@article {pmid40626882,
year = {2025},
author = {Bello-López, E and Kawabata, A and Cantero, J and Mendoza, S and Pertile, E and Perez-Osegura, A and Cevallos, MA and Peralta, H and Aguilar-Vera, A and Castillo-Ramirez, S},
title = {Genomic epidemiology reveals antibiotic resistance transfer and polyclonal dissemination of Acinetobacter baumannii in a Paraguayan hospital.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0007725},
doi = {10.1128/aac.00077-25},
pmid = {40626882},
issn = {1098-6596},
abstract = {Acinetobacter baumannii is a major nosocomial pathogen worldwide and, specifically, in Latin America. Genomic epidemiology has been instrumental in determining the transmission dynamics of A. baumannii in many countries of the world, yet some Latin American countries have conducted no genomic epidemiology studies. Here, we conduct the first genomic epidemiology study about this pathogen in Paraguay. We sequenced 43 isolates from a big tertiary hospital in Paraguay collected from different wards in 2021 and 2022. Our genomic epidemiology analyses, including almost 200 genomes and considering the main international clones (ICs), show that IC1, IC2, IC4, IC5, and IC7 were found in the hospital. We found novel genetic variation (three novel sequence types as per the Oxford MLST scheme and one as per the Pasteur scheme) within IC7. Antibiotic susceptibility tests show that all but one of the Paraguayan isolates were resistant to carbapenems. Notably, 98% were classified as multidrug-resistant. We detected plasmids in almost all the Paraguayan isolates. Furthermore, we detected cases of recent horizontal transfer of important antibiotic resistance genes between different ICs. On a general note, our findings highlight polyclonal spreading across different hospital wards and horizontal transfer of clinically relevant antibiotic resistance genes among the different clones. On a more local note, this is the first genomic epidemiology study of A. baumannii in Paraguay and will be a reference point for future studies in the country and the region.},
}

@article {pmid40623962,
year = {2025},
author = {Monte, DFM and de Lima Rocha, AD and Lemos, MLP and de Lima, LA and Cabrera, JM and da Silva, NJ and Huang, X and Chen, Z and Brown, EW and Allard, MW and Bell, RL and Toro, M and Meng, J and de Oliveira, CJB},
title = {High Prevalence of Plasmid-Mediated Quinolone Resistance in Salmonella enterica Serovars Isolated From Surface Water.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70140},
doi = {10.1111/1462-2920.70140},
pmid = {40623962},
issn = {1462-2920},
support = {U01FDU001418//U.S. Department of Health and Human Services/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 420755/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 3136678/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 88887.898770/2023-00//Fundação de Apoio à Pesquisa do Estado da Paraíba (FAPESQ)/ ; //Financiadora de Estudo e Projetos (FINEP)/ ; },
mesh = {*Quinolones/pharmacology ; *Salmonella enterica/genetics/drug effects/isolation & purification/classification ; *Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; Brazil ; *Drug Resistance, Bacterial/genetics ; Serogroup ; Multilocus Sequence Typing ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Fresh Water/microbiology ; Prevalence ; },
abstract = {Considering the increasing reports of Salmonella enterica strains resistant to quinolones, antimicrobials frequently employed as therapeutic agents globally, our goal was to investigate the occurrence of plasmid-mediated quinolone resistance (PMQR) determinants in S. enterica recovered from natural surface waters in Paraíba state, Brazil. Water samples (n = 230) were collected monthly in triplicate using modified Moore swabs from 29 sampling sites belonging to 10 large dams. After conventional microbial isolation, representative isolates (n = 938) were submitted to whole genome sequencing, assembly and annotation. Antimicrobial resistance genes (ARGs) were identified, and core genome multilocus sequence typing (cgMLST) was used to infer phylogenetic relationships. Among recovered S. enterica, 130 (13.9%) isolates harboured PMQR determinants; 124 (95.4%) harboured qnrB19, while 6 (4.6%) harboured qnrS1. Multiple other ARGs associated with resistance to aminoglycosides, β-lactams, sulphonamides, tetracyclines and fosfomycin were identified. The diversity of ARGs and plasmids suggests a highly complex resistance landscape. Phylogenetic analysis revealed clustering by serovar and sequence type but not by resistance profile or geographic origin. The absence of association between phylogeny and ARGs highlights the potential role of horizontal gene transfer in disseminating resistance genes in water. Our findings reinforce the importance of antimicrobial resistance surveillance in surface waters.},
}

*Quinolones/pharmacology
*Salmonella enterica/genetics/drug effects/isolation & purification/classification
*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
Phylogeny
Brazil
*Drug Resistance, Bacterial/genetics
Serogroup
Multilocus Sequence Typing
Microbial Sensitivity Tests
Whole Genome Sequencing
*Fresh Water/microbiology
Prevalence

@article {pmid40623055,
year = {2025},
author = {Frazão, N and Seixas, E and Mischler, M and Moura-de-Sousa, J and Barreto, HC and Gordo, I},
title = {Clonal interference and genomic repair during strain coexistence in the gut.},
journal = {PLoS genetics},
volume = {21},
number = {7},
pages = {e1011777},
doi = {10.1371/journal.pgen.1011777},
pmid = {40623055},
issn = {1553-7404},
abstract = {Humans and other mammals are colonized by multiple strains of Escherichia coli, but the tempo and mode of evolution of different coexisting strains, between whom horizontal gene transfer (HGT) can occur, is poorly understood. Here, we follow in real time the evolution of two phylogenetic distinct strains of E. coli that co-colonize the mouse gut with different population sizes. We find qualitative differences in evolutionary dynamics between strains within the same host. In the strain with larger population size intense clonal interference occurs and polymorphism at a neutral marker locus is maintained, while in the strain with lower population size complete selective sweeps and loss of neutral marker polymorphism occurs. Strain coexistence is also accompanied by rich dynamics of HGT from one strain to the other. Strikingly, a rare HGT event could restore a previously lost genomic region in the recipient strain. Furthermore, we detect for the first time a case of phage piracy in the gut, where a putative phage satellite, lacking essential genes for their own replication, was likely mobilized by a helper phage to transfer between bacterial hosts. Our results show that HGT is a key mechanism underlying genetic exchanges and adaptive genomic repair in the mammalian gut.},
}

@article {pmid40622509,
year = {2025},
author = {Can, A and Baysal, Ö},
title = {A Chitinase Gene Belonging to Serratia marcescens GBS19 Reveals Horizontal Gene Transfer within Bacterial Strains Besides its Biocontrol Potential Against Myzus persicae.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40622509},
issn = {1573-4927},
abstract = {Microorganisms produce diverse enzymes with applications in biological control and pest management. Chitinase enzymes degrade chitin, a structural component of insect exoskeletons and fungal cell walls, offering sustainable and environmentally friendly solutions for agricultural pest and pathogen management. This study focused on the chiA gene from our original strain belonging to Serratia marcescens identified using multi locus sequencing and ribosomal DNA analysis, amplified via PCR, cloned into expression vectors, and expressed as a recombinant protein. The chiA enzyme was purified using His-tag affinity chromatography and showed optimal activity at 40 °C and pH 5. The purified chiA enzyme exhibited strong insecticidal activity against Myzus persicae, with an lethal dose50 of 15.8 ppm. The comparative genomic analysis using MUMMER4 and MAUVE, identified horizontal gene transfer (HGT) events and genomic rearrangements within reference strain and our strain GBS19. The recombinant chiA enzyme exhibited 98.4% similarity with reference chiA sequences, highlighting its evolutionary conservation. Molecular docking studies confirmed a binding affinity of - 5.74 kcal/mol between the enzyme and chitin monomers, supported by interaction studies with modeled chitin layer. In addition, we have also predicted the most variable mutations required for enzyme stability and enzymatic activity enhancement in cloned amino acid sequence using protein AI tool, which will also guide us further studies linked to site-directed mutagenesis. This study demonstrates the potential of S. marcescens chitinase as an effective biocontrol agent against Myzus persicae. It underscores the importance of recombinant DNA technology in sustainable agriculture and sheds light on the evolutionary adaptation of chitinase genes through HGT and mutational events.},
}

@article {pmid40621911,
year = {2025},
author = {Yu, J and Gao, J-W and Cao, K and He, D-Y and Xu, L and Fu, G-Y and Sun, C},
title = {Characterization of two novel species of the genus Flagellimonas reveals the key role of vertical inheritance in the evolution of alginate utilization loci.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0091725},
doi = {10.1128/spectrum.00917-25},
pmid = {40621911},
issn = {2165-0497},
abstract = {Flavobacteriaceae is the major participant in the degradation of algal polysaccharides. With diverse polysaccharide utilization loci (PULs) and specific carbohydrate-active enzymes (CAZymes), Flavobacteriaceae strains appear to have different abilities in algal polysaccharide degradation and therefore change their roles in the bacterial community. Here, we identified two novel isolates as two novel species of genus Flagellimonas with the names Flagellimonas alginolytica sp. nov. and Flagellimonas cixiensis sp. nov. Furthermore, the comprehensive genomic comparison of 41 Flagellimonas genomes revealed that Flagellimonas strains were diverse in the CAZymes and PUL profiles and exhibited a preference for polysaccharides derived from brown algae. The evolutionary analysis of alginate utilization loci (AUL) in this genus illuminated that the function genes in AULs, that is, PL7 and PL17, were more reliant on the stable inheritance from ancestors associated with gene duplication and loss rather than horizontal gene transfer (HGT) from outside, and the AUL structures exhibited a trend of simplification which resulted in the incidental decrease in alginate degradation ability. This study highlights the important role of vertical inheritance in the evolution of AULs and proves that the discrepancy in AUL structure can arouse phenotypic differences, providing a new perspective on the evolution of AUL and the niche adaptation mechanism of Flavobacteriaceae strains.IMPORTANCEFlavobacteriaceae play an important role in the marine carbon cycle with their noteworthy ability in algal polysaccharides degradation, which is primarily reliant on diverse polysaccharide utilization loci (PULs). Our study highlights the crucial role of vertical inheritance in the evolution of alginate utilization loci (AUL) in Flagellimonas strains and reveals the AUL structural simplification found in Flagellimonas strains that will lead to the reduction of alginate degradation ability. These insights advance understanding of niche adaptation strategy and related evolutionary mechanisms of Flavobacteriaceae strains.},
}

@article {pmid40619778,
year = {2025},
author = {Bhide, AJ},
title = {Redefining the nitroplast: Recent insights into the endosymbiontto- organelle transition.},
journal = {Journal of biosciences},
volume = {50},
number = {},
pages = {},
pmid = {40619778},
issn = {0973-7138},
mesh = {*Symbiosis/genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; *Plastids/genetics ; Cyanobacteria/genetics ; Rhodophyta/genetics ; Mitochondria/genetics ; Chlorophyta/genetics ; Alphaproteobacteria/genetics ; Biological Evolution ; Evolution, Molecular ; Dinoflagellida/genetics ; },
abstract = {One of the most remarkable events in cellular evolution is the endosymbiosis of α-proteobacteria with a single archaean host cell, a rare evolutionary process, which eventually led to the transformation of symbionts into fully functional mitochondrial organelles in eukaryotes. Evolutionary events related to plants occurred almost 1.6 billion years ago, when eukaryotic heterotrophs acquired a β-cyanobacterium (containing 1B RUBISCO) in what is termed as primary endosymbiosis. Further, this composite cell lineage evolved into three photosynthetic lineages: green algae (plants), red algae and the glaucophytes. Thereafter, a secondary, and tertiary endosymbiosis event occurred giving rise to distinct kinds of green and red-derived photosynthetic plastids, which can be observed in a few haptophytes and dinoflagellates respectively. Eventually, these endosymbionts acquired characteristic cellular properties such as two/multiple envelope membranes and reduction of their genomes through either loss or concerted endosymbiotic gene transfer (EGT) into the nucleus, which ultimately led to the decline of more than three quarters of coding capacity and complete loss of several metabolic pathways. This loss, however, is partly compensated by import of nuclearencoded proteins as well as proteins acquired by horizontal gene transfer (HGT). For most proteins, specific transport mechanisms from nucleus/cytoplasm to organelle exist. The proteins are typically translated as a preprotein with specific signal sequences targeted to the organelle membrane. These membranes harbour receptors, in some cases soluble receptors, for recognition of these signal sequences. Proteins are then internalised using a set of translocation machineries (Gould et al. 2006).},
}

*Symbiosis/genetics
Gene Transfer, Horizontal
Photosynthesis/genetics
*Plastids/genetics
Cyanobacteria/genetics
Rhodophyta/genetics
Mitochondria/genetics
Chlorophyta/genetics
Alphaproteobacteria/genetics
Biological Evolution
Evolution, Molecular
Dinoflagellida/genetics

@article {pmid40614847,
year = {2025},
author = {Wang, R and Chen, H and Liu, Y},
title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122285},
doi = {10.1016/j.envres.2025.122285},
pmid = {40614847},
issn = {1096-0953},
abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.},
}

@article {pmid40612915,
year = {2025},
author = {Vasta, GR and Bianchet, MA},
title = {F-type lectins: Structural and functional aspects, and potential biomedical applications.},
journal = {BBA advances},
volume = {8},
number = {},
pages = {100166},
pmid = {40612915},
issn = {2667-1603},
abstract = {Among the multiple animal lectin families recognized to date, F-type lectins (FTLs), fucose-binding lectins characterized by an FTL domain (FTLD), constitute the most recent lectin family to be identified and structurally characterized. The structure of the FTL from the European eel Anguilla anguilla revealed a novel jellyroll lectin fold (the "F-type" fold) with unique fucose- and calcium-binding sequence motifs. The FTL lectin family comprises proteins that may exhibit single or multiple FTLD, in combination with structurally and functionally distinct domains, and can form oligomeric associations that display high-avidity multivalent binding. Differences in fine carbohydrate specificity among tandemly arrayed FTLDs present in any FTL polypeptide subunit, together with the expression of multiple FTL isoforms in a single individual supports a broad diversity in ligand recognition. Widely distributed in invertebrates, protochordates, ectothermic vertebrates, birds, and monotreme and marsupial mammals, the FTLD is also present in some bacterial proteins and viruses but absent in placental mammals. The taxonomically broad, and discontinuous distribution of the FTLD, suggests an extensive structural and functional diversification of this lectin family, including horizontal gene transfer in viruses and prokaryotic organisms, together with possible gene loss and/or cooption along the lineages leading to the mammals. FTLs' biological roles range from pathogen recognition in innate immunity to fertilization, cell adhesion and cell aggregation, and as bacterial virulence factors, among others. The specificity of FTLs for fucosylated moieties should provide ample opportunities for novel applications in glycan and cell separation, and innovative diagnostic, preventive, and therapeutic approaches in cancer and infectious disease.},
}

@article {pmid40479505,
year = {2025},
author = {Pianezza, R and Scarpa, A and Haider, A and Signor, S and Kofler, R},
title = {Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.},
journal = {Molecular biology and evolution},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/molbev/msaf143},
pmid = {40479505},
issn = {1537-1719},
support = {NSF-EPSCoR-1826834 and NSF-EPSCoR-2032756//National Science Foundation/ ; P35093 and P34965//Austrian Science Fund (FWF)/ ; },
mesh = {Animals ; *DNA Transposable Elements ; *Drosophila melanogaster/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Genome, Insect ; },
abstract = {Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a significant influence on evolution throughout the tree of life. Using a novel approach that does not require prior knowledge of the sequence of repeats, we identified three novel TE invasions in Drosophila melanogaster: McLE spread between 1990-2000, Souslik between 2009-2012, and Transib1 between 2013-2016. We recapitulate previous findings, revealing that a total of 11 TEs invaded D. melanogaster over the past two centuries. These 11 invasions increased the fly genome by ∼1 Mbp. Using data from over 1,400 arthropod genomes, we provide evidence that these TE invasions were triggered by horizontal transfers, with Drosophila simulans and species of the Drosophila willistoni group acting as putative donors. Through the analysis of ∼600 short-read datasets spanning diverse geographic regions, we reveal the rapidity of TE invasions: Transib1 swiftly multiplied from three isolated epicenters in 2014 to all investigated populations in just 2 years. Our findings suggest that anthropogenic activities, which facilitate the range and population expansions of D. melanogaster, could have accelerated the rate of horizontal transposon transfer as well as the spread of the TEs into the worldwide population. Given the significant impact of TEs on evolution and the potential involvement of humans in their dispersal, our research has crucial implications for both evolution and ecology.},
}

Animals
*DNA Transposable Elements
*Drosophila melanogaster/genetics
Gene Transfer, Horizontal
Evolution, Molecular
Genome, Insect

@article {pmid40612392,
year = {2025},
author = {Ma, Y and Lei, Z and Zhang, Y and Liu, Q and Zhang, F and Zu, H and Yang, X and Li, Z and Lu, B},
title = {Tracing the evolutionary trajectory of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1: an outbreak of Pseudomonas aeruginosa co-producing IMP-45 and VIM-1 carbapenemases in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1623241},
pmid = {40612392},
issn = {2235-2988},
mesh = {*beta-Lactamases/genetics/metabolism ; *Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification ; *Plasmids/genetics ; Humans ; China/epidemiology ; *Pseudomonas Infections/epidemiology/microbiology ; *Bacterial Proteins/genetics/metabolism ; *Disease Outbreaks ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Evolution, Molecular ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a significant global health risk, particularly for immunocompromised individuals. This study documents an outbreak of CRPA strains co-harboring bla VIM-1 and bla IMP-45 on IncP-2 plasmids in a Chinese tertiary hospital, resulting in poor outcomes for transplant patients.

METHODS: 17 ST313 VIM-1-IMP-45 CRPA strains were collected from transplant patients, and antibiotic susceptibility was tested via microbroth dilution. Whole genome sequencing (WGS) identified drug resistance and virulence mechanisms, analyzed ST313 P. aeruginosa phylogeny, and traced bla VIM-1 and bla IMP-45 origins. Conjugation experiments were conducted to assess the conjugative potential of the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45. Structural and molecular docking studies explored the PBP3 (P527S) mutation's role in aztreonam resistance.

RESULTS: From February 2022 to July 2024, 17 ST313 VIM-1-IMP-45 CRPA strains from 10 transplant patients were identified. All strains were extensively drug-resistant but sensitive to colistin and cefiderocol. WGS showed bla IMP-45 and bla VIM-1 on an IncP-2 megaplasmid. Phylogenetic analysis indicated high homology with plasmids carrying bla IMP-45. Further analysis of the genetic environment showed that the IncP-2 plasmid co-harboring bla VIM-1 and bla IMP-45 was formed by the insertion of a Tn3-family transposon carrying bla VIM-1 into the IncP-2 plasmid carrying bla IMP-45. In addition aztreonam-resistant strains (14/15) had a PBP3 (P527S) mutation, with molecular docking studies suggesting reduced aztreonam binding.

