, Bacterial

@article {pmid40210157,
year = {2025},
author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY},
title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126209},
doi = {10.1016/j.envpol.2025.126209},
pmid = {40210157},
issn = {1873-6424},
mesh = {*Aquaculture ; Ponds/microbiology ; Animals ; Metagenomics ; *Brachyura ; *Drug Resistance, Microbial/genetics ; China ; Bacteria/genetics ; Environmental Monitoring ; },
abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58 %) and Acidobacteria (6.04 %) were identified as the dominant phyla and Thiobacillus (1.84 %) and Lysobacter (0.99 %) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r > 0.7, p < 0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p < 0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.},
}

*Aquaculture
Ponds/microbiology
Animals
Metagenomics
*Brachyura
*Drug Resistance, Microbial/genetics
China
Bacteria/genetics
Environmental Monitoring

@article {pmid40209969,
year = {2025},
author = {Dündar, T and Köksal Çakırlar, F},
title = {Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104298},
doi = {10.1016/j.resmic.2025.104298},
pmid = {40209969},
issn = {1769-7123},
abstract = {Coagulase-negative staphylococci (CNS) are emerging as significant contributors to antimicrobial resistance, yet their genomic characteristics remain incompletely understood. This study presents a whole-genome analysis of 12 multidrug-resistant CNS strains (Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis) isolated from blood cultures, focusing on antimicrobial resistance genes, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) mechanisms. We identified 22 resistance genes conferring resistance to 11 antimicrobial classes, many of which were plasmid-associated. Notably, we report the first detection of the ISSha1 insertion sequence in S. hominis, along with novel resistance plasmids, including pGO1 and VRSAp in S. haemolyticus and pAMα1 in S. hominis. The identification of bacteriophage-derived sequences in S. haemolyticus and S. hominis suggests a role for phages in genetic exchange. CRISPR sequences and a Cas gene were detected in S. hominis, suggesting a potential but unconfirmed role in restricting gene transfer. Additionally, pGO1 was identified as a conjugative plasmid, while pAMα1 and VRSAp were determined to be mobilizable, reinforcing the role of CNS in resistance dissemination. These results highlight CNS as reservoirs of antimicrobial resistance genes and emphasize the importance of species-specific genomic surveillance. Proactive monitoring of CNS is crucial for controlling antimicrobial resistance in clinical settings.},
}

@article {pmid40209228,
year = {2025},
author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ},
title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.},
journal = {Environmental science & technology},
volume = {59},
number = {15},
pages = {7600-7612},
doi = {10.1021/acs.est.4c10888},
pmid = {40209228},
issn = {1520-5851},
mesh = {*Lakes/microbiology ; *Saxitoxin ; *Cyanobacteria/genetics ; *Harmful Algal Bloom ; },
abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.},
}

*Lakes/microbiology
*Saxitoxin
*Cyanobacteria/genetics
*Harmful Algal Bloom

@article {pmid40207493,
year = {2025},
author = {Swain, PP and Sahoo, RK},
title = {Blocking horizontal transfer of antibiotic resistance genes: an effective strategy in combating antibiotic resistance.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/1040841X.2025.2489463},
pmid = {40207493},
issn = {1549-7828},
abstract = {Antimicrobial resistance (AMR) poses a significant public health threat, with emerging and novel forms of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) potentially crossing international borders and challenging the global health systems. The rate of development of antibiotic resistance surpasses the development of new antibiotics. Consequently, there is a growing threat of bacteria acquiring resistance even to newer antibiotics further complicating the treatment of bacterial infections. Horizontal gene transfer (HGT) is the key mechanism for the spread of antibiotic resistance in bacteria through the processes of conjugation, transformation, and transduction. Several compounds, other than antibiotics, have also been shown to promote HGT of ARGs. Given the crucial role of HGT in the dissemination of ARGs, inhibition of HGT is a key strategy to mitigate AMR. Therefore, this review explores the contribution of HGT in bacterial evolution, identifies specific hotspots andhighlights the role of HGT inhibitors in impeding the spread of ARGs. By specifically focusing on the HGT mechanism and its inhibition, these inhibitors offer a highly promising approach to combating AMR.},
}

@article {pmid40207084,
year = {2025},
author = {Katonge, JH and Ally, ZK},
title = {Evolutionary relationships and genetic diversity in the BlaTEM gene among selected gram-negative bacteria.},
journal = {Biochemistry and biophysics reports},
volume = {42},
number = {},
pages = {101985},
pmid = {40207084},
issn = {2405-5808},
abstract = {This study investigates the genetic diversity and evolutionary relationships of the blaTEM gene, a major determinant of beta-lactam antibiotic resistance. We analyzed nucleotide sequences of 32 β-lactamase-producing strains from Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, and Acinetobacter baumannii obtained from public databases. Sequence analysis revealed 32 distinct sequences with 298 segregating sites and 303 mutations, indicating substantial genetic variability. A high level of haplotype diversity was observed, with 24 distinct haplotypes, reflecting evolutionary pressures and horizontal gene transfer. Phylogenetic analysis showed clear clades, suggesting the evolutionary relationships among blaTEM variants and interspecies gene transfer. The resistance profiles correlated with the genetic findings, particularly mutations. This analysis draws attention to the ongoing adaptive evolution of antibiotic resistance mechanisms, as well as the need for continued monitoring and novel therapeutic strategies. Further research with larger sample sizes and functional validation is needed to fully understand the implications of these variants in antibiotic resistance.},
}

@article {pmid40204742,
year = {2025},
author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB},
title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12156},
pmid = {40204742},
issn = {2045-2322},
mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; },
abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.},
}

*Gene Transfer, Horizontal
Animals
Humans
*Metagenomics/methods
Feces/microbiology
*Bacteria/genetics/drug effects
Nepal
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
Virulence Factors/genetics
Birds/microbiology
Metagenome

@article {pmid40204671,
year = {2025},
author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH},
title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.},
journal = {Environmental science & technology},
volume = {59},
number = {15},
pages = {7722-7735},
doi = {10.1021/acs.est.5c00246},
pmid = {40204671},
issn = {1520-5851},
mesh = {*Microplastics ; Biodegradation, Environmental ; Biodegradable Plastics ; *Drug Resistance, Microbial/genetics ; },
abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.},
}

*Microplastics
Biodegradation, Environmental
Biodegradable Plastics
*Drug Resistance, Microbial/genetics

@article {pmid40202301,
year = {2025},
author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J},
title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149624},
doi = {10.1128/msystems.01496-24},
pmid = {40202301},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.

IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.},
}

@article {pmid40199202,
year = {2025},
author = {Ferheen, I and Cimarelli, L and Marcheggiani, S and Klümper, U and Spurio, R},
title = {Plastic-mediated transformation: A new route to navigate plasmid-borne antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {976},
number = {},
pages = {179125},
doi = {10.1016/j.scitotenv.2025.179125},
pmid = {40199202},
issn = {1879-1026},
mesh = {*Plasmids/genetics ; *Plastics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Transformation, Bacterial ; },
abstract = {Among the anthropogenic sources of pollution, accumulation of plastic polymers in aquatic ecosystems is scaling at unprecedented rates and emerging as a new niche for bacterial colonization and horizontal gene transfer (HGT). The current study focuses on determining the ability of bacteria to acquire plasmid DNA from the extracellular environment under exposure to different treatments (soil, CaCl2 salt solution, soil plus CaCl2, Escherichia coli cell-free extract, and plastic debris) that simulate possible conditions experienced by microorganisms in natural environments. The transformation frequency of two plasmids (pACYC:Hyg and pBAV-1k) was tested following two experimental approaches: single species microcosm of E. coli cells (SSM) and bacterial consortium microcosm (BCM) of strains isolated from freshwater ecosystems. Plastic fragments (with consistent results obtained using polypropylene) proved to be remarkably efficient in increasing the bacterial competence towards plasmid DNA uptake as compared to the other conditions. Moreover, the effects of different plastic polymers and four incubation conditions on bacterial DNA transformation were analyzed to gain deeper insight into the exchange of genetic material. Our findings from both experimental approaches demonstrate that simultaneous incubation of microorganisms, plasmids, and plastic fragments enhances the bacterial ability to uptake plasmids and to express genes required for survival under stress conditions. The two microcosm models prove to be promising tools to mimic natural transformation events leading to the dissemination of antibiotic-resistant genes via HGT in the environment.},
}

*Plasmids/genetics
*Plastics
Escherichia coli/genetics
Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
*Transformation, Bacterial