CONCLUSIONS: This study reports a clonal outbreak of ST313 P. aeruginosa strains co-producing IMP-45 and VIM-1 carbapenemases in a tertiary hospital. The evolutionary path of the IncP-2 plasmid co-harboring bla IMP-45 and bla VIM-1 was elucidated.},
}

*beta-Lactamases/genetics/metabolism
*Pseudomonas aeruginosa/genetics/drug effects/enzymology/isolation & purification
*Plasmids/genetics
Humans
China/epidemiology
*Pseudomonas Infections/epidemiology/microbiology
*Bacterial Proteins/genetics/metabolism
*Disease Outbreaks
Phylogeny
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Microbial Sensitivity Tests
Molecular Docking Simulation
Evolution, Molecular
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid40609725,
year = {2025},
author = {Chen, M and Song, L and Ye, C and Grossart, HP and Yang, Y and Li, S and Liao, H and Gong, Y and Che, R and Zhang, Q},
title = {Dynamic relationships of antibiotic resistomes and greenhouse gas-functioning microbes across diverse habitats.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122272},
doi = {10.1016/j.envres.2025.122272},
pmid = {40609725},
issn = {1096-0953},
abstract = {Reservoir ecosystems with diverse habitats form critical interfaces where antibiotic resistance genes (ARGs) and greenhouse gas (GHG) emissions converge. Despite their distribution and ecological implications of ARGs across diverse habitats remain greatly unknown. There is a critical gap in dissecting the interlinkages between antibiotic resistomes and GHG-functioning microbes. Thus, we aimed to investigate the relationship between antibiotic resistomes and GHG-functioning microbes in various habitats of the Three Gorges reservoir, encompassing water, sediment, and riparian top- and sub-soil. We provide a comprehensive assessment of ARG abundance and diversity across four habitats. Significant differences in ARG, with riparian zones exhibiting more than twice the ARG abundance of water. Horizontal gene transfer of ARGs was more frequent in water, suggesting a pivotal role in aquatic ARG dissemination. The GHG-functioning microbes displayed habitat-specific composition and diversity, with key genera like Neisseria and Azoarcus in riparian subsoil, contrasting with Streptomyces in other habitats. The dynamic relationship of antibiotic resistomes and GHG-functioning microbes ranges from synergistic to competitive in varied habitats, reflecting antibiotic resistomes can influence ecological function stability. This study emphasizes the importance of considering resistomes in the context of global change, advancing our understanding of environmental management and conservation strategies in these critical ecosystems.},
}

@article {pmid40607640,
year = {2025},
author = {Jia, X and Zhang, X and Chen, X and Fernie, AR and Wen, W},
title = {The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13957},
pmid = {40607640},
issn = {1744-7909},
support = {32161133017//National Natural Science Foundation of China/ ; 32494781//National Natural Science Foundation of China/ ; },
abstract = {Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10[-5]). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosine and S-adenosylhomocysteine to release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.},
}

@article {pmid40607638,
year = {2025},
author = {Hou, J and Liu, M and Yang, K and Liu, B and Liu, H and Liu, J},
title = {Genetic variation for adaptive evolution in response to changed environments in plants.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13961},
pmid = {40607638},
issn = {1744-7909},
support = {No. 32030006//National Natural Science Foundation of China/ ; No. 32270302//National Natural Science Foundation of China/ ; 2024NSFSC0340//Natural Science Foundation of Sichuan Province/ ; },
abstract = {Plants adapt to their local environments through natural or artificial selection of optimal phenotypes. Recent advances in genomics and computational biology, which integrate phenotypic and multi-omics data, have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes. Understanding the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats, including various biotic and abiotic stresses. In this review, we highlight recent progress in elucidating the genetic basis of phenotypic variation in morphological traits and stress responses, as well as the emergence of new ecotypes, subspecies, and species during adaptive evolution across varied environments. This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants. Furthermore, the terrestrialization and early diversification of land plants involved the acquisition of additional genes, primarily through horizontal gene transfer and whole-genome duplication, which facilitated the development of complex molecular pathways to adapt to increasingly diverse environments. Finally, we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adaptation, to guide crop breeding efforts in response to global climate change.},
}

@article {pmid40606176,
year = {2025},
author = {Du, H and Lu, C and Latif, MZ and Du, J and Liu, Y and Li, H and Ding, X},
title = {Thermophilic microbial agents promote the fermentation progression of spent mushroom compost and pig manure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575397},
pmid = {40606176},
issn = {1664-302X},
abstract = {Livestock and poultry manure, as a significant organic resource, had an enormous annual production but a utilization rate of less than 50%. Improperly managed manure had become the primary source of agricultural non-point pollution, posing severe challenges to the ecological environment. Achieving efficient resource utilization of livestock manure was a critical step in promoting green agricultural development. Existing research indicated that microbial activity significantly influences the transfer and dissemination of antibiotic resistance genes (ARGs) and the community dynamics of human pathogenic bacteria (HPB) during pig manure composting. However, the specific mechanisms remain unclear. This study innovatively introduced two thermophilic microbial agents (TMS1 and CTMS2) into a pig manure-spent mushroom compost (SMC) aerobic composting system to systematically investigate their regulatory effects on pollutant reduction. The results showed that persistent ARGs (ErmF, ErmQ, ErmX, blaR1, QnrA1, QnrA6, bla-F, QnrA2, QnrA5, Qnra4 and bla-VIM) primarily rely on vertical gene transfer (VGT) for dissemination, whereas easily removable ARGs (tetX, tetW, tetG, tetC, suI1 and suI2) were regulated by both horizontal gene transfer (HGT) and VGT. Notably, the co-addition of thermophilic microbial agents and SMC reduced persistent ARGs by lg0.45-3.73, significantly decreased the abundances of HPB such as Bacteroides and Treponema, and reduced the enrichment of related metabolic pathways, greatly improving compost quality. In stark contrast, the control group (with only SMC and no thermophilic microbial agents) exhibited ARG proliferation. Overall, the application of thermophilic microbial agents not only extended the high temperature phase of composting by over 30% and shortened the composting cycle by 50%, but more importantly, it achieved comprehensive improvement in compost quality by selectively enriching functional microbial communities such as Pseudomonas. This study provides a theoretical foundation and data support for the industrial application of CTMS2 in the safe production of organic fertilizers and the synergistic control of environmental risks.},
}

@article {pmid40606165,
year = {2025},
author = {Jers, C and Mišetić, H and Ravikumar, V and Garg, A and Franjević, D and Domazet-Lošo, T and Mijakovic, I},
title = {Gene age and genome organization in Escherichia coli and Bacillus subtilis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1512923},
pmid = {40606165},
issn = {1664-302X},
abstract = {Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer. Interestingly, while most bacterial transcription regulators belong to the oldest phylostrata, they regulate expression of both older and more recent genes alike. A large fraction of bacterial operons contains genes from different phylostrata. This suggests that newer genes are integrated in the existing framework for regulating gene expression, and that the establishment of new regulatory circuits typically do not accompany acquisition of new genes. One striking difference between E. coli and B. subtilis genomes was observed. About 87.0% of all E. coli genes belong to the evolutionary oldest physlostratum. In B. subtilis, this number is only 71.8%, indicating a more eventful evolutionary past in terms of acquisition of new genes, either by gene emergence or by horizontal transfer.},
}

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@article {pmid40602897,
year = {2025},
author = {Liang, S and Zhang, W and Semaha, P and Rocher, D and Liu, L and Gao, Y},
title = {Microelectrolysis facilitated the plasmid-mediated horizontal transfer of antibiotic resistance genes at the microbial community level.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {470-477},
doi = {10.1016/j.jes.2025.01.029},
pmid = {40602897},
issn = {1001-0742},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Wastewater/microbiology ; },
abstract = {The escalating global dissemination of plasmid-mediated antibiotic resistance poses a formidable threat to global health. Conjugation stands as a pivotal mechanism for horizontal gene transfer among bacterial populations, facilitating the spread of antibiotic resistance genes (ARGs). Microelectrolysis has garnered attention as an efficacious strategy for mitigating antibiotic concentrations in wastewater, yet its potential impact on ARG horizontal transfer remain largely unexplored. This comprehensive investigation unveils that microelectrolysis not only influences but significantly accelerates the conjugative transfer of ARG-harboring plasmids. Remarkably, this phenomenon is corroborated at the microbial community scale, underscoring its ecological relevance. Alarmingly, the study highlights the vulnerability of intestinal microorganisms to acquire antibiotic resistance under electrolytic stimulation, posing heightened risks to both animal and human health. Delving deeper, the study elucidates the underlying mechanisms responsible for this enhanced conjugative transfer. It reveals that microelectrolysis augments the abundance of mating-competent cells, triggers the generation of reactive oxygen species, inflicts modest membrane damage, and upregulates the expression of genes critical for conjugation. These findings collectively contribute to a more profound comprehension of the environmental dissemination dynamics and associated public health implications of ARGs in the context of wastewater treatment employing microelectrolytic technologies.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents
Wastewater/microbiology

@article {pmid40602895,
year = {2025},
author = {Li, S and Xi, Y and Wang, K and Wan, N and Liu, H and Ho, SH},
title = {Responses of antibiotic resistance genes and microbial community in the microalgae-bacteria system under sulfadiazine: Mechanisms and implications.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {443-456},
doi = {10.1016/j.jes.2024.12.003},
pmid = {40602895},
issn = {1001-0742},
mesh = {*Microalgae/physiology ; *Sulfadiazine/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Anti-Bacterial Agents ; Genes, Bacterial ; Sewage/microbiology ; },
abstract = {Microalgae-bacteria system is an emerging alternative for sustainable wastewater treatment. Exploring the structure and diversity of microbial community in microalgae-bacteria system under sulfadiazine stress can contribute to the understanding of the sulfadiazine behavior in environments. Furthermore, as important carriers of antibiotic resistance genes (ARGs), microalgae can influence the profiles of ARGs either directly or indirectly through the secretion of metabolites. However, the effects of sulfadiazine on ARGs dissemination of microalgae-bacteria systems remain underreported. Herein, the impacts of sulfadiazine (1 mg/L) on the structural diversity and metabolic activity of microorganisms were examined in microalgae-bacteria systems. Results showed that microalgae-bacteria system could remove NH4[+]-N better (about 72.3 %) than activated sludge system, and hydrolysis was the first step in sulfadiazine degradation. A high level of intI1 (5.7 × 10[4] copies/mL) was detected in the initial media of the microalgae-bacteria system. Microalgae could hamper the rate of horizontal gene transfer activation. Compared with activated sludge system, the abundance of sul genes (sul1, sul2, sul3, and sulA) was significantly lowered after treating with microalgae-bacteria system. Additionally, the number of proteins and the sum of polysaccharides in the extracellular polymeric substances of the activated sludge system were lower than those of the microalgae-bacteria system. Microalgae can alter microbial communities. The genus Rozellomycota predominated all samples. Fungi with relatively high abundance increased in the microalgae-bacteria system, including Dipodascaceae, Rhodotorula, and Geotrichum. These results offer valuable insights into the application processes involving microalgae-bacteria system.},
}

*Microalgae/physiology
*Sulfadiazine/toxicity
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects
*Water Pollutants, Chemical/toxicity
Waste Disposal, Fluid/methods
*Microbiota/drug effects
Anti-Bacterial Agents
Genes, Bacterial
Sewage/microbiology

@article {pmid40601807,
year = {2025},
author = {Wang, Y and Feng, Z and Wu, W and Zhan, Z and Huang, J and Guo, C and He, J},
title = {Emergence of highly virulent Aeromonas dhakensis in channel catfish aquaculture: Genomic insights into pathogenicity and antimicrobial resistance.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2525933},
doi = {10.1080/21505594.2025.2525933},
pmid = {40601807},
issn = {2150-5608},
mesh = {Animals ; *Fish Diseases/microbiology/pathology ; *Ictaluridae/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary/pathology ; Virulence ; *Aeromonas/pathogenicity/genetics/drug effects/isolation & purification ; Aquaculture ; Virulence Factors/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Genomics ; *Drug Resistance, Bacterial ; },
abstract = {Aeromonas dhakensis has emerged as a significant pathogen in aquaculture, causing severe disease outbreaks and resulting in substantial economic losses. However, its pathogenic mechanism and virulence factors remain largely unexplored. In this study, we isolated a highly virulent strain of A. dhakensis, CWH5, from a severe disease outbreak in farmed channel catfish (Ictalurus punctatus). Through comprehensive whole-genome analysis, we elucidated its pathogenicity and the genetic basis for its high virulence and multi-antimicrobial resistance in channel catfish. Experimental infections showed that CWH5 exhibited exceptional virulence, with an LD50 of (5.37 ± 0.31) ×10[5] CFU/fish and causing 100% mortality within 24 h at a concentration of 10[7] CFU/fish. Histopathological examinations revealed severe multi-organ damage, including extensive hepatocellular necrosis, gill epithelial destruction, and fin tissue deterioration. Whole-genome sequencing revealed a 4.92 Mb circular chromosome encoding sophisticated virulence mechanisms, such as complete Type III, IV, and VI secretion systems, and a vast arsenal of 60 antibiotic resistance genes across 15 drug classes. Comparative genomic analysis positioned CWH5 within the A. dhakensis clade, sharing the highest sequence similarity with A. dhakensis CIP 107,500[T]. The co-localization of virulence and resistance determinants within mobile genetic elements suggests the potential for horizontal gene transfer. Our work underscored the importance of A. dhakensis CWH5 as an emerging pathogen in channel catfish aquaculture, providing crucial insights into the molecular mechanisms of its exceptional virulence and implying significant implications for disease management and antimicrobial resistance surveillance in aquaculture settings.},
}

Animals
*Fish Diseases/microbiology/pathology
*Ictaluridae/microbiology
*Gram-Negative Bacterial Infections/microbiology/veterinary/pathology
Virulence
*Aeromonas/pathogenicity/genetics/drug effects/isolation & purification
Aquaculture
Virulence Factors/genetics
Genome, Bacterial
Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Genomics
*Drug Resistance, Bacterial

@article {pmid40600175,
year = {2025},
author = {Etesami, H},
title = {The dual nature of plant growth-promoting bacteria: Benefits, risks, and pathways to sustainable deployment.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100421},
pmid = {40600175},
issn = {2666-5174},
abstract = {Plant growth-promoting bacteria (PGPB) are pivotal in sustainable agriculture, enhancing crop productivity and reducing reliance on chemical inputs. However, their dual role as beneficial agents and potential stressors remains underexplored. This review examines the paradoxical adverse effects of PGPB, challenging the predominantly optimistic narrative surrounding their use. At the plant level, unintended consequences include hormonal imbalances (e.g., auxin-induced root inhibition), phytotoxic metabolite production (e.g., hydrogen cyanide), and trade-offs between growth and defense mechanisms. At the soil level, risks encompass disrupted microbial diversity, altered nutrient cycling, and horizontal gene transfer that may foster pathogenicity. These outcomes are driven by environmental factors (soil pH and moisture), host-specific interactions, and application practices. Mitigation strategies emphasize rigorous strain selection, optimized dosing, and integrated soil management to balance efficacy with ecological safety. Advances in multi-omics technologies and synthetic consortia design offer predictive insights into strain behavior, while long-term ecological assessments are critical to address legacy impacts. The review underscores the necessity of a nuanced, evidence-based approach to PGPB deployment, harmonizing agricultural benefits with environmental stewardship. By addressing knowledge gaps in microbial ecology and risk assessment, this work supports strategies prioritizing both agricultural resilience and soil biodiversity to ensure PGPB contribute sustainably to global food security.},
}

@article {pmid40600145,
year = {2025},
author = {Piispa, M and Vainio, A and Halkilahti, J and Lyytikäinen, O and Räisänen, K},
title = {Detecting plasmid-mediated dissemination of bla KPC-3 and bla OXA-48-like genes in Enterobacterales across Finnish healthcare organizations using hybrid genome assembly.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1567913},
pmid = {40600145},
issn = {1664-302X},
abstract = {The spread of carbapenemase-producing Enterobacterales (CPE) is a global concern. While the majority of the CPE outbreaks are due to clonal spread, recent findings highlight the transmission of carbapenemase gene-carrying plasmids across various bacterial species, exacerbated by extensive antibiotic use in hospitals. This study aimed to identify plasmid-mediated horizontal transfer of carbapenemase genes among Enterobacterales isolated from patient samples and hospital environment samples in three healthcare organizations in Finland. Using a hybrid assembly of short and long reads, we could complete the genome assembly and compare the plasmids harboring the bla KPC-3 and bla OXA-48-like genes. Our findings reveal indications of interspecies and intraspecies plasmid-mediated gene transfer of bla KPC-3 and bla OXA-48-like, emphasizing the role of horizontal gene transfer (HGT) in outbreaks. The study underscores the need for comprehensive infection control and surveillance beyond specific species to prevent the spread of antimicrobial resistance genes. These results suggest that expanding outbreak investigations to an interspecies level could be beneficial.},
}

@article {pmid40600140,
year = {2025},
author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV},
title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537826},
pmid = {40600140},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.},
}

@article {pmid40600027,
year = {2025},
author = {Lewicka, AJ and Lyczakowski, JJ and Pardyak, L and Dubniewicz, K and Latowski, D and Arent, Z},
title = {Beyond serology: saccharide profiling enables identification of antigenically similar Leptospira and prompts re-evaluation of bacterial lipopolysaccharide evolution.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1581587},
pmid = {40600027},
issn = {2296-889X},
abstract = {Leptospirosis is a zoonotic infectious disease of growing importance in both human and veterinary medicine. Gram-negative spirochetes of Leptospira are traditionally classified into serovars based on their antigenic identity, which must be ascertained to design effective treatment procedures for humans and appropriate vaccination strategies in pets and livestock. Unfortunately, identifying Leptospira serovars is challenging and currently requires access to a wide panel of reference strains, animal-derived antisera, or monoclonal antibodies. Here, we describe a new method for the identification of Leptospira serovars that is based on monosaccharide composition analysis of the polysaccharide part of bacterial lipopolysaccharide (LPS) structures. Our approach requires no animal sacrifice and can be implemented in any laboratory equipped for chromatographic analysis. An LPS sugar fingerprint that is specific to each bacterial isolate that we studied can be generated. Importantly, sugar profiling of LPS enables distinguishing Leptospira serovars that are antigenically very similar. Using our new approach, we discover that the LPS structures of two cattle pathogens belonging to two different species: Leptospira interrogans and Leptospira borgpetersenii, and to one serovar: Hardjo, can be distinguished despite sharing major similarities. Through extensive phylogenetic analysis, we reveal which specific glycosyltransferases of the LPS biosynthesis rfb locus likely drove the emergence of these similarities and identify a single glycosyltransferase that might have contributed to the formation of saccharide differences in the LPS structure. Our findings have implications for future work on the evolution of bacterial polysaccharide synthesis and highlight the importance of preventing horizontal gene transfer between pathogenic bacteria.},
}

@article {pmid40597104,
year = {2025},
author = {Blais, C and Colp, MJ and Sarre, LA and de Mendoza, A and Archibald, JM},
title = {Epigenetic silencing and genome dynamics determine the fate of giant virus endogenizations in Acanthamoeba.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {171},
pmid = {40597104},
issn = {1741-7007},
support = {GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; GBMF5782//Gordon and Betty Moore Foundation/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-05058//Natural Sciences and Engineering Research Council of Canada/ ; ERC-StG 950230/ERC_/European Research Council/International ; ERC-StG 950230/ERC_/European Research Council/International ; },
mesh = {*Acanthamoeba/virology/genetics ; *Giant Viruses/genetics/physiology ; *Epigenesis, Genetic ; *Gene Silencing ; *Virus Integration/genetics ; *Genome, Protozoan ; *Genome, Viral ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Endogenized giant viruses are emerging as major contributors to the genome evolution of microbial eukaryotes, with both degraded and fully functional latent viruses being found integrated in diverse lineages. The mechanisms that determine the fate of viral integrants are poorly understood, however. Acanthamoeba is a unicellular eukaryote known for undergoing lateral gene transfer (LGT) with viruses. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba, Neff and C3, to investigate the genomic mechanisms that mediate the fate of viral integrations in eukaryotic genomes.

RESULTS: Viral integrations in the C3 and Neff genomes are largely non-overlapping and disproportionately found in sub-telomeric regions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed, do not obviously encode functions associated with their own mobility, and are colonized by host mobile elements. Viral regions are hypermethylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions.

CONCLUSIONS: We propose a model for the trajectory of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, allowing them to persist in the genome, and (iii) deterioration of viral genomes by point mutation, mobile element colonization, and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the amoeba. Our work highlights the importance of host genome dynamics and epigenetic silencing for understanding the evolution of endogenized viral elements.},
}

*Acanthamoeba/virology/genetics
*Giant Viruses/genetics/physiology
*Epigenesis, Genetic
*Gene Silencing
*Virus Integration/genetics
*Genome, Protozoan
*Genome, Viral
Gene Transfer, Horizontal

@article {pmid40596330,
year = {2025},
author = {Puangseree, J and Hein, ST and Prathan, R and Srisanga, S and Chuanchuen, R},
title = {Genomic insights into multidrug - resistant Salmonella enterica isolates from pet dogs and cats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22104},
pmid = {40596330},
issn = {2045-2322},
support = {N42A660897//National Research Council of Thailand/ ; HEAF67310045//Thailand Science Research and Innovation Fund Chulalongkorn University (Fundamental Fund) Fiscal year 2567/ ; },
mesh = {Animals ; Dogs ; Cats ; *Salmonella enterica/genetics/drug effects/isolation & purification ; *Drug Resistance, Multiple, Bacterial/genetics ; *Pets/microbiology ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Plasmids/genetics ; *Salmonella Infections, Animal/microbiology ; *Dog Diseases/microbiology ; Microbial Sensitivity Tests ; *Cat Diseases/microbiology ; Genomics ; Genome, Bacterial ; },
abstract = {Companion animals are recognized as potential reservoirs and transmitters of antimicrobial resistance (AMR) within the One Health framework. However, in-depth knowledge on AMR in pet animals remains limited. This study aimed to characterize Salmonella from companion dogs and cats using Whole Genome Sequencing (WGS). A total of 25 Salmonella obtained from clinically healthy household dogs and cats were serotyped and had their antimicrobial susceptibility tested. A discrepancy between the serovars identified by traditional slide agglutination tests and those determined by WGS analysis was observed. The isolates exhibited multidrug resistance (MDR) (n = 18) and harbored several resistance genes either chromosomally encoded or plasmid associated. Tn3 and IS26 were commonly found flanking AMR genes and class 1 integrons, while an unusual qacL-IS256-sul3 arrangement was also frequently observed. Similar AMR genes and insertion sequences were found among dogs and cats from different provinces, suggesting clonal spread and horizontal gene transfer of AMR. The similarity between plasmids (i.e., IncX1 and IncI1 plasmid) carrying AMR genes (e.g., aadA1, qacL, sul3, blaTEM-1B, qnrS1, dfrA, tetA) in Salmonella from pets in this study and those from other sources (e.g., humans, food producing animals and environment) in different countries was revealed, suggesting that pet dogs and cats may play a significant role in the global spread of AMR. The finding underscores the role of household pets as silent reservoirs of MDR Salmonella and the need for a One Health approach to tackle the issue. Public health campaigns promoting hygiene practices among pet owners should be encouraged. Pet animals should be incorporated into AMR monitoring and surveillance programs as a component of One Health framework.},
}

Animals
Dogs
Cats
*Salmonella enterica/genetics/drug effects/isolation & purification
*Drug Resistance, Multiple, Bacterial/genetics
*Pets/microbiology
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Plasmids/genetics
*Salmonella Infections, Animal/microbiology
*Dog Diseases/microbiology
Microbial Sensitivity Tests
*Cat Diseases/microbiology
Genomics
Genome, Bacterial

@article {pmid40595289,
year = {2025},
author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT},
title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20953},
pmid = {40595289},
issn = {2045-2322},
support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; },
abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.},
}

Animals
*Chickens/microbiology
*Interspersed Repetitive Sequences/genetics
Aquaculture
Fishes
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/pathogenicity/drug effects
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Virulence/genetics
Bangladesh

@article {pmid40595025,
year = {2025},
author = {Wedell, N},
title = {Harnessing lateral gene transfer and endosymbiosis for adaptation.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40595025},
issn = {1471-0064},
}

@article {pmid40594904,
year = {2025},
author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z},
title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22915},
pmid = {40594904},
issn = {2045-2322},
mesh = {*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; },
abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.},
}

*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects
*Wastewater/microbiology
Bangladesh
*Drug Resistance, Multiple, Bacterial/genetics
Phylogeny
Hospitals
Virulence/genetics
Genome, Bacterial
Whole Genome Sequencing
Genomics/methods
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Humans

@article {pmid40592271,
year = {2025},
author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F},
title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139054},
doi = {10.1016/j.jhazmat.2025.139054},
pmid = {40592271},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.},
}

@article {pmid40592212,
year = {2025},
author = {Byczkowska-Rostkowska, Z and Gajewska, J and Chajęcka-Wierzchowska, W},
title = {Whole genome analysis and antimicrobial resistance assessment of Staphylococcus epidermidis isolated from food sources.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {179999},
doi = {10.1016/j.scitotenv.2025.179999},
pmid = {40592212},
issn = {1879-1026},
abstract = {Coagulase-negative staphylococci (CoNS), including Staphylococcus epidermidis, are commonly occurrence in a variety of food products. Historically considered non-pathogenic, these microorganisms were excluded from routine food safety monitoring protocols. However, their increasing involvement in nosocomial infections underscores their pathogenic potential. Emerging evidence suggests that the food chain may serve as a reservoir and transmission route for antibiotic-resistant bacteria. In this study, 26 S. epidermidis isolates obtained from ready-to-eat food were subjected to whole-genome sequencing and comprehensive bioinformatics analyses. The antimicrobial susceptibility of the isolates was also evaluated against a broad spectrum of agents including aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, lincosamides, macrolides, nitrofurantoins, oxalidinones, phenicols, steroids, sulphonamides and tetracyclines. Sequence typing revealed the presence of 17 distinct sequence types (STs), with ST329 being the most frequently identified (8/26, 30.77 %), followed by ST88 and ST152 (each 2/26; 7.69 %). Notably, one isolate harbored a novel multi-locus sequence type. Phenotypically resistance to erythromycin was most prevalent (21/26, 80.77 %), followed by resistance to clindamycin (19/26, 73.08 %). Genomic analysis confirmed the presence of multiple antimicrobial resistance genes including norA/C, vanT, mecA, dfrC and multidrug resistance genes. The carrying of mobile genetic elements was demonstrated by 25/26 (96.15 %) strains. These findings indicate that S. epidermidis strains isolated from ready-to-eat foods not only exhibit multidrug resistance but also carry a diverse array of antimicrobial resistance genes. The potential for horizontal gene transfer to commensal or pathogenic bacteria highlights the need for increased surveillance and risk assessment concerning CoNS in the food supply.},
}

@article {pmid40407375,
year = {2025},
author = {Lyra de Holanda Fonseca, D and Scheunemann, GS and Fortes, BN and Ishida, K and Galhardo, RS},
title = {Interaction of the SXT/R391 element ICEPmiJpn1 with its natural host Proteus mirabilis.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0033925},
pmid = {40407375},
issn = {2165-0497},
support = {2019/19435-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/00535-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/15170-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/10577-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/03986-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; finance code 01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology ; Conjugation, Genetic ; Gene Transfer, Horizontal ; Biofilms/growth & development ; Escherichia coli/genetics ; *DNA Transposable Elements/genetics ; Proteus Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Interspersed Repetitive Sequences ; Bacterial Proteins/genetics ; },
abstract = {Integrative and conjugative elements (ICEs) of the SXT/R391 family are mobile genetic elements that integrate into the bacterial host chromosome and can be transferred horizontally, spreading antimicrobial resistance genes. Our study aimed to evaluate aspects of the relationship between ICEPmiJpn1, one of the most widespread SXT/R391 variants, with its natural host Proteus mirabilis. For this investigation, we used isogenic strains (containing or not the ICEPmiJpn1) that enabled us to evaluate the influence of this element on several physiological aspects of P. mirabilis as well as the effect of different P. mirabilis genetic backgrounds on the conjugative transmission of the element. ICEPmiJpn1 did not impact the fitness, self-recognition, swarming, pathogenicity, and persistence abilities of this bacterium but increased biofilm formation in one strain. Additionally, conjugative transfer of the element to Escherichia coli is widely variable when different P. mirabilis strains are used as donors in mating assays. Our results indicate that ICEPmiJpn1 has no adverse effects on the physiology or pathogenicity of P. mirabilis, reflecting a stable association between this element and its host. Furthermore, the findings support the notion that ICE transfer between bacteria is influenced not only by element-specific regulators but also by strain-specific factors.IMPORTANCEMobile genetic elements play a key role in the spread of antimicrobial resistance, raising concerns about multidrug-resistant bacteria, yet their interactions with bacterial hosts are not well characterized. This study explores the relationship between ICEPmiJpn1, a globally distributed SXT/R391 integrative and conjugative element (ICE), and its natural host Proteus mirabilis, revealing minimal effects on bacterial fitness and pathogenicity. Nevertheless, strain-specific factors significantly influence conjugative transfer. These findings highlight the need for further research on host-dependent regulatory mechanisms that drive the spread of these elements. Understanding these dynamics is essential for developing strategies to mitigate the dissemination of antibiotic resistance in clinically relevant bacterial populations.},
}

*Proteus mirabilis/genetics/pathogenicity/drug effects/physiology
Conjugation, Genetic
Gene Transfer, Horizontal
Biofilms/growth & development
Escherichia coli/genetics
*DNA Transposable Elements/genetics
Proteus Infections/microbiology
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
*Interspersed Repetitive Sequences
Bacterial Proteins/genetics

@article {pmid40590551,
year = {2025},
author = {Renno, AJ and Shields, RC and McLellan, LK},
title = {Bacterial evolution in the oral microbiome: the role of conjugative elements and horizontal gene transfer.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0006625},
doi = {10.1128/jb.00066-25},
pmid = {40590551},
issn = {1098-5530},
abstract = {As one of the most diverse bacterial populations within the human body, the oral microbiome encodes a wealth of genetic information. Horizontal gene transfer, driven by mobile genetic elements, takes advantage of this information to influence bacterial evolution and the spread of phenotypes (antibiotic resistances, virulence attributes, and metabolic capabilities) among oral microbes. Although widespread within microbial communities, fundamental aspects of the mobile elements that drive horizontal gene transfer within the oral cavity remain poorly understood. In this review, we explore what is known about the role of horizontal gene transfer in bacterial evolution within the oral microbiome and the elements that facilitate this transfer, with a specific focus on conjugative DNA transfer. Conjugative elements are found in virtually all bacterial phylogenetic clades, and some can mediate genetic exchange between distantly related organisms. This is of particular interest in the diverse microcosm of the oral cavity, specifically how it drives the evolution and virulence of dental pathogens. Finally, we highlight advances in our understanding of the unique biology within dental plaque and how these might influence our understanding of bacterial gene transfer, and thus human health and disease.},
}

@article {pmid40589066,
year = {2025},
author = {Collins, N and Levy, Y and Kolomeisky, AB},
title = {Theoretical Understanding of Target Search Dynamics in Horizontal Gene Transfer in Bacteria.},
journal = {The journal of physical chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jpcb.5c02436},
pmid = {40589066},
issn = {1520-5207},
abstract = {Horizontal gene transfer (HGT) is a fundamental process of increasing genetic diversity in microbial species. It allows bacterial cells to acquire new beneficial traits quickly by incorporating new genetic material into existing genomes. Despite the critical importance of HGT phenomena, the underlying molecular mechanisms are still poorly understood. Recent experiments investigated the dynamics of conjugation HGT processes in which DNA is transmitted directly from the donor to the recipient bacterial cell. It is accomplished by special mobile genetic particles known as integrative and conjugative elements (ICE). However, the molecular picture of how ICE can efficiently find the unique integration sites in a new genome is not yet clear. We present a novel theoretical model to explain the dynamic processes in HGT after ICE reaches the recipient cell. It is shown that the target search for integration sites can be viewed as a set of stochastic transitions between discrete states, allowing us to obtain an explicit description of the dynamic properties using analytical calculations supported by Monte Carlo computer simulations. Search times are found to depend on the location of integration sites, the size of the genome, the effective diffusion rate of mobile genetic elements, and the binding/unbinding transitions between ICE and DNA. Theoretical estimates for search times agree well with experimental observations for integration in Bacillus subtilis bacterial species. Physical-chemical arguments are presented to explain the dynamics of the ICE target search. This study clarifies some important mechanistic aspects of HGT phenomena.},
}

@article {pmid40588591,
year = {2025},
author = {Mancuso, CP and Baker, JS and Qu, EB and Tripp, AD and Balogun, IO and Lieberman, TD},
title = {Intraspecies warfare restricts strain coexistence in human skin microbiomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40588591},
issn = {2058-5276},
support = {1DP2GM140922//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Determining why only a fraction of encountered or applied strains engraft in a given person's microbiome is crucial for understanding and engineering these communities. Previous work has established that metabolic competition between bacteria can restrict colonization success in vivo, but other mechanisms may also prevent successful engraftment. Here we combine genomic analysis and high-throughput agar competition assays to demonstrate that intraspecies warfare presents a significant barrier to strain coexistence in the human skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis isolates cultured from 18 people from 6 families. We find that intraspecies antagonisms are abundant, mechanistically diverse, independent of strain relatedness and consistent with rapid evolution via horizontal gene transfer. Critically, these antagonisms are significantly depleted among strains residing on the same person relative to random assemblages, indicating a significant in vivo role. Wide variation in antimicrobial production and resistance suggests trade-offs between these factors and other fitness determinants. Together, our results emphasize that accounting for intraspecies warfare may be essential to the design of long-lasting probiotic therapeutics.},
}

@article {pmid40587929,
year = {2025},
author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S},
title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126425},
doi = {10.1016/j.jenvman.2025.126425},
pmid = {40587929},
issn = {1095-8630},
abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.},
}

@article {pmid40585299,
year = {2025},
author = {Chai, Z and Guo, Z and Chen, X and Yang, Z and Wang, X and Zhang, F and Kang, F and Liu, W and Liang, S and Ren, H and Yue, J and Jin, Y},
title = {Comprehensive profiling of integrative conjugative elements (ICEs) in Mollicutes: distinct catalysts of gene flow and genome shaping.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf083},
pmid = {40585299},
issn = {2631-9268},
mesh = {*Genome, Bacterial ; Gene Transfer, Horizontal ; *Conjugation, Genetic ; *Gene Flow ; *Tenericutes/genetics ; Evolution, Molecular ; Phylogeny ; },
abstract = {Mollicutes, known as the simplest bacteria with streamlined genomes, were traditionally thought to evolve mainly through gene loss. Recent studies have highlighted their rapid evolutionary capabilities and genetic exchange within individual genomes; however, their evolutionary trajectory remains elusive. By comprehensive screening 1433 available Mollicutes genomes, we revealed widespread horizontal gene transfer (HGT) in 83.9% of investigated species. These genes involve type IV secretion systems and DNA integration, inferring the unique role of integrative conjugative elements (ICEs) or integrative and mobilizable elements (IMEs) as self-transmissible genetic elements. We systematically identified 263 ICEs/IMEs across most Mollicutes genera, being intact or fragmented, showing a strong correlation with HGT frequency (cor 0.573, P = .002). Their transfer tendency was highlighted across species sharing ecological niches, notably in livestock-associated mycoplasmas and insect-vectored spiroplasmas. ICEs/IMEs not only act as gene shuttles ferrying various phenotypic genes, but also promote increased large-scale chromosomal transfer events, shaping the host genomes profoundly. Additionally, we provided novel evidence that Ureaplasma ICE facilitates genetic exchange and the spread of antibiotic resistance gene tet(M) among other pathogens. These findings suggest that, despite the gene-loss pressure associated with the compact genomes of Mollicutes, ICEs/IMEs play a crucial role by introducing substantial genetic resources, providing essential opportunities for evolutionary adaptation.},
}

*Genome, Bacterial
Gene Transfer, Horizontal
*Conjugation, Genetic
*Gene Flow
*Tenericutes/genetics
Evolution, Molecular
Phylogeny

@article {pmid40584034,
year = {2025},
author = {Alhejaili, AY and Zhou, G and Halawa, H and Huang, J and Fallatah, O and Hirayban, R and Iftikhar, S and AlAsmari, A and Milner, M and Banzhaf, M and Alzaidi, AA and Rajeh, AA and Al-Otaiby, MA and Alabbad, SS and Bukhari, D and Aljurayyan, AN and Aljasham, AT and Alzeyadi, ZA and Alajel, SM and Alanazi, RH and Alghoribi, M and Almutairi, MM and Pain, A and Senok, A and Moradigaravand, D and Al Salem, W},
title = {Methicillin-resistant Staphylococcus aureus in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602985},
pmid = {40584034},
issn = {1664-302X},
abstract = {OBJECTIVES: Staphylococcus aureus is a leading cause of hospital-acquired infections worldwide. Over recent decades, methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to multiple antimicrobials, has emerged as a significant pathogenic strain in both hospital and community settings. The rapid emergence and dissemination of MRSA clones are driven by a dynamic and evolving population, spreading swiftly across regions on epidemiological time scales. Despite the vast geographical expanse and diverse demographics of the Kingdom of Saudi Arabia and the broader West Asia region, the population diversity of MRSA in hospitals in these areas remains underexplored.