@article {pmid40199074,
year = {2025},
author = {Li, ZY and Cui, YW and Liang, HK and Yan, HJ and Yang, RC},
title = {Tetracycline degradation by a mixed culture of halotolerant fungi-bacteria under static magnetic field: Mechanism and antibiotic resistance genes transfer.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138181},
doi = {10.1016/j.jhazmat.2025.138181},
pmid = {40199074},
issn = {1873-3336},
abstract = {Efficient antibiotics removal lowers the transmission risk of antibiotic resistance genes (ARGs). However, low efficiency limits the application of biological methods for antibiotics removal. Herein, a mixed culture of halotolerant fungi-bacteria was used for treatment of saline wastewater containing tetracycline (TC). Furthermore, static magnetic field (SMF) was used to increase TC removal. The study examined the effectiveness of SMF in removing antibiotics from saline wastewater and the associated risk of ARGs transmission. The results demonstrated that the application of a 40 mT SMF significantly improved the TC removal efficiency by 37.09 %, compared to the control (SMF=0) The TC was mainly removed through biodegradation and adsorption. In biodegradation, SMF enhanced electron transport system activity, and activities of lignin-degrading enzymes which led to higher TC biodegradation. The activity of lactate dehydrogenase and malondialdehyde decreased, lowering the damage of microbial cell membranes by TC. During the adsorption process, higher generation of extracellular polymeric substances was observed under SMF, which caused an increase in TC removal via adsorption. Microbial community analysis revealed that SMF facilitated the enrichment of TC-degrading microorganisms. Under SMF, vertical gene transfer of ARGs increased, while horizontal gene transfer risk decreased due to a reduction in mobile genetic elements (intl1) abundance. This study demonstrates that SMF is a promising strategy for enhancing TC removal efficiency, providing a basis for improved antibiotic wastewater management.},
}

@article {pmid40195311,
year = {2025},
author = {Rao, BD and Gomez-Gil, E and Peter, M and Balogh, G and Nunes, V and MacRae, JI and Chen, Q and Rosenthal, PB and Oliferenko, S},
title = {Horizontal acquisition of prokaryotic hopanoid biosynthesis reorganizes membrane physiology driving lifestyle innovation in a eukaryote.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3291},
pmid = {40195311},
issn = {2041-1723},
support = {ALTF 712-2022//European Molecular Biology Organization (EMBO)/ ; CC0102/ARC_/Arthritis Research UK/United Kingdom ; 103741/Z/14/Z//Wellcome Trust (Wellcome)/ ; 220790/Z/20/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Schizosaccharomyces/genetics/metabolism/physiology ; *Gene Transfer, Horizontal ; Sterols/metabolism/biosynthesis ; *Intramolecular Transferases/genetics/metabolism ; *Cell Membrane/metabolism ; *Triterpenes/metabolism ; },
abstract = {Horizontal gene transfer is a source of metabolic innovation and adaptation to new environments. How new metabolic functionalities are integrated into host cell biology is largely unknown. Here, we probe this fundamental question using the fission yeast Schizosaccharomyces japonicus, which has acquired a squalene-hopene cyclase Shc1 through horizontal gene transfer. We show that Shc1-dependent production of hopanoids, mimics of eukaryotic sterols, allows S. japonicus to thrive in anoxia, where sterol biosynthesis is not possible. We demonstrate that glycerophospholipid fatty acyl asymmetry, prevalent in S. japonicus, is crucial for accommodating both sterols and hopanoids in membranes and explain how Shc1 functions alongside the sterol biosynthetic pathway to support membrane properties. Reengineering experiments in the sister species S. pombe show that hopanoids entail new traits in a naïve organism, but the acquisition of a new enzyme may trigger profound reorganization of the host metabolism and physiology.},
}

*Schizosaccharomyces/genetics/metabolism/physiology
*Gene Transfer, Horizontal
Sterols/metabolism/biosynthesis
*Intramolecular Transferases/genetics/metabolism
*Cell Membrane/metabolism
*Triterpenes/metabolism

@article {pmid40190753,
year = {2025},
author = {Nahum, Y and Muhvich, J and Morones-Ramirez, JR and Casillas-Vega, NG and Zaman, MH},
title = {Biofilms as potential reservoirs of antimicrobial resistance in vulnerable settings.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1568463},
pmid = {40190753},
issn = {2296-2565},
mesh = {*Biofilms/drug effects/growth & development ; Humans ; *Wastewater/microbiology ; *Drug Resistance, Bacterial ; *Vulnerable Populations ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial ; },
abstract = {Antimicrobial resistance is a major global health threat, characterized by the ability of microorganisms to withstand the effects of antimicrobial agents. Biofilms, as unique microbial communities, significantly contribute to this threat. They provide a protective environment for pathogens, facilitate horizontal gene transfer, and create an ideal setting for the persistence and evolution of resistant bacteria. This issue can be particularly important in low-income settings and vulnerable communities, such as formal and informal refugee and migrant camps. These settings usually have limited access to healthcare resources and appropriate treatments, contributing to the selective pressure that promotes the survival and proliferation of resistant bacteria. Thus, biofilms formed in wastewater in these areas can play a critical role in spreading antimicrobial resistance or acting as hidden reservoirs for future outbreaks. While emerging efforts focus on detecting antibiotic resistance genes and planktonic bacteria in wastewater, biofilms may be a source of under-appreciated antimicrobial resistance, creating a significant gap in our understanding of resistance dynamics in wastewater systems. Incorporating biofilm surveillance into wastewater monitoring strategies in vulnerable settings can help develop a more comprehensive understanding of resistance transmission and more effective intervention measures in these settings.},
}

*Biofilms/drug effects/growth & development
Humans
*Wastewater/microbiology
*Drug Resistance, Bacterial
*Vulnerable Populations
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial

@article {pmid40189939,
year = {2025},
author = {Wang, H and Wang, D and Shao, B and Li, J and Li, Z and Chase, MW and Li, J and Feng, Y and Wen, Y and Qin, S and Chen, B and Wu, Z and Jin, X},
title = {Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera.},
journal = {Molecular biology and evolution},
volume = {42},
number = {4},
pages = {},
pmid = {40189939},
issn = {1537-1719},
support = {2022YFF1301704//National Key Research and Development Program of China/ ; 2023-QYCX-02//Linzhi Science and Technology Program/ ; 31870195//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; *Chromosomes, Plant/genetics ; *Gastrodia/genetics ; Evolution, Molecular ; Phylogeny ; Genome, Plant ; DNA Copy Number Variations ; *Orchidaceae/genetics ; Heterotrophic Processes ; },
abstract = {The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel the evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1 Mb, each consisting of numerous, unequally abundant chromosomes or contigs. Size variation might have evolved through chromosome rearrangements followed by stochastic loss of "dispensable" chromosomes, with deletion-biased mutations. The discovery of a hyper-abundant (∼15 times intragenomic average) chromosome in two assemblies represents the hitherto most extreme copy number variation in any mitogenomes, with similar architectures discovered in two metazoan lineages. Transferred sequence contents highlight asymmetric evolutionary consequences of heterotrophy: despite drastically reduced intracellular plastome transfers convergent across heterotrophic plants, their rarity of horizontally acquired sequences sharply contrasts parasitic plants, where massive transfers from their hosts prevail. Rates of sequence evolution are markedly elevated but not explained by copy number variation, extending prior findings of accelerated molecular evolution from parasitic to heterotrophic plants. Putative evolutionary scenarios for these mitogenomic convergence and divergence fit well with the common (e.g. plastome contraction) and specific (e.g. host identity) aspects of the two heterotrophic types. These idiosyncratic mycoheterotrophs expand known architectural variability of plant mitogenomes and provide mechanistic insights into their content and size variation.},
}

*Genome, Mitochondrial
*Chromosomes, Plant/genetics
*Gastrodia/genetics
Evolution, Molecular
Phylogeny
Genome, Plant
DNA Copy Number Variations
*Orchidaceae/genetics
Heterotrophic Processes

@article {pmid40188791,
year = {2025},
author = {Huang, X and Tan, Z and Wei, J and Bai, X},
title = {Super-robust synthetic microorganism can get chlorine resistance in advance and transfer their inserted DNA sequence in genome to indigenous bacteria in water.},
journal = {Water research},
volume = {281},
number = {},
pages = {123594},
doi = {10.1016/j.watres.2025.123594},
pmid = {40188791},
issn = {1879-2448},
abstract = {CRISPR-Cas gene editing tools have brought us to an era of synthetic biology that will change the world. Synthetic microorganisms (SMs) have brought enormous economic benefits and will contribute more in the future. Among them, super-robust SMs can overcome the stresses in bioproduction and further increase yield. However, when they are released into the environments, little is known about their fates and risks to human health. In this study, it was found that the gene editing super-robust SM could transfer its inserted DNA sequence in genome to the indigenous bacteria in surface water and showed stronger resistance to chlorine compared with wild-type bacteria. Chlorine disinfection did slight damage on cell membrane of super-robust SM, which decreased ATP leakage and DNA damage, and thereby promoted bacterial survival. Chlorine-injured super-robust SM retained high respiratory activity, and could resuscitate and regenerate. Less damage on super-robust SM cell membrane could prevent chlorine from entering the cells and resulted in lower ROS generation. Its DNA repair system and antioxidant system could still function under high concentrations of chlorine exposure. These findings provided new insights into the fates and environmental risks of SMs as an emerging biological pollutant in water supply system.},
}