METHODS: We conducted a large-scale genomic analysis of a systematic Staphylococcus aureus collection obtained from 34 hospitals across all provinces of KSA, from diverse body sites between 2022 and 2024. The dataset comprised 581 MRSA and 31 methicillin-susceptible Staphylococcus aureus (MSSA) isolates, all subjected to whole-genome sequencing. A combination of phylogenetic and population genomics approaches was utilized to analyze the genomic data. Hybrid sequencing approach was employed to retrieve the complete plasmid content.

RESULTS: The population displayed remarkable diversity, comprising 48 distinct sequence types (STs), with the majority harboring community-associated SCCmec loci (types IVa, V/VII, and VI). Virulence factors associated with community-acquired MRSA (CA-MRSA), including Panton-Valentine Leukocidin (PVL) genes, were identified in 12 distinct STs. Dominant clones, including ST8-t008 (USA300), ST88-t690, ST672-t3841, ST6-t304, and ST5-t311, were associated with infections at various body sites and were widely disseminated across the country. Linezolid and vancomycin resistance were mediated by cfr-carrying plasmids and mutations in the vraR gene (involved in cell-wall stress response) and the murF gene (involved in peptidoglycan biosynthesis) in five isolates, respectively. Phylodynamic analysis revealed rapid expansion of the dominant clones, with their emergence estimated to have occurred 10-20 years ago. Plasmidome analysis uncovered a diverse repertoire of blaZ-containing plasmids and the sharing of erm(C)-encoding plasmids among major clades. The acquisition of plasmids coincided with clonal expansion.

CONCLUSIONS: Our results highlight the recent concurrent expansion and geographical dissemination of CA-MRSA clones across hospitals. These findings also underscore the interplay between clonal spread and horizontal gene transfer in shaping the resistance landscape of MRSA.},
}

@article {pmid40434128,
year = {2025},
author = {Zhao, R and Nawrocki, A and Møller-Jensen, J and Liu, G and Olsen, JE and Thomsen, LE},
title = {Mechanistic divergence between SOS response activation and antibiotic-induced plasmid conjugation in Escherichia coli.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0009025},
pmid = {40434128},
issn = {2165-0497},
support = {//China Scholarship Council/ ; },
mesh = {*SOS Response, Genetics/drug effects ; *Escherichia coli/genetics/drug effects/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Plasmids/genetics/metabolism ; *Conjugation, Genetic/drug effects ; Escherichia coli Proteins/genetics/metabolism ; Cefotaxime/pharmacology ; Ciprofloxacin/pharmacology ; Gene Expression Regulation, Bacterial/drug effects ; Mitomycin/pharmacology ; Gene Transfer, Horizontal ; },
abstract = {The SOS response is a critical DNA damage repair mechanism in bacteria, designed to counteract genotoxic stress and ensure survival. This system can be activated by different classes of antimicrobial agents, each inducing the SOS response through different mechanisms. Moreover, it has been observed that certain antibiotics can enhance conjugative plasmid transfer frequencies. However, while previous studies have suggested that the SOS response contributes to horizontal transfer of certain genes, its role in plasmid conjugation remains unclear. In this study, we investigated the relationship between the SOS response and conjugation of IncI1 and IncFII plasmids harboring various blaCTX-M resistance genes. Results showed that cefotaxime and mitomycin C induced both the SOS response and conjugation, while ciprofloxacin induced the SOS response without affecting conjugation frequencies. Further analysis of SOS mutants, ranging from constitutively inactive to hyper-induced states, revealed no correlation between SOS levels and conjugation frequencies, despite upregulation of tra gene expression in a SOS hyper-induced strain. Proteomic analysis revealed that cefotaxime-induced conjugation was associated with increased transfer and pilus protein expression. In contrast, the SOS hyper-induced strain displayed limited upregulation of plasmid-encoded proteins, suggesting post-transcriptional regulation. Additionally, putative LexA binding sites on the IncI1 plasmid revealed potential SOS-mediated regulation of plasmid genes, highlighting the interaction between the SOS response and plasmid, although it did not significantly affect conjugation.IMPORTANCEPlasmids play a critical role in the dissemination of antibiotic resistance through conjugation. Recent research suggests that the use of antibiotics not only selects for already resistant variants but further increases the rate of plasmid-encoded conjugative transmission by increasing expression of the conjugative system. At the same time, these antibiotics are known to induce the stress-related SOS response in bacteria. To be able to counteract an antibiotic-induced increase in conjugative transfer of resistance plasmid, there is a need for a fundamental understanding of the regulation of transmission, including whether this happens through activation of the SOS response. In this research, we show that antibiotic-induced conjugation and induction of the SOS response happen through different mechanisms, and thus that future strategies to control the spread of antibiotics cannot interfere with the SOS response as its target.},
}

*SOS Response, Genetics/drug effects
*Escherichia coli/genetics/drug effects/metabolism
*Anti-Bacterial Agents/pharmacology
*Plasmids/genetics/metabolism
*Conjugation, Genetic/drug effects
Escherichia coli Proteins/genetics/metabolism
Cefotaxime/pharmacology
Ciprofloxacin/pharmacology
Gene Expression Regulation, Bacterial/drug effects
Mitomycin/pharmacology
Gene Transfer, Horizontal

@article {pmid40408992,
year = {2025},
author = {Zhang, S and Li, J and Lai, J and Zhang, Q and Zhao, Z and Li, B},
title = {Transfer dynamics of intracellular and extracellular last-resort antibiotic resistome in hospital wastewater.},
journal = {Water research},
volume = {283},
number = {},
pages = {123833},
doi = {10.1016/j.watres.2025.123833},
pmid = {40408992},
issn = {1879-2448},
mesh = {*Wastewater/microbiology ; Hospitals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; },
abstract = {The increasing prevalence of last-resort antibiotic resistance genes (LARGs) has posed severe public health hazards. Previous studies focused primarily on the profiles of intracellular LARGs (iLARGs) in hospital wastewater (HWW), while largely neglecting the expression patterns of iLARGs and the presence of extracellular LARGs (eLARGs). Currently, wastewater resistomes and transfer dynamics of LARGs are still poorly characterized. This study integrates Nanopore-metagenomic and metatranscriptomic sequencing to conduct the comprehensive longitudinal analysis of both iLARGs and eLARGs in HWW. Our study firstly revealed the distinct seasonal patterns of iLARGs and eLARGs. Specifically, iLARGs showed higher abundance during colder seasons, whereas eLARGs showed higher abundance in warm seasons. Both clinical pathogens and functional bacteria of wastewater treatments were identified as important hosts of LARGs, while clinical pathogens played predominant roles in the high expression levels of LARGs. Acinetobacter spp. was identified as major host of blaNDM-1 in HWW, which is unrestricted by plasmid host range compatibility. However, HWW treatments could not remove LARGs effectively and instead facilitated their transmission by enhancing the expression and horizontal transfer of mobile genetic element (MGE)-derived LARGs. Our study provides comprehensive insights for the atlas and transfer dynamics of LARGs in HWW for the development of control strategies under worldwide spread of antibiotic resistance.},
}

*Wastewater/microbiology
Hospitals
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal

@article {pmid40582582,
year = {2025},
author = {Munshi, ID and Mathuria, A and Sharma, H and Acharya, M and Chaudhary, A and Jain, K and Ragini, and Dahiya, S and Arora, R and Singh, V and Saini, A and Mani, I},
title = {Emerging concept of genomic islands in bacterial adaptation and pathogenicity.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104303},
doi = {10.1016/j.resmic.2025.104303},
pmid = {40582582},
issn = {1769-7123},
abstract = {Genomic Islands (GEIs) are distinct DNA segments acquired through horizontal gene transfer (HGT), driving bacterial evolution and adaptation. These include Pathogenicity Islands (PAIs), Symbiosis Islands, Antibiotic Resistance Islands, Xenobiotic-Degradation Islands, and Nitrogen Fixation Islands. GEIs contribute to genetic diversity, enhancing bacterial pathogenicity, symbiosis, antibiotic resistance, and xenobiotic degradation. Characterized by variations in GC content, codon bias, and integration sites, they distinguish themselves from the core genome. Advances in genome sequencing and bioinformatics have deepened our understanding of GEIs in bacteria like Salmonella, Vibrio, E. coli, and many more, offering insights into microbial evolution, pathogenicity, and antibiotic resistance mechanisms.},
}

@article {pmid40581000,
year = {2025},
author = {Fraikin, N and Samuel, B and Burstein, D and Lesterlin, C},
title = {Strategies for zygotic gene expression during plasmid establishment.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102754},
doi = {10.1016/j.plasmid.2025.102754},
pmid = {40581000},
issn = {1095-9890},
abstract = {Conjugative plasmids are key drivers of horizontal gene transfer and the spread of antimicrobial resistance. Their successful establishment in new hosts requires overcoming diverse bacterial defence mechanisms, such as restriction-modification systems, CRISPR-Cas systems, and the SOS response. Plasmids achieve this through a leading region-encoded zygotic program of anti-defence genes expressed early in conjugation. This program employs diverse strategies, including single-stranded promoters, repressed double-stranded promoters, and protein translocation. This review explores the diversity of these zygotic programs, the mechanisms underlying their timely regulation, and the array of anti-defence functions they encode. Further investigation of leading region genes is crucial for discovering novel counter-defence strategies and understanding their tailored regulation across diverse plasmid and bacterial species, ultimately enabling us to better understand and potentially manipulate plasmid transfer.},
}

@article {pmid40580037,
year = {2025},
author = {},
title = {Correction to 'GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf654},
pmid = {40580037},
issn = {1362-4962},
}

@article {pmid40579721,
year = {2025},
author = {O'Donnell, S and Rezende, G and Vernadet, JP and Snirc, A and Ropars, J},
title = {Harbouring Starships: The accumulation of large Horizontal Gene Transfers in Domesticated and Pathogenic Fungi.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf125},
pmid = {40579721},
issn = {1759-6653},
abstract = {Human-related environments, including food and clinical settings, present microorganisms with atypical and challenging conditions that necessitate adaptation. Several cases of novel horizontally acquired genetic material associated with adaptive traits have been recently described, contained within giant transposons named Starships. While a handful of Starships have been identified in domesticated species, their abundance has not yet been systematically explored in human-associated fungi. Here, we investigated whether Starships have shaped the genomes of two major genera of fungi occurring in food and clinical environments, Aspergillus and Penicillium, providing a unique opportunity to study several independent events of adaptation to similar niches. We found in all cases that the domesticated strains or species exhibited significantly greater Starship content compared with close relatives from non-human-related environments, containing an enrichment in genes involved in adaptation to food. We found a similar pattern in clinical contexts. Our findings have clear implications for agriculture, human health and the food industry as we implicate Starships as a widely recurrent mechanism of gene transfer aiding the rapid adaptation of fungi to novel environments.},
}

@article {pmid40578739,
year = {2025},
author = {Yang, Y and Tang, X and Zhang, P and Mo, C and Huang, F and Wen, Z},
title = {Effect of microplastics on antibiotic resistome risk in composting.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122241},
doi = {10.1016/j.envres.2025.122241},
pmid = {40578739},
issn = {1096-0953},
abstract = {Microplastics are a growing concern worldwide because of their impact on the environment and human health. Composting is an effective method for managing antibiotic resistome risk in organic waste, yet the effects of microplastics on antibiotic resistome risk in composting are not well understood. In this study of laying hen manure, the microplastic polypropylene increased the temperature of the compost but did not significantly affect the total composition, abundance and risk score of antibiotic resistance genes (ARGs) during composting. The dominant phyla on microplastics and manure were Actinobacteria, Firmicutes and Proteobacteria. Escherichia (bin.70), Oceanobacillus (bin.85) and Mycobacterium (bin.79) were the main ARG hosts. Among them, the abundance of the ARG host Mycobacterium (bin.79) was significantly higher in microplastics than in manure. Furthermore, ARG transfer occurred between the ARG host Mycobacterium (bin.79) and other microorganisms on microplastics and manure. These findings indicate that while microplastics may not strongly affect the overall antibiotic resistome risk during composting, they increase the likelihood of horizontal gene transfer in specific ARG hosts. This underscores the critical need to control both microplastic and resistance contamination.},
}

@article {pmid40578617,
year = {2025},
author = {Villarroel, CA and Gonzalez-Gonzalez, A and Chamorro, M and Villarreal, P and Cubillos, FA and Ramírez, CC},
title = {Discovery of the first aphid-infecting nudiviruses reveal bidirectional host-virus gene transfer.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108393},
doi = {10.1016/j.jip.2025.108393},
pmid = {40578617},
issn = {1096-0805},
abstract = {Nudiviruses are double-stranded DNA viruses that infect invertebrate species, ranging from aquatic arthropods to insects from diverse orders. Remnants of nudiviral infections have been found as introgressions in the genome of several insect hosts, such as aphids pest species (Hemiptera: Aphididae). However, a nudivirus infecting aphids has yet to be reported. Here, we describe the complete genome sequences of two nudiviruses found in the aphid Neuquenaphis staryi, a species that branched out early in the Aphididae family and is endemic to southern beech forests in South America. These nudiviruses (NsNV-1 and NsNV-2) share 98% of nucleotide identity between them and belong to the Alphanudivirus genus. Notably, we found that the prevalence of NsNV-1 was 16 times higher than NsNV-2 in natural N. staryi populations, and co-infections were not observed. Furthermore, we show that horizontal gene transfer between aphids and nudiviruses has been bidirectional, providing evidence of their dynamic co-evolutionary relationship. This study provides the first documentation of nudivirus infections in aphids and expands our understanding of the evolutionary interactions between nudiviruses and their insect hosts.},
}

@article {pmid40578104,
year = {2025},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.},
journal = {Water research},
volume = {285},
number = {},
pages = {124074},
doi = {10.1016/j.watres.2025.124074},
pmid = {40578104},
issn = {1879-2448},
abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.},
}

@article {pmid40576355,
year = {2025},
author = {López, L and Jumbo, M and Mosquera, P and Donoso, G and Graham, J and Trueba, G},
title = {Oral and parenteral treatment with a third-generation cephalosporin promotes the proliferation of diverse ESBL-producing Escherichia coli in the chicken intestinal tract.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0022725},
doi = {10.1128/msphere.00227-25},
pmid = {40576355},
issn = {2379-5042},
abstract = {The global rise of antimicrobial resistance is a major public health threat, with Escherichia coli facilitating the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study examines the impact of 3GC treatment on resistant E. coli clones and horizontal gene transfer (HGT) of ESBL genes in broiler chickens in Quito, Ecuador. Fifteen-day-old Ross broilers were divided into three groups: oral ceftriaxone (100 mg/kg), parenteral ceftriaxone (100 mg/kg intramuscular), and control (no treatment). The study included three phases: baseline, antimicrobial administration (5 days), and recovery (15 days). Fecal cultures on McConkey agar, with and without ceftriaxone (2 µg/mL), measured the ratio of 3GC-resistant lactose fermenters. Regardless of the administration route, ceftriaxone significantly increased resistant coliforms (>80%). Five E. coli colonies per animal and time point were analyzed using single-gene typing, with clonal candidates subjected to whole-genome sequencing. Clonal analysis revealed high genetic diversity, averaging three distinct clones per animal. A unique lineage (H34) emerged exclusively during treatment, and new clones appeared post-treatment. The blaCTX-M-55 variant was the most abundant ESBL gene, persisting despite fluctuations in other blaCTX-M variants. Comparative plasmid analysis suggested blaCTX-M-55 HGT, as plasmids were identified in two genetically distinct E. coli isolates from the same host. Most plasmids belonged to IncFII, with IncX1 and IncN also present. These findings highlight how 3GC treatments rapidly impact ESBL-producing E. coli diversity in the intestine.IMPORTANCEThe global rise of antimicrobial resistance (AMR) poses a critical public health challenge, with Escherichia coli playing a central role in the spread of extended-spectrum beta-lactamase (ESBL) genes like blaCTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study highlights the significant impact of 3GC treatment on the frequency and diversity of 3GC-resistant E. coli clones and horizontal gene transfer of ESBL genes in the intestinal microbiota of broiler chickens. Understanding how antimicrobial treatments drive resistance dynamics in animal populations is crucial for developing strategies to mitigate AMR in both human and veterinary settings.},
}

@article {pmid40573425,
year = {2025},
author = {Lewandowska, N and Bloch, S and Łukasiak, A and Wesołowski, W and Węgrzyn, G and Nejman-Faleńczyk, B},
title = {The Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060834},
pmid = {40573425},
issn = {1999-4915},
support = {2018/29/B/NZ1/00549//National Science Center/ ; 2018/30/E/NZ1/00400//National Science Center/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *RNA, Small Untranslated/genetics/metabolism ; *RNA, Viral/genetics/metabolism ; Gene Expression Regulation, Bacterial ; *Host Microbial Interactions ; RNA, Bacterial/genetics ; Host-Pathogen Interactions ; Gene Transfer, Horizontal ; },
abstract = {Small regulatory RNAs (sRNAs) play a critical role in bacterial gene expression, modulating various cellular processes, including stress responses, metabolism, virulence, and many others. While well-characterized in bacterial systems, an emerging class of phage-derived sRNAs has been identified, suggesting an underexplored regulatory network at phage-host interactions. These sRNAs, encoded within phage genomes, influence both bacterial and viral life cycles by modulating transcriptional and post-transcriptional gene expression processes. The interplay between phage-derived sRNAs and the host genome reveals a complex network of gene regulation, with an impact on bacterial fitness, pathogenesis, and horizontal gene transfer. This review explores the diverse functions of phage-encoded sRNAs, highlighting recent discoveries and their impact on bacterial physiology and phage-host interactions.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*RNA, Small Untranslated/genetics/metabolism
*RNA, Viral/genetics/metabolism
Gene Expression Regulation, Bacterial
*Host Microbial Interactions
RNA, Bacterial/genetics
Host-Pathogen Interactions
Gene Transfer, Horizontal

@article {pmid40572258,
year = {2025},
author = {Gonzalez Moreno, PJ and Nishiguchi, MK},
title = {The Competitive Edge: T6SS-Mediated Interference Competition by Vibrionaceae Across Marine Ecological Niches.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572258},
issn = {2076-2607},
support = {NSF DBI-2214028//U.S. National Science Foundation/ ; EXO 80NSSC18K1053/NASA/NASA/United States ; School of Natural Sciences//University of California, Merced/ ; },
abstract = {Interference competition, wherein bacteria actively antagonize and damage their microbial neighbors, is a key ecological strategy governing microbial community structure and composition. To gain a competitive edge, bacteria can deploy a diverse array of antimicrobial weapons-ranging from diffusible toxins to contact-mediated systems in order to eliminate their bacterial rivals. Among Gram-negative bacteria, the type VI secretion system (T6SS) has emerged as a potent and sophisticated contact-dependent mechanism that enables the delivery of toxic cargo into neighboring cells, thereby promoting the colonization and dominance of a bacterial taxon within an ecological niche. In this review, we examine the ecological significance of T6SS-mediated interference competition by members of the Vibrionaceae family across a range of marine habitats that include free-living microbial communities and host-associated niches such as coral and squid symbioses. Additionally, we explore the ecological impact of T6SS-mediated competition in modulating biofilm community structure and promoting horizontal gene transfer within those complex microbial populations. Together, these insights underscore the ecological versatility of the T6SS and emphasize its role in driving antagonistic bacterial interactions and shaping microbial community dynamics within marine ecosystems.},
}

@article {pmid40572209,
year = {2025},
author = {Antequera-Zambrano, L and Parra-Sánchez, Á and González-Paz, L and Fernandez, E and Martinez-Navarrete, G},
title = {Distribution of Genetic Determinants Associated with CRISPR-Cas Systems and Resistance to Antibiotics in the Genomes of Archaea and Bacteria.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572209},
issn = {2076-2607},
abstract = {The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, cas gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material-reflected in the higher complexity and diversity of CRISPR loci in Archaea-and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures.},
}

@article {pmid40572139,
year = {2025},
author = {Balata, D and Rosado, T and Pina-Martins, F and Manageiro, V and Menezes, C and Ferreira, E and Paulo, OS and Caniça, M and Dias, E},
title = {Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572139},
issn = {2076-2607},
support = {PTDC/BIA-BMA/31451/2017; UIDB/00211/2020//Portuguese Foundation for Science and Technology/ ; },
abstract = {Cyanobacteria are ubiquitous in freshwater environments, but their role in aquatic resistome remains unclear. In this work, we performed whole genome sequencing on 43 cyanobacterial strains isolated from Portuguese fresh/wastewaters. From 43 available non-axenic unicyanoabacterial cultures (containing only one cyanobacterial strain and their co-occurring bacteria), it was possible to recover 41 cyanobacterial genomes from the genomic assemblies using a genome binning software, 26 of which were classified as high-quality based on completeness, contamination, N50 and contig number thresholds. By using the comprehensive antibiotic resistance database (CARD) on the assembled samples, we detected four antibiotic resistance gene (ARG) variants, conferring resistance in pathogenic bacteria to tetracyclines, fluoroquinolones (adeF-type) and macrolides (ermF-type, mefC-type and mphG-type). Among these, adeF-type was the most prevalent gene, found across 11 cyanobacterial genomes from the Nostocales order. Planktothrix presented the highest variety of close ARG matches, with hits for the macrolide resistance genes ermF-type, mefC-type and mphG-type. An analysis of the genomic assemblies also revealed an additional 12 ARGs in bacteria from the phyla Firmicutes, Proteobacteria and Bacteroidetes, present in the cyanobacterial cultures, foreseeing the horizontal gene transfer of ARGs with cyanobacteria. Additionally, more than 200 partial ARGs were detected on each recovered cyanobacterial genome, allowing for future studies of antibiotic resistance genotype/phenotype in cyanobacteria. These findings highlight the importance of further efforts to understand the role of cyanobacteria on the aquatic resistome from a One Health perspective.},
}

@article {pmid40572111,
year = {2025},
author = {Lucero, J and Nishiguchi, MK},
title = {Host-Associated Biofilms: Vibrio fischeri and Other Symbiotic Bacteria Within the Vibrionaceae.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572111},
issn = {2076-2607},
support = {1T32GM141862-24S3/NH/NIH HHS/United States ; DBI 2214038//National Science Foundation/ ; },
abstract = {Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies.},
}

@article {pmid40571945,
year = {2025},
author = {Elmahdy, MH and Azmy, AF and Dishisha, T and El-Gendy, AO and Sebak, M},
title = {Fundamental changes in the antimicrobial resistance profile of Klebsiella quasipneumoniae ATCC 700603 in response to meropenem stress.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {369},
pmid = {40571945},
issn = {1471-2180},
mesh = {*Meropenem/pharmacology ; *Klebsiella/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; Bacterial Proteins/genetics/metabolism ; beta-Lactamases/genetics/metabolism ; *Drug Resistance, Bacterial/genetics ; Stress, Physiological ; Gene Transfer, Horizontal ; Gene Expression Regulation, Bacterial/drug effects ; },
abstract = {BACKGROUND: Klebsiella is one of the most challenging superbugs having a high tendency to acquire rapid resistance to many antibiotics, even the ones recognized as the last resort. In several hospitals and environmental niches, Klebsiella is continuously exposed to residual amounts of antibiotics at sub-inhibitory concentrations forming an environmental stress motivating them to adapt and evolve antimicrobial resistance. In the present study, meropenem (MEM) resistance was induced experimentally in a MEM-sensitive strain of K. quasipneumoniae ATCC 700603 through sequential sub-culturing in presence of sub-inhibitory concentrations of MEM over a period of 20 days. To uncover the possible mechanisms standing behind the evolution of antimicrobial resistance upon successive exposure to stress of MEM rather than horizontal gene transfer (HGT) of antibiotic resistance genes.

RESULTS: Fully adapted cells of the 20th generation (G20) showed MEM-resistance with elevated minimum inhibitory concentration (MIC) by 256-fold compared to the parent cells (G0). The main mechanism of resistance was the production of carbapenemases, which was assured by different tests including nitrocefin, modified-Hodge test (MHT), and modified carbapenem inactivation method (mCIM). The degradation of MEM reached 65.93% by the produced carbapenemases of G20 as determined by the HPLC analysis. Transcriptomics analysis of the class D carbapenemase encoding gene, blaOXA-2, revealed that it was significantly over-expressed by a 3.12-fold (p < 0.05) in G20 compared to G0.

CONCLUSION: The evolved MEM resistance aroused mainly from MEM degradation by carbapenemases, neither increased efflux nor decreased influx of MEM. The rational use of antibiotics is essential to reduce bacterial exposure to the environmental basal levels of antibiotics and decreasing the evolution of antimicrobial resistance.},
}

*Meropenem/pharmacology
*Klebsiella/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Bacterial Proteins/genetics/metabolism
beta-Lactamases/genetics/metabolism
*Drug Resistance, Bacterial/genetics
Stress, Physiological
Gene Transfer, Horizontal
Gene Expression Regulation, Bacterial/drug effects

@article {pmid40570498,
year = {2025},
author = {Zhang, X and Jiao, P and Li, B and Zhang, XX and Ma, L},
title = {Phage lysis-mediated reduction of antibiotic-resistant bacteria alleviates micro/nanoplastic-driven antimicrobial resistance dissemination in anaerobic digestion.},
journal = {Water research},
volume = {285},
number = {},
pages = {124046},
doi = {10.1016/j.watres.2025.124046},
pmid = {40570498},
issn = {1879-2448},
abstract = {Micro/nanoplastics (MPs/NPs) prevalent in anaerobic digestion (AD) have posed escalating threats to antimicrobial resistance (AMR) dissemination, yet mechanistic insights remain insufficient. Here we investigated polypropylene (PP)-MPs (200 μm) and PP-NPs (100 nm) at environmentally relevant concentrations (10, 50, and 100 mg/g TS) on antibiotic resistance gene (ARG) dynamics and transfer mechanisms using metagenomics and bioinformatic modeling. PP-MPs/NPs significantly elevated (6.4-17.8 %, p < 0.05) ARG abundance through selective enrichment of aminoglycoside, mupirocin, multidrug, polymyxin, sulfonamide, tetracycline, and novobiocin ARGs. Metagenomic assembly revealed the particle-induced ecological niche specialization of antibiotic-resistant bacteria (ARB), notably the multi-resistant ESKAPE pathogen Enterobacter hormaechei (53.4-69.4 % enrichment, p < 0.05), which harbored mobile aadA, qacEdelta1, and sul1 via conjugative plasmids. Mechanistically, MPs/NPs facilitated horizontal gene transfer (HGT) through synergism of plasmids and phages. The enhanced abundance of conjugation elements, enriched plasmid-borne ARGs, and extensive HGT events promoted plasmid-conjugative transfer, while the strongly correlated ARG-carrying lysogenic phage-host pairs highlighted phage-mediated transfer under MPs/NPs. The significant increase of phage-to-host-ratio (1.0-1.2 folds) revealed the underestimated role of phages lysing ARB under MPs/NPs stress, thereby contributing to ARG load reduction. A novel risk assessment framework prioritizing prevalence, enrichment, mobility, and host pathogenicity identified dfrA3, mefB, OXA-347, and tet44 as high-risk biomarkers and quantified 1.5-9.9 % increased health risks in digestate-exposed scenarios. These findings reveal the neglected role of phage lysis driving ARG reduction, providing actionable targets for mitigating plastic-driven resistance in AD.},
}

@article {pmid40452436,
year = {2025},
author = {Tannier, E and Tricou, T and Benali, S and de Vienne, DM},
title = {HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.},
journal = {Molecular biology and evolution},
volume = {42},
number = {6},
pages = {},
doi = {10.1093/molbev/msaf128},
pmid = {40452436},
issn = {1537-1719},
support = {ANR-19-CE45-0010//Agence Nationale de la Recherche/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Models, Genetic ; Evolution, Molecular ; Computer Simulation ; },
abstract = {When a gene is horizontally transferred (HGT), under the "replacement" model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the "recipient branch" is moved from its initial position to attach to the "donor branch". Based on this observation, various methods have used SPRs to infer HGTs. We examine this apparent equivalence in the light of ghost lineages, i.e. related species absent from the phylogeny because they are extinct, unknown, or have not been sampled. In this case, an SPR is not directly interpretable by an HGT from the donor branch, because HGTs can have ghost lineages as donors. A possible and frequent interpretation-that we call "induced HGT"-is that the transferred gene leaves the sampled phylogeny for a ghost lineage at the donor branch and is transferred back from a ghost lineage at the recipient branch. We show by simulations that this interpretation is misleading in a significant number of cases. For instance, if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then SPRs do not correspond to induced HGTs in around 50% of the cases. This leaves the question of a coherent interpretation of SPR in the presence of ghosts open and applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation, or phylogenetic networks.},
}

*Gene Transfer, Horizontal
*Phylogeny
*Models, Genetic
Evolution, Molecular
Computer Simulation

@article {pmid40568145,
year = {2025},
author = {Brezner, S and Garushyants, SK and Wolf, YI and Koonin, EV and Snir, S},
title = {Evolution of gene order in prokaryotes is driven primarily by gene gain and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.03.647019},
pmid = {40568145},
issn = {2692-8205},
abstract = {UNLABELLED: Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order relying on the recently developed "jump" model of gene translocation. The jump model has been completely solved analytically and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.

SIGNIFICANCE: Evolution of bacterial and archaeal genomes is a highly dynamic process that includes extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, so that gene order is not highly conserved even among closely related organisms. We developed a theoretical framework to quantify the contributions of different genome dynamics processes to the evolution of the gene order and found that in most groups of bacteria and archaea, the genome rearrangement to gene flux (combined gain and loss) is on the order of 0.1. Thus, the loss of genomic synteny in the evolution of bacteria and archaea appears to be driven primarily by gene gain and loss rather than by gene translocation.},
}

@article {pmid40565594,
year = {2025},
author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C},
title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/genes16060702},
pmid = {40565594},
issn = {2073-4425},
mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; },
abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.},
}

Humans
*Evolution, Molecular
Animals
*Eukaryota/genetics
Gene Duplication
Gene Transfer, Horizontal
Selection, Genetic

@article {pmid40565227,
year = {2025},
author = {Fu, W and Wang, Y and Ge, Y and Gao, H and Sun, X and Deng, Z and Wang, L and Chen, S and He, X and Wu, G},
title = {Molecular Insight into the Recognition of DNA by the DndCDE Complex in DNA Phosphorothioation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125765},
pmid = {40565227},
issn = {1422-0067},
support = {32170030//National Natural Science Foundation of China/ ; 2020YFA0907300//National Key R&D Program of China/ ; 2022YFA0912200//National Key R&D Program of China/ ; },
mesh = {Escherichia coli/metabolism/genetics ; *Escherichia coli Proteins/metabolism/chemistry/genetics ; Protein Binding ; *DNA, Bacterial/metabolism/chemistry ; *DNA/metabolism/chemistry ; Streptomyces lividans/metabolism/genetics ; *Bacterial Proteins/metabolism/chemistry ; Models, Molecular ; },
abstract = {In a vast variety of prokaryotes such as Escherichia coli and Streptomyces lividans, the DNA degradation (Dnd) CDE protein complex (consisting of DndC, DndD, and DndE), together with the DndA/IscS protein and the DndFGH complex, function as a defense barrier to prevent the invasion of non-self-DNA. The DndCDE complex introduces phosphorothioation (PT) modifications into DNA, and the DndFGH complex specifically cleaves non-PT DNA and, thus, restricts horizontal gene transfer and phage invasion. Despite the central importance of the DndCDE complex in DNA PT modification, which catalyzes the oxygen-sulfur swap on DNA, our understanding of this key complex remains poor. Here, we employed protein structure prediction to provide a reasonably reliable prediction of the structure of the DndCDE complex and a 23 bp DNA-DndCDE complex. We found that among the three proteins in the DndCDE complex, DndC, especially its "specificity loop", plays a key role in recognizing the consensus PT modification sequence. In addition, the DndD protein is found to possess a highly conserved structural surface on its globular domain, presumably mediating the dimerization of DndD as well as the DndCDE complex. Furthermore, our normal mode analysis showed that there exists a dynamic transition between a closed and an open state for the DndCDE complex, facilitating its association and release of DNA. Our conclusions were corroborated by biochemical assays using purified proteins. On the whole, we provide molecular insights into the assembly and DNA-recognition mechanism of a central protein complex involved in DNA phosphorothioation.},
}

Escherichia coli/metabolism/genetics
*Escherichia coli Proteins/metabolism/chemistry/genetics
Protein Binding
*DNA, Bacterial/metabolism/chemistry
*DNA/metabolism/chemistry
Streptomyces lividans/metabolism/genetics
*Bacterial Proteins/metabolism/chemistry
Models, Molecular

@article {pmid40560800,
year = {2025},
author = {Ruf, A and Blumenkamp, P and Ludwig, C and Lippegaus, A and Brachmann, A and Klingl, A and Goesmann, A and Brinkrolf, K and Papenfort, K and Robatzek, S},
title = {Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells.},
journal = {Journal of extracellular vesicles},
volume = {14},
number = {6},
pages = {e70102},
pmid = {40560800},
issn = {2001-3078},
support = {EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; INST 95/1435-1 FUGG//Deutsche Forschungsgemeinschaft/ ; RO 3550/16-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/17-1//Deutsche Forschungsgemeinschaft/ ; RO 3550/18-1//Deutsche Forschungsgemeinschaft/ ; SPP2389 - Project-ID 503931087//Deutsche Forschungsgemeinschaft/ ; ERC Adv Grant 884235//H2020 European Research Council/ ; },
mesh = {*Extracellular Vesicles/metabolism/genetics ; *Genomic Islands/genetics ; *Xylella/genetics/pathogenicity/metabolism ; *RNA, Small Untranslated/genetics/metabolism ; Plant Diseases/microbiology ; Gene Transfer, Horizontal ; RNA, Bacterial/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Virulence ; RNA-Binding Proteins/metabolism ; },
abstract = {Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF's stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.},
}

*Extracellular Vesicles/metabolism/genetics
*Genomic Islands/genetics
*Xylella/genetics/pathogenicity/metabolism
*RNA, Small Untranslated/genetics/metabolism
Plant Diseases/microbiology
Gene Transfer, Horizontal
RNA, Bacterial/genetics/metabolism
Bacterial Proteins/metabolism/genetics
Virulence
RNA-Binding Proteins/metabolism

@article {pmid40559614,
year = {2025},
author = {Martz, K and Alomar, D and Karim, M and Knezevic, S and D'Costa, VM},
title = {Characterization of the Diversity in Host Range of an Extensively Drug-Resistant (XDR) Type IV Secretion System-Encoding Plasmid in Acinetobacter.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559614},
issn = {2076-0817},
support = {PJ4-175369/CAPMC/CIHR/Canada ; PJT-178191/CAPMC/CIHR/Canada ; },
mesh = {*Plasmids/genetics ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Type IV Secretion Systems/genetics ; Acinetobacter Infections/microbiology ; *Host Specificity ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The World Health Organization (WHO) cites antimicrobial resistance as among the greatest threats to human health. The multidrug-resistant pathogen Acinetobacter baumannii, recognized as a priority pathogen for healthcare and research, is responsible for a diverse array of infections including respiratory tract, soft tissue and wound, and bloodstream infections. Despite this importance, the mechanisms of its pathogenesis remain poorly understood. Conjugation represents a central mechanism for bacterial adaptation and evolution and is responsible for the spread of genes that promote pathogen survival, antibiotic resistance, virulence, and biofilm formation. Our laboratory recently characterized a large group of almost 120 Type IV Secretion System (T4SS)-encoding plasmids in Acinetobacter, distributed globally across 20 countries spanning four continents, and demonstrated that an XDR A. baumannii plasmid from this family was transmissible to another A. baumannii strain. This research investigated the potential diversity of host strains for this representative member plasmid. Using the GC1 lineage strain A. baumannii AB5075-UW harbouring the XDR plasmid p1AB5075 and a series of previously characterized clinical and environmental Acinetobacter strains, conjugative analyses demonstrated transfer of the XDR plasmid to both A. baumannii strains of more genetically divergent sequence types and to non-baumannii Acinetobacter species both inside and outside the Acinetobacter calcoaceticus-baumannii (ACB) complex. Successful recipients included diverse strains of both clinical and environmental origin within the Acinetobacter genus. Collectively, this research could provide insights into an important genetic element for future surveillance.},
}