@article {pmid40188040,
year = {2025},
author = {Yang, Y and Liu, W and Zhao, Z and Guo, K and Wang, X and Lou, Z and Yang, X and Gong, L and Wang, K and Liu, X and Xu, H and Liu, Q and Zheng, B and Jiang, X},
title = {Genomic insights and epidemiology of mcr-1-Carrying Escherichia albertii isolated from agricultural soil in China.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {344},
pmid = {40188040},
issn = {1471-2164},
mesh = {China/epidemiology ; *Soil Microbiology ; Phylogeny ; *Escherichia/genetics/isolation & purification/drug effects/classification ; *Genomics ; Humans ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; *Escherichia coli Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Agriculture ; },
abstract = {BACKGROUND: Polymyxins are critical in treating multidrug-resistant Gram-negative bacteria infections, yet their overuse has spurred the emergence of polymyxin-resistant pathogens globally. This study aims to analyze the genomic characteristics of the Escherichia albertii strain 6S-65-1 carrying the mcr-1 gene and to investigate the global epidemiology of mcr-1-carrying E. albertii strains.

RESULTS: In this study, we identified and analyzed a polymyxin-resistant Escherichia albertii strain (6S-65-1) carrying the mcr-1 gene, isolated from agricultural soil in China. Whole-genome sequencing and comparative genomic analyses revealed two chromosomal integrations of the mcr-1 gene within Tn6330 transposon structures, indicating its capacity for horizontal gene transfer. Strain 6S-65-1 also harbors other antimicrobial resistance genes, including tet(A), sul3, and aph (3')-Ia, enhancing its resistance profile. Comparative genomic analysis of E. albertii genomes in the NCBI database revealed that mcr-1-carrying E. albertii strains are geographically restricted to China and Japan, and have been isolated from both animals and humans. Phylogenetic analysis revealed that strain 6S-65-1 was most closely related to a human-derived strain from Japan (SAMD00164101), with both strains carried virulence genes (cdt, paa, and eae) that enable them to form attaching and effacing (A/E) lesions. Among all publicly available ST4619 E. albertii genomes, strain 6S-65-1 is the first to carry the mcr-1 gene.

CONCLUSION: Our findings offer new insights into the epidemiology and genomic features of mcr-1-carrying E. albertii, underscoring the need for targeted management strategies to curb its spread. These findings underscore the importance of "One Health" approaches to antimicrobial resistance, which require coordinated efforts across human, animal and the environmental health sectors.},
}

China/epidemiology
*Soil Microbiology
Phylogeny
*Escherichia/genetics/isolation & purification/drug effects/classification
*Genomics
Humans
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
*Escherichia coli Proteins/genetics
Drug Resistance, Bacterial/genetics
Agriculture

@article {pmid40186988,
year = {2025},
author = {Liu, L and Zhang, QH and Li, MZ and Li, RT and He, Z and Dechesne, A and Smets, BF and Sheng, GP},
title = {Single-cell analysis reveals antibiotic affects conjugative transfer by modulating bacterial growth rather than conjugation efficiency.},
journal = {Environment international},
volume = {198},
number = {},
pages = {109385},
doi = {10.1016/j.envint.2025.109385},
pmid = {40186988},
issn = {1873-6750},
mesh = {*Anti-Bacterial Agents/pharmacology ; Single-Cell Analysis ; *Conjugation, Genetic/drug effects ; *Escherichia coli/drug effects/genetics/growth & development ; *Gene Transfer, Horizontal/drug effects ; Drug Resistance, Bacterial/genetics ; Plasmids ; },
abstract = {Antibiotic resistance genes (ARGs) pose a significant threat to human health and the environment. Quantifying the efficiency of horizontal gene transfer (HGT) is challenging due to diverse biological and environmental influences. Single-cell level approaches are well-suited for investigating conjugative transfer, given its reliance on cell-to-cell contact nature and its capacity to offer insights into population-level responses. This study introduces a self-developed system for automated time-lapse image acquisition and analysis. Using a custom dual-chamber microfluidic chip and Python-based image analysis pipeline, we dynamically quantify the ARGs conjugation efficiency at single-cell level. By combining experiments with individual-based modelling, we isolate the effects of subinhibitory antibiotic concentrations on conjugation efficiency from those related to bacterial growth dynamics. No significant variation in Escherichia coli conjugation efficiency was observed across kanamycin concentrations (0 to 50 mg l[-1]). Moreover, recipient cells with higher growth rates show a greater propensity for plasmid acquisition, suggesting the physiological state of cells pre-conjugation influences their susceptibility to gene transfer. Our methodology eliminates population growth bias, revealing the intrinsic nature of conjugation efficiency. This approach advances our understanding of the factors influencing HGT efficiency and holds promise for studying other microbial interactions. SYNOPSIS: This study employs single-cell analysis to reveal that subinhibitory concentrations of antibiotics affect the conjugative transfer of antibiotic resistance genes by modulating bacterial growth rate rather than conjugation efficiency.},
}