*Plasmids/genetics
*Acinetobacter baumannii/genetics/drug effects/pathogenicity
*Drug Resistance, Multiple, Bacterial/genetics
Humans
*Type IV Secretion Systems/genetics
Acinetobacter Infections/microbiology
*Host Specificity
Anti-Bacterial Agents/pharmacology

@article {pmid40559557,
year = {2025},
author = {Enciso-Martínez, Y and Barrios-Villa, E and Ballesteros-Monrreal, MG and Navarro-Ocaña, A and Valencia, D and González-Aguilar, GA and Martínez-Téllez, MA and Palomares-Navarro, JJ and Ayala-Zavala, F},
title = {Virulence and Antibiotic Resistance of aEPEC/STEC Escherichia coli Pathotypes with Serotype Links to Shigella boydii 16 Isolated from Irrigation Water.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/pathogens14060549},
pmid = {40559557},
issn = {2076-0817},
mesh = {Humans ; Virulence ; Serogroup ; *Shigella boydii/genetics/isolation & purification/drug effects/pathogenicity/classification ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; *Drug Resistance, Bacterial ; HeLa Cells ; *Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation & purification/pathogenicity/classification ; Agricultural Irrigation ; Virulence Factors/genetics ; Microbial Sensitivity Tests ; },
abstract = {Irrigation water can serve as a reservoir and transmission route for pathogenic Escherichia coli, posing a threat to food safety and public health. This study builds upon a previous survey conducted in Hermosillo, Sonora (Mexico), where 445 samples were collected from a local Honeydew melon farm and associated packing facilities. Among the 32 E. coli strains recovered, two strains, A34 and A51, were isolated from irrigation water and selected for further molecular characterization by PCR, due to their high pathogenic potential. Both strains were identified as hybrid aEPEC/STEC pathotypes carrying bfpA and stx1 virulence genes. Adhesion assays in HeLa cells revealed aggregative and diffuse patterns, suggesting enhanced colonization capacity. Phylogenetic analysis classified A34 within group B2 as associated with extraintestinal pathogenicity and antimicrobial resistance, while A51 was unassigned to any known phylogroup. Serotyping revealed somatic antigens shared with Shigella boydii 16, suggesting possible horizontal gene transfer or antigenic convergence. Antibiotic susceptibility testing showed resistance to multiple β-lactam antibiotics, including cephalosporins, linked to the presence of blaCTX-M-151 and blaCTX-M-9. Although no plasmid-mediated quinolone resistance genes were detected, resistance may involve efflux pumps or mutations in gyrA and parC. These findings are consistent with previous reports of E. coli adaptability in agricultural environments, suggesting potential genetic adaptability. While our data support the presence of virulence and resistance markers, further studies would be required to demonstrate mechanisms such as horizontal gene transfer or adaptive evolution.},
}

Humans
Virulence
Serogroup
*Shigella boydii/genetics/isolation & purification/drug effects/pathogenicity/classification
Phylogeny
Anti-Bacterial Agents/pharmacology
*Water Microbiology
*Drug Resistance, Bacterial
HeLa Cells
*Shiga-Toxigenic Escherichia coli/genetics/drug effects/isolation & purification/pathogenicity/classification
Agricultural Irrigation
Virulence Factors/genetics
Microbial Sensitivity Tests

@article {pmid40558211,
year = {2025},
author = {Enshaie, E and Nigam, S and Patel, S and Rai, V},
title = {Livestock Antibiotics Use and Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060621},
pmid = {40558211},
issn = {2079-6382},
abstract = {Background/Objectives: Antibiotic resistance or antimicrobial resistance (AMR) in livestock is a growing global concern that threatens both human and animal health. The overuse and misuse of antibiotics in livestock production have led to an increased propensity for the development of AMR bacterial strains in animals, which can be spread to humans through the consumption of contaminated animal products, direct contact, or environmental exposure. This review aims to summarize the development and transmission of AMR in livestock, explore its underlying mechanisms and impact on human and animal health, and discuss current practices and potential strategies for mitigation and prevention. Methods: For this narrative review, we searched articles on PubMed and Google Scholar using the terms antibiotic resistance, livestock, and environment, alone or in combination. Results: The history of antibiotic use in livestock and its link to increased AMR, along with the involved mechanisms, including the enzymatic breakdown of antibiotics, alterations in bacterial targets, horizontal gene transfer, and efflux pumps, are important. Antibiotics in livestock are used for growth promotion, disease prevention and control, and metaphylactic use. The role of livestock and the environment as reservoirs for resistant pathogens, their impact on human health, chronic infections, allergic reactions, toxicity, and the development of untreatable diseases is important to understand AMR. Conclusions: Given the widespread use of antibiotics and the potential consequences of AMR, collaborative global efforts, increased public awareness, coordinated regulations, and advancements in biological technology are required to mitigate the threat AMR poses to human and animal health. Regulatory solutions and the development of new therapeutic alternatives like antimicrobial peptides and bacteriophage therapy, and preventive measures such as DNA and mRNA vaccines, are future perspectives.},
}

@article {pmid40558188,
year = {2025},
author = {Mohammed, EAH and Kovács, B and Kuunya, R and Mustafa, EOA and Abbo, ASH and Pál, K},
title = {Antibiotic Resistance in Aquaculture: Challenges, Trends Analysis, and Alternative Approaches.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060598},
pmid = {40558188},
issn = {2079-6382},
support = {TKP2021-NKTA-32//National Research, Development, and Innovation Fund of Hungary/ ; },
abstract = {Antibiotic resistance in aquaculture has emerged as a global crisis, representing a serious threat to the health of aquatic animals, environment, and human. The extensive use of antibiotics in aquaculture has led to rapid development of resistant bacterial strains, resulting in environmental contamination and the dissemination of resistant genes. Understanding of the research trends, key contributors, and thematic evolution of this field is essential for guiding future studies and policy interventions. The study aimed to conduct a bibliometric analysis of research on antibiotic resistance development in aquaculture, identifying key areas of research, leading contributors, emerging challenges, and alternative solutions. Data were extracted from the Web of Science (WoS) database covering the period from 2000 to 2025. A systematic search strategy was employed, utilizing terms including "antibiotic resistance" AND "bacteria," AND "aquaculture". Relevant publications were extracted from the WoS using these keywords. R-tool was then used to analyze the obtained metadata including keywords, citation patterns, and co-authored country. The analysis revealed a remarkable increase in publications over the past 25 years, with key contributions from China, India, and the USA. The most significant articles focused on the presence of multidrug resistant bacteria in the aquatic environments and, antibiotic-resistant genes, and horizontal gene transfer. Probiotics are the alternative solution to overcome the antibiotic resistance and enhance aquaculture sustainability. Future research should focus on the interdisciplinary collaboration, novel antimicrobial alternatives, and global monitoring approaches.},
}

@article {pmid40558133,
year = {2025},
author = {Ye, Z and Li, M and Jing, Y and Liu, K and Wu, Y and Peng, Z},
title = {What Are the Drivers Triggering Antimicrobial Resistance Emergence and Spread? Outlook from a One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060543},
pmid = {40558133},
issn = {2079-6382},
support = {2022YFF1103100//National Key Research and Development Program of China/ ; 32172314//National Natural Science Foundation of China/ ; 22193064//National Natural Science Foundation of China/ ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global public health threat, exacerbating healthcare burdens and imposing substantial economic costs. Currently, AMR contributes to nearly five million deaths annually worldwide, surpassing mortality rates of any single infectious disease. The economic burden associated with AMR-related disease management is estimated at approximately $730 billion per year. This review synthesizes current research on the mechanisms and multifaceted drivers of AMR development and dissemination through the lens of the One Health framework, which integrates human, animal, and environmental health perspectives. Intrinsic factors, including antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), enable bacteria to evolve adaptive resistance mechanisms such as enzymatic inactivation, efflux pumps, and biofilm formation. Extrinsic drivers span environmental stressors (e.g., antimicrobials, heavy metals, disinfectants), socioeconomic practices, healthcare policies, and climate change, collectively accelerating AMR proliferation. Horizontal gene transfer and ecological pressures further facilitate the spread of antimicrobial-resistant bacteria across ecosystems. The cascading impacts of AMR threaten human health and agricultural productivity, elevate foodborne infection risks, and impose substantial economic burdens, particularly in low- and middle-income countries. To address this complex issue, the review advocates for interdisciplinary collaboration, robust policy implementation (e.g., antimicrobial stewardship), and innovative technologies (e.g., genomic surveillance, predictive modeling) under the One Health paradigm. Such integrated strategies are essential to mitigate AMR transmission, safeguard global health, and ensure sustainable development.},
}

@article {pmid40558095,
year = {2025},
author = {Milhomem Pilati Rodrigues, B and Janssen, L and da Silva, LA and Acacio, SSVG and Magalhães, MT and Ribeiro, BM},
title = {Experimental and evolutionary evidence for horizontal transfer of an envelope fusion protein gene between thogotoviruses and baculoviruses.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0214824},
doi = {10.1128/jvi.02148-24},
pmid = {40558095},
issn = {1098-5514},
abstract = {Baculoviruses are insect-specific viruses with large, double-stranded DNA genomes classified into four genera. Alphabaculoviruses, which infect lepidoptera, are further divided into group I (G1-α) and group II (G2-α). The GP64 protein, essential for cell attachment and viral entry in G1-α baculoviruses, is thought to have originated through horizontal gene transfer (HGT) from thogotoviruses (family Orthomyxoviridae). This study investigates the functional substitution of GP64 by thogotovirus fusion proteins. Through RNA-seq data mining, we identified a novel thogotovirus, Melitaea didyma thogotovirus 1 (MediTHOV-1), in lepidopteran hosts. Phylodynamic analysis of G1-α baculovirus and thogotovirus glycoproteins suggests that the HGT event occurred during the Mesozoic era. To test functional substitution, we constructed recombinant Autographa californica multiple nucleopolyhedrovirus (AcMNPV) carrying either the envelope fusion protein (EFP) genes from MediTHOV-1 or Apis thogotovirus 1 (ATHOV-1), while deleted for its native gp64 gene. Our results show that, while the MediTHOV-1 glycoprotein failed to rescue AcMNPV infectivity, the ATHOV-1 fusion protein (EFP) partially restored infectivity, albeit with reduced efficiency. Cryo-electron microscopy revealed lower incorporation of ATHOV-1 EFP into viral envelopes compared to GP64. The recombinant AcMNPV carrying ATHOV-1 EFP (Ac-ATHOVGPgp64Δ) displayed delayed replication kinetics and lower viral titers. Interestingly, ATHOV-1 EFP significantly enhanced baculovirus entry and gene transduction in mosquito cells. These findings provide experimental support for the HGT hypothesis, demonstrating the functional incorporation of a thogotovirus glycoprotein into a baculovirus. This study sheds light on the evolutionary relationship between baculovirus GP64 and glycoproteins, offering insights into viral evolution and potential biotechnological applications in gene delivery and protein expression.IMPORTANCEBaculoviruses are widely utilized for the biological control of insect pests and as versatile biotechnological tools, with their effectiveness largely dependent on the activity of their envelope fusion proteins (EFPs). Thogotoviruses, in contrast, are emerging vector-borne pathogens of significant concern. In this study, we present the first successful functional substitution of the baculovirus GP64 protein with a thogotovirus EFP, alongside the identification of what appears to be a lepidopteran-associated thogotovirus, Melitaea didyma thogothovirus 1. Our work provides functional and phylogenetic insights into the evolutionary relationship between these distantly related viral groups, particularly the hypothesized horizontal gene transfer event that gave rise to baculoviral gp64 gene. These findings offer a deeper understanding of the determinants underlying the adaptation of baculoviral glycoproteins to novel hosts. Furthermore, the discovery of novel viral genes highlights promising opportunities for biotechnological advancements, including the development of enhanced baculovirus-based gene delivery systems and tools for protein expression.},
}

@article {pmid40556893,
year = {2025},
author = {Di Marcantonio, L and Chiatamone Ranieri, S and Toro, M and Marchegiano, A and Cito, F and Sulli, N and Del Matto, I and Di Lollo, V and Alessiani, A and Foschi, G and Platone, I and Paoletti, M and D'Alterio, N and Garofolo, G and Janowicz, A},
title = {Comprehensive regional study of ESBL Escherichia coli: genomic insights into antimicrobial resistance and inter-source dissemination of ESBL genes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595652},
pmid = {40556893},
issn = {1664-302X},
abstract = {INTRODUCTION: The global dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) poses a significant public health challenge, particularly in regions with high antimicrobial resistance (AMR) occurrence. This study investigated the occurrence, genomic characteristics, and dissemination dynamics of ESBL-producing E. coli in Abruzzo, Italy, by analyzing 956 isolates from humans, livestock, wildlife, and food products.

METHODS: Phenotypic and genomic analyses were performed on the isolates to assess ESBL-E. coli occurrence and characteristics. Multilocus sequence typing (MLST) was used to identify sequence types (STs), and plasmid profiling alongside synteny analysis was conducted to investigate horizontal gene transfer and resistance gene integration. Spatial analysis was also carried out to identify hotspots of ESBL-positive isolates.

RESULTS: An overall ESBL-E. coli occurrence of 14.1% (135/956 samples) was found, with significant variation across hosts: companion animals exhibited the highest occurrence (16.2%), followed by livestock and food matrices (14.6%), and wildlife (7.0%). Spatial analysis identified a hotspot in northeastern Abruzzo, where ESBL-positive isolates were 5.34 times more likely to occur (p < 0.001). MLST identified 58 sequence types (STs), with ST131 dominating human isolates (12/19). In cattle, predominant sequence types were ST16565 (5 isolates) and ST540 (4 isolates); in poultry, ST43 (5 isolates), ST10 (4 isolates), and ST6215 (3 isolates) were most common; ST206 (8 isolates) was predominant in swine; and in dogs, ST10 (4 isolates) and ST3580 (3 isolates) were most prevalent. Genomic analysis revealed host-specific distributions of ESBL genes: bla CTX-M-15 predominated in humans and dogs, while bla CTX-M-1 was most common in pigs. Plasmid profiling revealed IncF and IncI plasmids as key vectors for horizontal gene transfer. Synteny analysis showed identical flanking regions of bla CTX-M-1 and bla CTX-M-15 across phylogenetically distant strains, suggesting chromosomal integration and stable maintenance of resistance genes.

DISCUSSION: These findings underscore the interconnectedness of human, animal, and environmental reservoirs in AMR dissemination. The high genetic diversity observed within farms and the detection of shared clusters across hosts emphasize the need for integrated One Health interventions, including reduced antibiotic use in livestock and enhanced surveillance of high-risk environments. This study provides critical insights into local AMR dynamics, offering a model for regional mitigation strategies.},
}

@article {pmid40556891,
year = {2025},
author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U},
title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597580},
pmid = {40556891},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.},
}

@article {pmid40556499,
year = {2025},
author = {Yang, Y and Jin, X and Zhao, Z},
title = {Distribution and Evolutionary Trajectories of β-Lactamases in Vibrio: Genomic Insights from CARB-Type Enzymes in the Harveyi and Cholerae Clades.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf128},
pmid = {40556499},
issn = {1759-6653},
abstract = {Antibiotic resistance mediated by β-lactamases (BLs), encoded by bla genes, is a significant global health threat, necessitating systematic studies of their diversity and evolution, particularly among pathogenic bacteria lineages. Leveraging over 6,000 quality-filtered Vibrio genomes alongside six newly sequenced marine symbiotic strains representing 128 nominal and 57 unclassified Vibrio species, our study extends taxonomic breadth and resolution for investigating BL diversity. We identified 4,431 BLs across 41 species, encompassing all four Ambler Classes (A∼D). Among these, CARBenicillin-hydrolyzing Class A BLs (CARBs encoded by blaCARB family) were the most prevalent (60.7%) and exhibited a clade-centric distribution particularly in Harveyi clade and V. cholerae, underscoring influence of specific ecological and evolutionary pressures. We refined CARB classification into two subfamilies: CARB-17-like (blaCARB-17-like) confined to Harveyi clade, and CARB-1-like (blaCARB-1-like) found exclusively outside Harveyi clade, based on phylogenetic placement, sequence similarity, and inheritance patterns, providing a clearer framework for delineating their functional and phylogenetic nuances. Notably, blaCARB-17-like genes in non-pathogenic Harveyi Subclade II showed significantly relaxed selection, accompanied by unusual mutations within key conserved motifs especially catalytic serine residues, suggesting evolutionary drift that may compromise canonical enzymatic activity. Furthermore, blaCARB-17-like genes, present as a single copy, emerged as a core gene in Harveyi clade, showing promise as a diagnostic marker for clinically significant Harveyi clade species, despite limited yet significant interspecies genetic exchanges mediated by recombination or mobile genetic elements. Our study advances the understanding of BL evolution and genomic distribution in Vibrio, with broad implications for diagnostic applications and resistance management strategies.},
}

@article {pmid40556036,
year = {2025},
author = {Li, Y and Liu, X and Yang, J and Li, R and Wang, M and Kuang, S},
title = {Characteristics of intracellular/extracellular antibiotic resistance genes and microbial community in sludge compost under sulfadiazine stress.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2522480},
pmid = {40556036},
issn = {1479-487X},
abstract = {The accumulation of emerging antibiotics in sewage sludge, which serves as a repository for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), is raising growing concern. To accurately assess the environmental risks, it is essential to separately investigate intracellular and extracellular ARGs (iARGs and eARGs) due to their distinct roles in resistance persistence and horizontal gene transfer. However, the impact of sulfadiazine (SDZ) on iARGs and eARGs, and the mechanisms involved in the composting process remain under further investigation. In this study, composts with SDZ concentrations of 5 and 50 mg/kg were constructed, and ARGs, microbial community composition and functional pathways were analyzed. The results showed that the abundance of iARGs varied significantly under SDZ selective pressure, while eARGs showed no significant differences. Specifically, i-erm decreased in the 50SDZ group, likely due to competition for ecological niches. The abundance of ermA, ermB and ermF decreased by approximately 97%, 85%, and 84%, respectively. i-sul increased by 127% to 156% in SDZ-added groups but not dose-dependently. Bacillus, Paracoccus, Pseudomonas, and Caproiciproducens were predominant in the SDZ-added groups. The abundance of potential ARG hosts, such as Bacillus and Paracoccus, increased significantly, with Paracoccus showing 2.3-fold and 1.8-fold higher abundance in the 50SDZ and 5SDZ treatments, respectively, compared to the CK. Functional genes related to the ABC-2 type transport system, signal transduction, and genome maintenance decreased with SDZ application. These findings suggested that the dynamics of ARGs should be continuously monitored during sludge composting and land application of compost products to reduce their environmental risks.},
}

@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.

METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.

RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.

CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}

@article {pmid40459279,
year = {2025},
author = {Parras-Moltó, M and Lund, D and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {The transfer of antibiotic resistance genes between evolutionarily distant bacteria.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0011425},
doi = {10.1128/msphere.00114-25},
pmid = {40459279},
issn = {2379-5042},
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects/classification ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Evolution, Molecular ; *Genes, Bacterial ; Humans ; },
abstract = {UNLABELLED: Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionarily distant bacteria, defined here based on their phylum. We implemented an algorithm that identified inter-phylum transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million ARGs identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3), while the levels for beta-lactamases were generally lower. ARGs involved in IPTs also differed between phyla, where, for example, tetracycline ARGs were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or underrepresented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline ARGs involved in IPTs almost always were >95% identical between phyla, corresponding β-lactamases showed a median identity of <60%. We conclude that inter-phylum transfer is recurrent, and our results offer new insights into how ARGs are disseminated between evolutionarily distant bacteria.

IMPORTANCE: Antibiotic-resistant infections pose a growing threat to global health. This study reveals how genes conferring antibiotic resistance can move between bacteria that belong to different phyla lineages previously thought to be too evolutionarily distant for frequent gene exchange. By analyzing nearly 1 million resistance genes from over 400,000 bacterial genomes, the researchers uncovered hundreds of inter-phylum transfer events, exposing surprising patterns in how different classes of resistance genes spread. The findings highlight that conjugative systems are less common than expected in cross-phyla transfers and suggest that alternative mechanisms may play key roles. This new understanding of how resistance genes leap between vastly different bacterial groups can inform strategies to slow the emergence of drug-resistant infections, aiding in the development of more effective public health interventions.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects/classification
Phylogeny
*Drug Resistance, Bacterial/genetics
Genome, Bacterial
Anti-Bacterial Agents/pharmacology
Evolution, Molecular
*Genes, Bacterial
Humans

@article {pmid40298963,
year = {2025},
author = {Karki, S and Barth, ZK and Aylward, FO},
title = {Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.},
journal = {Journal of molecular evolution},
volume = {93},
number = {3},
pages = {295-305},
pmid = {40298963},
issn = {1432-1432},
support = {2141862//National Science Foundation/ ; },
mesh = {Phylogeny ; *DNA Viruses/genetics ; Evolution, Molecular ; *Eukaryota/genetics/virology ; *Gene Transfer, Horizontal ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; },
abstract = {The details surrounding the early evolution of eukaryotes and their viruses are largely unknown. Several key enzymes involved in DNA synthesis and transcription are shared between eukaryotes and large DNA viruses in the phylum Nucleocytoviricota, but the evolutionary relationships between these genes remain unclear. In particular, previous studies of eukaryotic DNA and RNA polymerases often show deep-branching clades of eukaryotes and viruses indicative of ancient gene exchange. Here, we performed updated phylogenetic analysis of eukaryotic and viral family B DNA polymerases, multimeric RNA polymerases, and mRNA-capping enzymes to explore their evolutionary relationships. Our results show that viral enzymes form clades that are typically adjacent to eukaryotes, suggesting that they originate prior to the emergence of the Last Eukaryotic Common Ancestor (LECA). The machinery for viral DNA replication, transcription, and mRNA capping are all key processes needed for the maintenance of virus factories, which are complex structures formed by many nucleocytoviruses during infection, indicating that viruses capable of making these structures are ancient. These findings hint at a diverse and complex pre-LECA virosphere and indicate that large DNA viruses may encode proteins that are relics of extinct proto-eukaryotic lineages.},
}

Phylogeny
*DNA Viruses/genetics
Evolution, Molecular
*Eukaryota/genetics/virology
*Gene Transfer, Horizontal
DNA-Directed DNA Polymerase/genetics
DNA-Directed RNA Polymerases/genetics

@article {pmid40197024,
year = {2025},
author = {Gillett, DL and Selinidis, M and Seamons, T and George, D and Igwe, AN and Del Valle, I and Egbert, RG and Hofmockel, KS and Johnson, AL and Matthews, KRW and Masiello, CA and Stadler, LB and Chappell, J and Silberg, JJ},
title = {A roadmap to understanding and anticipating microbial gene transfer in soil communities.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {2},
pages = {e0022524},
doi = {10.1128/mmbr.00225-24},
pmid = {40197024},
issn = {1098-5557},
mesh = {*Soil Microbiology ; *Microbiota/genetics ; *Gene Transfer, Horizontal ; Soil/chemistry ; Bacteria/genetics ; Synthetic Biology ; Biotechnology ; },
abstract = {SUMMARYEngineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. We propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.},
}

*Soil Microbiology
*Microbiota/genetics
*Gene Transfer, Horizontal
Soil/chemistry
Bacteria/genetics
Synthetic Biology
Biotechnology

@article {pmid40553200,
year = {2025},
author = {Xie, X and Ren, Z and Wang, R and Tian, K and Huang, X and Lyu, Y and Cao, G and Fu, J},
title = {Mobile Genomic Island GEI-FN1A in Aeromonas salmonicida FN1 Contributes to the Spread of Antibiotic-Resistance Genes.},
journal = {Current microbiology},
volume = {82},
number = {8},
pages = {345},
pmid = {40553200},
issn = {1432-0991},
support = {ZR2022MH107//Shandong Provincial Natural Science Foundation/ ; M-2023040//TCM science and technology project of Shandong Province/ ; },
mesh = {*Genomic Islands ; Anti-Bacterial Agents/pharmacology ; Animals ; Gene Transfer, Horizontal ; *Aeromonas salmonicida/genetics/drug effects/isolation & purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Chickens ; Whole Genome Sequencing ; Genome, Bacterial ; Feces/microbiology ; Soil Microbiology ; Genes, Bacterial ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotics are used to treat severe bacterial infections. However, owing to excessive antibiotic use, bacteria under high selective pressure for antibiotics develop resistance through spontaneous mutation or by acquiring antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Horizontal transfer of ARGs among bacteria in the environment can lead to the emergence of multidrug-resistant (MDR) bacteria that infect animals and humans, thus causing disease outbreaks. In this study, MDR strain FN1 was isolated from a feces-contaminated soil sample from a chicken farm under pressure from the antibiotic florfenicol (16 mg/L) and identified as Aeromonas salmonicida. Whole-genome sequencing and analysis revealed the 86.8-kb antibiotic-resistant genomic island, GEI-FN1A, in the FN1 genome. Genome annotation revealed that GEI-FN1A carried several ARGs, including two tetracycline-resistance genes [tetR and tet(A)], three aminoglycoside-resistance genes [aph(6), aph(3"), and aac(3)], one trimethoprim-resistance gene (dfrB4), two chloramphenicol/florfenicol-resistance genes (catB3 and floR), three macrolide-resistance genes [mphR(A), mrx(A), and mph(A)] and two sul1 genes. GEI-FN1A also contained genes encoding integrase, transposase, and recombinase, which mediate the horizontal transfer of MDR genes. These findings suggest that GEI-FN1A in A. salmonicida FN1 can potentially spread ARGs among environmental bacteria.},
}

*Genomic Islands
Anti-Bacterial Agents/pharmacology
Animals
Gene Transfer, Horizontal
*Aeromonas salmonicida/genetics/drug effects/isolation & purification
*Drug Resistance, Multiple, Bacterial/genetics
Chickens
Whole Genome Sequencing
Genome, Bacterial
Feces/microbiology
Soil Microbiology
Genes, Bacterial
Bacterial Proteins/genetics
Microbial Sensitivity Tests

@article {pmid40553195,
year = {2025},
author = {Sonkar, V and Devtalla, H and Kumar, S},
title = {Pesticide-driven antimicrobial resistance in water bodies: insights on environmental concerns, health implications and mitigation strategies.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {7},
pages = {282},
pmid = {40553195},
issn = {1573-2983},
mesh = {*Pesticides/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Drug Resistance, Microbial/drug effects ; Humans ; India ; Agriculture ; Water Microbiology ; },
abstract = {Pesticide contamination in water bodies is an emerging driver of antimicrobial resistance (AMR), posing severe environmental and public health risks. Due to excessive agricultural use, pesticides routinely end up in water bodies due to leaching, improper disposal, and agricultural runoff. Pesticides act as selective pressures, promoting resistant microbial strains by providing evolutionary pressure for the strains to thrive. Pesticides facilitate the dissemination of resistance genes through several mechanisms; horizontal gene transfer, bio-film formation, and co-selection with heavy metals. Pathogens carrying antibiotic resistance genes, are emerging as a threat to global populations exposed to contaminated water, as they are increasingly more challenging to treat with traditional antibiotics. Moreover, these issues escalate due to the overlap in disposal of agricultural runoffs and untreated hospital waste into water bodies leading to co-selection pressure facilitating multi drug resistance. Current review examines the critical role of pesticides contamination in driving AMR in Indian aquatic ecosystems, a novel intersection threatening global health and deteriorating aquatic life. However, existing policies are insufficient, necessitating stricter regulations to control the problem. There also needs to be stronger laws in place to limit and monitor pollution in the water bodies. The increasing incidences of health issues linked to resistant strains in Indian population, need to be tackled more comprehensively. Mitigation requires stringent agricultural regulations, improved waste management, and interdisciplinary strategies to curb this growing threat.},
}

*Pesticides/toxicity/analysis
*Water Pollutants, Chemical/toxicity/analysis
*Drug Resistance, Microbial/drug effects
Humans
India
Agriculture
Water Microbiology

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40551445,
year = {2025},
author = {Deshamukhya, C and Das, BJ and Dhar, D and Bhattacharjee, A},
title = {Influence of AHL and Imipenem on blaNDM Conjugation and sRNA Rydb Expression in Escherichia coli.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70074},
doi = {10.1002/jobm.70074},
pmid = {40551445},
issn = {1521-4028},
abstract = {The rise of carbapenem resistance in Escherichia coli is mainly due to the rapid spread of carbapenemase-encoding genes through horizontal gene transfer, particularly via bacterial conjugation. Recent research has highlighted the role of a small RNA molecule known as RydB in bacterial conjugation, specifically through its interaction with the protein SdiA. This study investigated the effects of sub-inhibitory concentrations of imipenem and N-acyl homoserine lactones (AHLs) on the expression of rydB in E. coli strains that overexpress sdiA. Additionally, we examined how AHLs influence the bacterial conjugation of plasmids that contain carbapenem resistance genes. We selected a carbapenem-resistant isolate of E. coli harbouring the blaNDM gene and its corresponding plasmid-cured derivative, based on the overexpression of the sdiA gene in response to AHLs. Conjugation experiments were conducted, both without AHL treatment and with AHL treatments, to assess the transferability of the blaNDM plasmid. The transcriptional response of rydB gene was evaluated in the plasmid-cured derivative, the native type, the transconjugant, and E. coli J53. Our findings indicated that AHLs and imipenem inhibit the expression of the rydB gene. Interestingly, while RydB does not seem to impact bacterial conjugation when suppressed by these agents, the combination of AHLs enhances the conjugation of plasmid that carry the blaNDM gene. This study enhances our understanding of the regulatory roles that quorum sensing signal molecules, including C4 AHL and C12AHL, as well as imipenem, play in bacterial conjugation and sRNA expression.},
}

@article {pmid40548977,
year = {2025},
author = {Bhadra, S and Das, C and Bawali, S and Bhattacharya, A},
title = {Evolutionary analysis of the Leishmania major orthologues for the newly identified cyclic AMP response proteins.},
journal = {Archives of microbiology},
volume = {207},
number = {8},
pages = {184},
pmid = {40548977},
issn = {1432-072X},
mesh = {*Leishmania major/genetics/metabolism ; Phylogeny ; *Evolution, Molecular ; *Protozoan Proteins/genetics/metabolism/chemistry ; *Cyclic AMP/metabolism ; Gene Transfer, Horizontal ; },
abstract = {Cyclic AMP (cAMP) signalling is largely noncanonical in kinetoplastids. With virtual absence of canonical cAMP effectors including cyclic nucleotide sensitive protein kinase A regulatory subunits. Through a number of RNAi screens, a group of novel cAMP-responsive effectors were identified from Trypanosoma with 11 members, assigned as cAMP Response Proteins (CARPs, CARP1 to 11). Four of the CARPs were reported earlier, recently the remaining seven were identified. Except for CARP3 and CARP11, the orthologues for other CARPs can be identified from Leishmania. An intricate evolutionary analysis performed earlier indicated CARP1 and CARP4 from Leishmania major comprise features of horizontally transferred genes. Aiming for comprehensive understanding of the evolution of CARPs, the study further extends the evolutionary analysis to newly annotated CARP orthologues from L. major. The study reveals the phylogenetic relation among kinetoplastid CARP orthologues and functional divergence. A systemic codon adaptation profiling suggested horizontal transfer for some of the CARPs. Alongside, structural analysis highlighted heterogeneity among the T. brucei and L. major orthologues.},
}

*Leishmania major/genetics/metabolism
Phylogeny
*Evolution, Molecular
*Protozoan Proteins/genetics/metabolism/chemistry
*Cyclic AMP/metabolism
Gene Transfer, Horizontal

@article {pmid40548945,
year = {2025},
author = {},
title = {Correction to 'Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome'.},
journal = {Nucleic acids research},
volume = {53},
number = {12},
pages = {},
doi = {10.1093/nar/gkaf631},
pmid = {40548945},
issn = {1362-4962},
}

@article {pmid40548717,
year = {2025},
author = {Xu, C and Li, X and Zhang, Y and Li, Y and Li, Y and Zhang, R and Dong, N},
title = {Interorder horizontal gene transfer of tet(X3) between Acinetobacter spp. and Enterobacteriaceae.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0194524},
doi = {10.1128/aac.01945-24},
pmid = {40548717},
issn = {1098-6596},
}

@article {pmid40544776,
year = {2025},
author = {Huang, W and Wang, F and Su, Y and Huang, H and Luo, J},
title = {Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139007},
doi = {10.1016/j.jhazmat.2025.139007},
pmid = {40544776},
issn = {1873-3336},
abstract = {Bacteriophages (phages) are vital components in biological wastewater ecosystems, whose concentrations are far exceeding those bacteria. Despite their importance, they are often overlooked and regarded as the "dark matter" in biological treatment processes. Phages play a pivotal role in shaping the dynamic evolution of host microbial communities within wastewater treatment plants (WWTPs), driving their functional evolution through interactions with host microorganisms. Phages are crucial in driving microbial ecological dynamics and regulating metabolic functions. At the macroscopic scale, the organic matters released through viral shunting demonstrate enhanced bioavailability and facilitated organic element cycling based on viral shuttle-mediated bio-pump. Additionally, at the micro-scale, gene transfer mediated by phages can assist functional microorganisms in enhancing metabolic efficiency and adapting to environmental stress. However, this process also introduces environmental risks, particularly the dissemination of antibiotic resistance genes through horizontal gene transfer and plasmids. Phages offer distinct advantages over conventional chemical and physical methods, including superior efficiency and environmental sustainability. Nonetheless, the development of phage-based biocontrol strategies is constrained by phage specificity and the complexity of biological treatment systems. Recent advances in artificial intelligence and genetic technologies provide promising avenues for optimizing phage applications. Further research into phage ecology is essential to lay a theoretical foundation for enhancing operational stability, treatment efficiency, and targeted biocontrol strategies.},
}

@article {pmid40544537,
year = {2025},
author = {Sinha, S and Upadhyay, LSB},
title = {Understanding antimicrobial resistance (AMR) mechanisms and advancements in AMR diagnostics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116949},
doi = {10.1016/j.diagmicrobio.2025.116949},
pmid = {40544537},
issn = {1879-0070},
abstract = {The overuse and abuse of antibiotics, which results in the evolution of resistant microorganisms, is the primary cause of the global health catastrophe known as antimicrobial resistance (AMR). The enzymatic breakdown of antibiotics, target site modification, efflux pump overexpression, and the formation of biofilm are some of the mechanisms responsible for acquiring antimicrobial resistance (AMR). These mechanisms enable bacteria to evade or neutralize the effects of antimicrobial agents, complicating treatment options and increasing mortality rates. The rapid dissemination of resistance genes via horizontal gene transfer further exacerbates the problem, necessitating urgent intervention. Advanced AMR diagnostics are transforming the fight against antimicrobial resistance. Biosensors enable rapid, point-of-care detection; Cluster regularly interspaced short palindromic repeat (CRISPR) technologies offer precise identification of resistance genes; and mass spectrometry provides fast, accurate profiling. Automated systems streamline workflows and boost throughput, while flow cytometry delivers real-time, single-cell analysis of phenotypic resistance. Together, these innovations accelerate detection and support targeted antimicrobial stewardship, essential for combating the global AMR threat. This review covers the mechanisms underlying antimicrobial resistance (AMR) and recent advancements in AMR diagnostic technologies.},
}

@article {pmid40542629,
year = {2025},
author = {Aristova, EO and Volkhin, IA and Denisova, AA and Nikitin, PA and Petrukhin, ER},
title = {[De Novo Gene Birth].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {1},
pages = {22-31},
pmid = {40542629},
issn = {0026-8984},
mesh = {*Evolution, Molecular ; Humans ; *Gene Duplication ; *Gene Transfer, Horizontal ; Animals ; },
abstract = {According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately.},
}

*Evolution, Molecular
Humans
*Gene Duplication
*Gene Transfer, Horizontal
Animals

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
mesh = {*Methane/metabolism ; Anaerobiosis ; Phylogeny ; *Evolution, Molecular ; Genome, Archaeal ; *Archaea/genetics/metabolism ; Metagenomics ; Gene Transfer, Horizontal ; },
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}

*Methane/metabolism
Anaerobiosis
Phylogeny
*Evolution, Molecular
Genome, Archaeal
*Archaea/genetics/metabolism
Metagenomics
Gene Transfer, Horizontal