*Anti-Bacterial Agents/pharmacology
Single-Cell Analysis
*Conjugation, Genetic/drug effects
*Escherichia coli/drug effects/genetics/growth & development
*Gene Transfer, Horizontal/drug effects
Drug Resistance, Bacterial/genetics
Plasmids

@article {pmid40183128,
year = {2025},
author = {Bolzoni, L and Scaltriti, E and Bracchi, C and Angelone, S and Menozzi, I and Taddei, R and Alba, P and Carfora, V and Diaconu, EL and Morganti, M and Dodi, A and Berni, M and Manni, L and Vinci, M and Tambassi, M and Mazzera, L and Venturelli, I and Ambretti, S and Battisti, A and Pongolini, S},
title = {Emergence of Salmonella enterica carrying bla OXA-181 carbapenemase gene, Italy, 2021 to 2024.},
journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin},
volume = {30},
number = {13},
pages = {},
pmid = {40183128},
issn = {1560-7917},
mesh = {*beta-Lactamases/genetics ; *Salmonella enterica/genetics/isolation & purification/enzymology ; Humans ; Animals ; *Bacterial Proteins/genetics ; Italy/epidemiology ; Swine/microbiology ; Phylogeny ; Plasmids/genetics ; Microbial Sensitivity Tests ; *Salmonella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {Between 2021 and 2024, we detected carbapenemase gene blaOXA-181 in 16 of 11,398 Salmonella enterica (SE) isolates: 10 SE 1,4,[5],12:i:-, three Bovismorbificans, two London and one Rissen from pigs, humans, pork meat and wild roe deer. The gene was first detected in pig isolates, later in humans, suggesting zoonotic transmission. Phylogenetic analysis indicated that horizontal transfer, mainly through plasmids, contributed to the spread. These findings highlight a possible emerging public health threat and the importance of One Health surveillance.},
}

*beta-Lactamases/genetics
*Salmonella enterica/genetics/isolation & purification/enzymology
Humans
Animals
*Bacterial Proteins/genetics
Italy/epidemiology
Swine/microbiology
Phylogeny
Plasmids/genetics
Microbial Sensitivity Tests
*Salmonella Infections/microbiology/epidemiology
Anti-Bacterial Agents/pharmacology
Gene Transfer, Horizontal

@article {pmid40173243,
year = {2025},
author = {Tsoi, R and Son, HI and Hamrick, GS and Tang, K and Bethke, JH and Lu, J and Maddamsetti, R and You, L},
title = {A predatory gene drive for targeted control of self-transmissible plasmids.},
journal = {Science advances},
volume = {11},
number = {14},
pages = {eads4735},
pmid = {40173243},
issn = {2375-2548},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; *Gene Drive Technology/methods ; },
abstract = {Suppressing plasmid transfer in microbial communities has profound implications due to the role of horizontal gene transfer (HGT) in spreading and maintaining diverse functional traits such as metabolic functions, virulence factors, and antibiotic resistance. However, existing tools for inhibiting HGT are limited in their modes of delivery, efficacy, and scalability. Here, we present a versatile denial-of-spread (DoS) strategy to target and eliminate specific conjugative plasmids. Our strategy exploits retrotransfer, whereby an engineered DoS plasmid is introduced into host cells containing a target plasmid. Acting as a predatory gene drive, DoS propagates itself at the expense of the target plasmid, through competition or active elimination. Once the target plasmid is eradicated, DoS is removed via induced plasmid suicide, resulting in a community containing neither plasmid. The strategy is tunable and scalable for various conjugative plasmids, different mechanisms of plasmid inheritance interruption, and diverse environmental contexts. DoS represents a new tool for precise control of gene persistence in microbial communities.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
Conjugation, Genetic
*Gene Drive Technology/methods

@article {pmid40173202,
year = {2025},
author = {Loyo, CL and Grossman, AD},
title = {A phage-encoded counter-defense inhibits an NAD-degrading anti-phage defense system.},
journal = {PLoS genetics},
volume = {21},
number = {4},
pages = {e1011551},
pmid = {40173202},
issn = {1553-7404},
support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM148343/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacillus subtilis/virology/genetics ; *NAD/metabolism ; *Bacteriophages/genetics ; *Bacterial Proteins/genetics/metabolism ; *Bacillus Phages/genetics/pathogenicity ; Gene Transfer, Horizontal ; },
abstract = {Bacteria contain a diverse array of genes that provide defense against predation by phages. Anti-phage defense genes are frequently located on mobile genetic elements and spread through horizontal gene transfer. Despite the many anti-phage defense systems that have been identified, less is known about how phages overcome the defenses employed by bacteria. The integrative and conjugative element ICEBs1 in Bacillus subtilis contains a gene, spbK, that confers defense against the temperate phage SPβ through an abortive infection mechanism. Using genetic and biochemical analyses, we found that SpbK is an NADase that is activated by binding to the SPβ phage portal protein YonE. The presence of YonE stimulates NADase activity of the TIR domain of SpbK and causes cell death. We also found that the SPβ-like phage Φ3T has a counter-defense gene that prevents SpbK-mediated abortive infection and enables the phage to produce viable progeny, even in cells expressing spbK. We made SPβ-Φ3T hybrid phages that were resistant to SpbK-mediated defense and identified a single gene in Φ3T (phi3T_120, now called nip for NADase inhibitor from phage) that was both necessary and sufficient to block SpbK-mediated anti-phage defense. We found that Nip binds to the TIR (NADase) domain of SpbK and inhibits NADase activity. Our results provide insight into how phages overcome bacterial immunity by inhibiting enzymatic activity of an anti-phage defense protein.},
}

*Bacillus subtilis/virology/genetics
*NAD/metabolism
*Bacteriophages/genetics
*Bacterial Proteins/genetics/metabolism
*Bacillus Phages/genetics/pathogenicity
Gene Transfer, Horizontal

@article {pmid40173128,
year = {2025},
author = {Sichert, A},
title = {A single enzyme becomes a Swiss Army knife.},
journal = {PLoS biology},
volume = {23},
number = {4},
pages = {e3003072},
pmid = {40173128},
issn = {1545-7885},
mesh = {Gene Transfer, Horizontal ; *Diatoms/genetics/enzymology ; Photosynthesis/genetics ; Phaeophyceae/genetics/enzymology/metabolism ; Alginates/metabolism ; },
abstract = {An alga that abandoned photosynthesis? This Primer explores a PLOS Biology study showing that a single horizontal gene transfer event allowed the diatom Nitzschia sing1 to evolve a complete enzymatic machinery to break down alginate from brown algae, unlocking a new ecological niche.},
}

Gene Transfer, Horizontal
*Diatoms/genetics/enzymology
Photosynthesis/genetics
Phaeophyceae/genetics/enzymology/metabolism
Alginates/metabolism

@article {pmid40168690,
year = {2025},
author = {Jaafar, T and Carvalhais, E and Shrestha, A and Cochrane, R and Meaney, J and Brumwell, S and Hamadache, S and Nasrollahi, V and Karas, BJ},
title = {Engineering conjugative plasmids for inducible horizontal DNA transfer.},
journal = {Canadian journal of microbiology},
volume = {71},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2024-0241},
pmid = {40168690},
issn = {1480-3275},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Conjugation, Genetic ; Promoter Regions, Genetic ; *Escherichia coli/genetics ; *Genetic Engineering/methods ; Arabinose/metabolism ; },
abstract = {Rapidly developing microbial resistance to existing antimicrobials poses a growing threat to public health and global food security. Current chemical-based treatments target cells by inhibiting growth or metabolic function, but their effectiveness is diminishing. To address the growing antimicrobial resistance crisis, there is an urgent need for innovative therapies. Conjugative plasmids, a natural mechanism of horizontal gene transfer in bacteria, have been repurposed to deliver toxic genetic cargo to recipient cells, showing promise as next-generation antimicrobial agents. However, the ecological risks posed by unintended gene transfer require robust biocontainment strategies. In this study, we developed inducible conjugative plasmids to solve these challenges. Utilizing an arabinose-inducible promoter, we evaluated 13 plasmids with single essential gene deletions, identifying trbC and trbF as strong candidates for stringent regulation. These plasmids demonstrated inducibility in both cis and trans configurations, with induction resulting in up to a 5-log increase in conjugation efficiency compared to uninduced conditions. Although challenges such as reduced conjugation efficiency and promoter leakiness persist, this work establishes a foundation for the controlled transfer of plasmids, paving the way for safer and more effective antimicrobial technologies.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Conjugation, Genetic
Promoter Regions, Genetic
*Escherichia coli/genetics
*Genetic Engineering/methods
Arabinose/metabolism

@article {pmid40168346,
year = {2025},
author = {Lim, ZH and Zheng, P and Quek, C and Nowrousian, M and Aachmann, FL and Jedd, G},
title = {Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization.},
journal = {PLoS biology},
volume = {23},
number = {4},
pages = {e3003038},
pmid = {40168346},
issn = {1545-7885},
mesh = {*Gene Transfer, Horizontal ; *Gene Duplication ; *Diatoms/genetics/metabolism ; *Polysaccharides/metabolism ; Phylogeny ; Heterotrophic Processes ; Alginates/metabolism ; Phaeophyceae/genetics ; Polysaccharide-Lyases/genetics/metabolism ; Evolution, Molecular ; },
abstract = {A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.},
}

*Gene Transfer, Horizontal
*Gene Duplication
*Diatoms/genetics/metabolism
*Polysaccharides/metabolism
Phylogeny
Heterotrophic Processes
Alginates/metabolism
Phaeophyceae/genetics
Polysaccharide-Lyases/genetics/metabolism
Evolution, Molecular

@article {pmid40166311,
year = {2025},
author = {Inglis, LK and Grigson, SR and Roach, MJ and Edwards, RA},
title = {Prophages as a source of antimicrobial resistance genes in the human microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166311},
issn = {2692-8205},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
abstract = {Prophages-viruses that integrate into bacterial genomes-are ubiquitous in the microbial realm. Prophages contribute significantly to horizontal gene transfer, including the potential spread of antimicrobial resistance (AMR) genes, because they can collect host genes. Understanding their role in the human microbiome is essential for fully understanding AMR dynamics and possible clinical implications. We analysed almost 15,000 bacterial genomes for prophages and AMR genes. The bacteria were isolated from diverse human body sites and geographical regions, and their genomes were retrieved from GenBank. AMR genes were detected in 6.6% of bacterial genomes, with a higher prevalence in people with symptomatic diseases. We found a wide variety of AMR genes combating multiple drug classes. We discovered AMR genes previously associated with plasmids, such as blaOXA-23 in Acinetobacter baumannii prophages or genes found in prophages in species they had not been previously described in, such as mefA-msrD in Gardnerella prophages, suggesting prophage-mediated gene transfer of AMR genes. Prophages encoding AMR genes were found at varying frequencies across body sites and geographical regions, with Asia showing the highest diversity of AMR genes.},
}

@article {pmid40166188,
year = {2025},
author = {Gonçalves, C and Steenwyk, JL and Rinker, DC and Opulente, DA and LaBella, AL and Harrison, MC and Wolters, JF and Zhou, X and Shen, XX and Covo, S and Groenewald, M and Hittinger, CT and Rokas, A},
title = {Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166188},
issn = {2692-8205},
support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; },
abstract = {Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing DNA repair genes. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina to examine the relationship between reduced DNA repair repertoires and elevated evolutionary rates. We identified three distantly related lineages-encompassing 12% of species-with substantially reduced sets of DNA repair genes and the highest evolutionary rates in the entire subphylum. Two of these "faster-evolving lineages" (FELs)-a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)-are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of DNA repair gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. Genomic signatures in the W/S clade are consistent with a substantial mutational burden, including pronounced A|T bias and signatures of endogenous DNA damage. The W/S clade appears to mitigate UV-induced damage through horizontal acquisition of a bacterial photolyase gene, underscoring how gene loss may be offset by nonvertical evolution. These findings highlight how the loss of DNA repair genes gave rise to hypermutators that persist across macroevolutionary timescales, with horizontal gene transfer as an avenue for partial functional compensation.},
}

@article {pmid40166157,
year = {2025},
author = {Gozashti, L and Corbett-Detig, R},
title = {Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40166157},
issn = {2692-8205},
support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; },
abstract = {Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal gene transfer (HGT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HGT since they often integrate into host genomes and have been implicated in widespread HGT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses as well as giant dsDNA viruses. By querying a previously annotated set of maverick-polinton-like proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements show the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HGT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.},
}

@article {pmid40165783,
year = {2025},
author = {Herbert, A and Hancock, CN and Cox, B and Schnabel, G and Moreno, D and Carvalho, R and Jones, J and Paret, M and Geng, X and Wang, H},
title = {Corrigendum: Oxytetracycline and streptomycin resistance genes in Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot in peach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1580418},
doi = {10.3389/fmicb.2025.1580418},
pmid = {40165783},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.821808.].},
}