@article {pmid40379877,
year = {2025},
author = {Gonzalez-Duran, E and Kroop, X and Schadach, A and Bock, R},
title = {Suppression of plastid-to-nucleus gene transfer by DNA double-strand break repair.},
journal = {Nature plants},
volume = {11},
number = {6},
pages = {1154-1164},
pmid = {40379877},
issn = {2055-0278},
mesh = {*DNA Breaks, Double-Stranded ; *Plastids/genetics ; *DNA Repair ; *Nicotiana/genetics ; *Cell Nucleus/genetics ; *Gene Transfer, Horizontal ; Symbiosis/genetics ; },
abstract = {Plant nuclear genomes contain thousands of genes of mitochondrial and plastid origin as the result of endosymbiotic gene transfer (EGT). EGT is a still-ongoing process, but the molecular mechanisms determining its frequency remain largely unknown. Here we demonstrate that nuclear double-strand break (DSB) repair is a strong suppressor of EGT. Through large-scale genetic screens in tobacco plants, we found that EGT from plastids to the nucleus occurs more frequently in somatic cells when individual DSB repair pathways are inactive. This effect is explained by the expected increase in the number and residence time of DSBs available as integration sites for organellar DNA. We also show that impaired DSB repair causes EGT to increase 5- to 20-fold in the male gametophyte. Together, our data (1) uncover DSB levels as a key determinant of EGT frequency, (2) reveal the strong mutagenic potential of organellar DNA and (3) suggest that changes in DNA repair capacity can impact EGT across evolutionary timescales.},
}

*DNA Breaks, Double-Stranded
*Plastids/genetics
*DNA Repair
*Nicotiana/genetics
*Cell Nucleus/genetics
*Gene Transfer, Horizontal
Symbiosis/genetics

@article {pmid40544427,
year = {2025},
author = {Lamberte, LE and Darby, EM and Kiu, R and Moran, RA and Acuna-Gonzalez, A and Sim, K and Shaw, AG and Kroll, JS and Belteki, G and Clarke, P and Felgate, H and Webber, MA and Rowe, W and Hall, LJ and Van Schaik, W},
title = {Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519700},
doi = {10.1080/19490976.2025.2519700},
pmid = {40544427},
issn = {1949-0984},
abstract = {Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n = 140) from 44 stool samples of 22 preterm infants from four hospitals in England. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 78/85 (91.7%) strains having Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were prevalent in the genomes. There was a strong association between the presence of mecA and phenotypic resistance to oxacillin, and the aacA-aphD gene and phenotypic resistance to gentamicin. While mecA was near-ubiquitous, none of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001 in multiple chromosomal and plasmid contexts. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonize the gut of preterm infants, and widespread horizontal gene transfer and recombination among this frequent colonizer of the preterm infant gut.},
}

@article {pmid40544087,
year = {2025},
author = {Bhattacharya, D and Van Etten, J and Panayotakis, G and McDermott, T and Stephens, TG},
title = {Gene transfer drives community cooperation in geothermal habitats.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.06.004},
pmid = {40544087},
issn = {1878-4380},
abstract = {Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.},
}

@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}

@article {pmid40541684,
year = {2025},
author = {Sies, AN and Nowlan, JP and Schnell, LJ and Lumsden, JS and Russell, S and Cameron, ADS},
title = {Discovery and assembly of plasmids in the fish pathogen Tenacibaculum.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102753},
doi = {10.1016/j.plasmid.2025.102753},
pmid = {40541684},
issn = {1095-9890},
abstract = {Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum, but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, and plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, highlighting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host species.},
}

@article {pmid40539803,
year = {2025},
author = {Mapiki, P and Laiser, E and Mufungwe, J and Shawa, M and Siamujompa, M and Johnson, T and Namukonde, N and Mwaanga, P and Hang'ombe, BM},
title = {Bacteriological quality of fresh and processed black soldier fly Hermetia illucens larvae reared on chicken manure in Kitwe, Zambia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057024},
doi = {10.1128/spectrum.00570-24},
pmid = {40539803},
issn = {2165-0497},
abstract = {UNLABELLED: Black soldier fly larvae (BSFL) have high nutrient content and are rapidly becoming an alternative protein source for animal feed. However, microbial contamination is a potential risk due to the environment in which they are reared. This study assessed the bacteriological quality of fresh and processed BSFL by comparing the processed BSFL using two traditional methods (oven-dried and sun-dried), on their effectiveness at reducing the bacterial load and further elucidated bacterial composition. PCR was used to identify extended-spectrum β-lactamase (ESBL) and mecA genes in Escherichia coli and Staphylococcus spp., respectively. A total of 51 fresh BSFL samples were collected from a commercial poultry farm in Kitwe, Zambia. The results showed various bacterial genera, with a higher diversity among gram-positive isolates. The comparison of the effectiveness of two traditional processing methods for BSFL, sun-drying and oven-drying, showed that both methods significantly reduced the bacterial load, with oven-drying causing a larger reduction. While various genera were identified, we focused on E. coli and Staphylococcus spp. This is because some E. coli harbor ESBLs that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. Similarly, the genus Staphylococcus was selected since some strains are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. Molecular characterization of the isolated strains revealed blaCTX-M and blaTEM genes among E. coli, but the mecA gene was not detected among Staphylococcus. This study revealed that BSFL harbor bacteria of zoonotic significance, emphasizing the need for good processing methods to eliminate potential risks.

IMPORTANCE: Isolation and identification of Escherichia coli and Staphylococcus spp. in processed black soldier fly larvae (BSFL) samples meant for animal feed indicate insufficient processing methods and pose a public health risk. For instance, some E. coli harbor extended-spectrum β-lactamases (ESBLs) that hydrolyze β-lactam antibiotics like cephalosporins and penicillin, leading to resistance. In addition, some E. coli commensals can transfer antimicrobial resistance genes to pathogenic bacteria through horizontal gene transfer using various mobile genetic elements, leading to resistance. Similarly, for Staphylococcus spp., some strains of the genus Staphylococcus are potentially pathogenic and contain the mecA gene that encodes resistance to β-lactam antibiotics. In this study, we used PCR to screen E. coli isolates for the two commonly reported ESBL genes in Zambia, blaCTX-M and blaTEM, and Sanger sequencing was used to reveal blaCTX-M gene alleles. Our results highlight the importance of using adequate processing methods for BSFL to eliminate potential health risks to animal feed.},
}

@article {pmid40535478,
year = {2025},
author = {Zhang, Y and Su, Z and Qiu, X and Liu, H and Wen, D and Chen, L},
title = {Distinct ARG profiles associated with class 1 integrons in municipal and industrial wastewater treatment plants.},
journal = {Environmental science and ecotechnology},
volume = {26},
number = {},
pages = {100586},
pmid = {40535478},
issn = {2666-4984},
abstract = {Class 1 integrons facilitate horizontal gene transfer, significantly influencing antibiotic resistance gene (ARG) dissemination within microbial communities. Wastewater treatment plants (WWTPs) are critical reservoirs of ARGs and integrons, yet the integron-mediated dynamics of ARG transfer across different WWTP types remain poorly understood. Here we show distinct ARG profiles associated with class 1 integrons in municipal and industrial WWTPs using a novel approach combining nested-like high-throughput qPCR and PacBio sequencing. Although industrial WWTPs contained higher absolute integron abundances, their relative ARG content was lower (1.27 × 10[7]-9.59 × 10[7] copies/ng integron) compared to municipal WWTPs (3.72 × 10[7]-1.98 × 10[8] copies/ng integron). Of the 132,084 coding sequences detected from integrons, 56.8 % encoded antibiotic resistance, with industrial plants showing lower ARG proportions, reduced ARG array diversity, and greater incorporation of non-ARG sequences. These findings suggest industrial WWTP integrons integrate a broader array of exogenous genes, reflecting adaptation to complex wastewater compositions. This work enhances our understanding of integron-driven ARG dynamics in wastewater and offers a robust strategy for environmental integron analysis.},
}

@article {pmid40533044,
year = {2025},
author = {Tian, Y and Li, J and Meng, J and Li, J},
title = {Deciphering antibiotic resistance gene transfer in activated sludge systems for piggery wastewater: behaviors, hosts and drivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122166},
doi = {10.1016/j.envres.2025.122166},
pmid = {40533044},
issn = {1096-0953},
abstract = {Understanding the transfer and driving mechanisms of antibiotic resistance genes (ARGs) in activated sludge is essential for mitigating environmental risks, particularly during real wastewater treatment where these processes remain poorly characterized. This study investigated the prevalence of ARGs in a sequencing batch reactor (SBR) - up-flow microaerobic sludge reactor (UMSR) system treating high-risk piggery wastewater and revealed critical pathways for resistance propagation. Ten prevalent ARG subtypes, categorized into three types, were selected as target genes, exhibiting a total relative abundance of 0.52 copies per 16S rRNA in raw wastewater. The SBR-UMSR system reduced total ARGs by 0.04 log in wastewater, with half of subtypes decreasing 0.14-1.30 log, despite 0.23-0.58 log enrichment in sludge. By integrating correlation analysis with partial least-squares path modeling, this study identified Burkholderiaceae as the primary potential host of ARGs and pinpointed other high-risk hosts. It further revealed two crucial mechanisms: (1) conjugation-mediated horizontal gene transfer dominated ARG propagation, and (2) bacterial community succession served as the main driving force for ARG transfer. This study advances mechanistic understanding of ARG transmission in real wastewater systems, providing critical insights for optimizing sludge management to mitigate antibiotic resistance risks.},
}

@article {pmid40530826,
year = {2025},
author = {Carolak, E and Czajkowska, J and Stypułkowska, A and Waszczuk, W and Dutkiewicz, A and Grzymajlo, K},
title = {Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2519696},
doi = {10.1080/19490976.2025.2519696},
pmid = {40530826},
issn = {1949-0984},
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genetic Engineering ; Animals ; *Microorganisms, Genetically-Modified/genetics ; *Bacteria/genetics ; },
abstract = {Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health through pathogen prevention and immune regulation. Although probiotics have emerged as promising therapeutic agents, their efficacy is limited by strain-dependent variations, survival challenges in the gastrointestinal tract, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems and their combinations with complementary technologies, such as Cre-lox and RecE/T, have enabled the precise modification of probiotic strains to enhance their therapeutic potential. These enhanced probiotics demonstrate improved functionality through multiple mechanisms, including increased adhesion via the expression of specific proteins (InlA, FnBPA, and LAP), targeted antimicrobial activity through engineered sensing systems (Lactococcus lactis detecting Vibrio cholerae CAI-1), and enhanced immunomodulation through cytokine production. Results have demonstrated the potential of genetically modified probiotics in preventing and treating gastrointestinal infections through mechanisms that include competitive exclusion, bacteriocin production, intestinal barrier reinforcement, and immune modulation. However, challenges remain in ensuring genetic stability and preventing horizontal gene transfer. Future research should focus on optimizing probiotic strains for targeted applications while addressing biosafety concerns. By understanding the complex interplay between probiotics, pathogens, and host immunity, innovative strategies can be developed to harness the full therapeutic potential of probiotic interventions in maintaining gut health.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome
Genetic Engineering
Animals
*Microorganisms, Genetically-Modified/genetics
*Bacteria/genetics

@article {pmid40529306,
year = {2025},
author = {Xu, J and Zhang, M and Yan, Y and Li, Z and Lu, X},
title = {Intestinal flora metabolites indole-3-butyric acid and disodium succinate promote IncI2 mcr-1-carrying plasmid transfer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564810},
pmid = {40529306},
issn = {2235-2988},
mesh = {*Plasmids/genetics ; Reactive Oxygen Species/metabolism ; *Indoles/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal/drug effects ; Conjugation, Genetic/drug effects ; *Succinic Acid/metabolism ; Cell Membrane Permeability/drug effects ; Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: Plasmid-driven horizontal transfer of resistance genes in bacterial communities is a major factor in the spread of resistance worldwide. The gut microbiome, teeming with billions of microorganisms, serves as a reservoir for resistance genes. The metabolites of gut microorganisms strongly influence the physiology of their microbial community, but the role of the metabolites in the transfer of resistance genes remains unclear.

METHODS: A dual-fluorescence conjugation model was established. We assessed the effects of different concentrations of indole-3-butyric acid (IBA) and disodium succinate (DS) on plasmid transfer using conjugation assays. The growth of bacteria (donors, recipients, and transconjugants), the reactive oxygen species (ROS) levels and membrane permeability were measured under IBA and DS exposure. The plasmid copy number, and transcriptional levels of conjugation-related genes (including the related genes of the regulation of ROS production, the SOS response, cell membrane permeability, pilus generation, ATP synthesis, and the type IV secretion system (T4SS)) were evaluated by qPCR.

RESULTS: In this study, we demonstrated that IBA and DS at low concentrations, which can also be ingested through diet, enhance the interspecies transfer ratio of IncI2 mcr-1-carrying plasmid in Escherichia coli. At 20 mg/L, the transfer ratios in the presence of IBA or DS increased by 2.5- and 2.7-fold compared to that of the control, respectively. Exposure to this concentration of IBA or DS increased the production of reactive oxygen species (ROS), the SOS response, cell membrane permeability, and plasmid copy number. The transcription of genes of the related pathways and of pilus, ATP, and the T4SS was upregulated.

DISCUSSION: Our findings revealed that low-dose gut microbiota metabolites-particularly those with dietary origins-promote plasmid-mediated resistance gene dissemination through multifaceted mechanisms involving oxidative stress, SOS activation, and conjugation machinery enhancement. This highlights potential public health risks associated with microbiota metabolites, especially those utilized in food production.},
}

*Plasmids/genetics
Reactive Oxygen Species/metabolism
*Indoles/metabolism/pharmacology
*Gastrointestinal Microbiome/drug effects
Escherichia coli/genetics/drug effects
*Gene Transfer, Horizontal/drug effects
Conjugation, Genetic/drug effects
*Succinic Acid/metabolism
Cell Membrane Permeability/drug effects
Drug Resistance, Bacterial/genetics

@article {pmid40528005,
year = {2025},
author = {Baker, BA and McCarthy, CGP and López-García, P and Leroy, RB and Susko, E and Roger, AJ and Eme, L and Moreira, D},
title = {Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40528005},
issn = {2058-5276},
support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101141745//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 812811//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.},
}

@article {pmid40527192,
year = {2025},
author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG},
title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109611},
doi = {10.1016/j.envint.2025.109611},
pmid = {40527192},
issn = {1873-6750},
abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.},
}

@article {pmid40520376,
year = {2025},
author = {Cao, H and Shen, Y and Ma, K and Zheng, D and Xu, Y and Qiao, X},
title = {Molecular characterization of clinical non-typhoidal Salmonella isolates shows high antimicrobial resistance burden in Jiangsu, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1587421},
pmid = {40520376},
issn = {1664-302X},
abstract = {Non-typhoidal Salmonella (NTS) poses a significant global health burden due to its association with gastroenteritis and rising antimicrobial resistance (AMR). This study conducted a genomic analysis of 62 Salmonella isolates from outpatient cases in Jiangsu, China, to monitor the epidemiological characteristics of NTS, including genetic diversity, AMR profiles, and resistance transmission mechanisms 18 serovars and 21 sequence types (STs) were identified by whole genome sequencing, with S. enteritidis (27.42%) and S. typhimurium (19.35%) predominating. 61 resistance genes from ten different antimicrobial categories were found by genotypic AMR screening. 90.32% of isolates had β-lactam resistance genes, indicating a high frequency of extended-spectrum β-lactamases (ESBL). Serovar-dependent resistance patterns were highlighted by the most varied AMR profile (40/61 genes) found in S. typhimurium. The co-occurrence of genes for aminoglycoside resistance, sul2, and blaTEM indicated clustering driven by mobile genetic elements. A plasmid in a S. Stanley isolate harbored 12 AMR genes, which showed structural changes suggestive of horizontal gene transfer and active recombination. These findings underscore the role of plasmids in disseminating MDR and the urgent need for enhanced antimicrobial stewardship, food safety protocols, and One Health interventions to mitigate the spread of resistant Salmonella clones.},
}

@article {pmid40517254,
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 = {Mobile DNA},
volume = {16},
number = {1},
pages = {25},
pmid = {40517254},
issn = {1759-8753},
support = {R35GM128932/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 transfer of transposable elements (HTT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HTT since they often integrate into host genomes and have been implicated in widespread HTT 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 in the family eupolintoviridae as well as giant dsDNA viruses. By querying a previously annotated set of eupolintoviral 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 shows 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 HTT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.},
}

@article {pmid40069292,
year = {2025},
author = {Lang, AS and Buchan, A and Burrus, V},
title = {Interactions and evolutionary relationships among bacterial mobile genetic elements.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {7},
pages = {423-438},
pmid = {40069292},
issn = {1740-1534},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Bacteria/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {Mobile genetic elements (MGEs) have profound influence on the ecology and evolution of organisms, including bacteria. During the past two decades, a great number of new types of MGEs have been discovered that now seem to be prevalent in diverse bacterial lineages. With the rapid discovery of new categories of MGEs comes an array of new acronyms that present a challenge to grasp. Moreover, it is now clear that there are complex evolutionary connections and molecular interactions among MGEs, and that these entities are not discrete, independent genetic elements acting in isolation. Different types of MGEs share and exchange genes, and coresident MGEs interact with each other within cells, in both cooperative and antagonistic ways. This all greatly affects the end results that are felt by the host organism. In this Review, we strive to clarify emerging bacterial MGE terms and elements while also presenting a comprehensive overview of the current knowledge landscape regarding MGEs in bacteria, their evolutionary relationships and interactions with their host and with one another.},
}

*Interspersed Repetitive Sequences/genetics
*Bacteria/genetics
*Evolution, Molecular
Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid40516885,
year = {2025},
author = {Cunha da Silva, G and Rossi, CC},
title = {Defense systems and mobile elements in Staphylococcus haemolyticus: a genomic view of resistance dissemination.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107808},
doi = {10.1016/j.micpath.2025.107808},
pmid = {40516885},
issn = {1096-1208},
abstract = {Staphylococcus haemolyticus is a multidrug-resistant opportunistic pathogen and a major reservoir of antimicrobial resistance (AMR) genes within the Staphylococcaceae family. Its high genomic plasticity, frequent association with mobile genetic elements (MGEs), and prevalence in clinical settings underscore its relevance as both a threat and a conduit for resistance dissemination. In this study, we performed a comprehensive pan-genomic analysis of the S. haemolyticus defensome - including restriction-modification (RM), abortive infection (Abi), and CRISPR-Cas systems - across 692 high-quality genomes. Our results reveal a highly diverse and modular repertoire of immune systems, often organized in physical clusters and frequently associated with MGEs. We identified evidence of antagonistic interactions, with both defense and anti-defense elements encoded on plasmids and prophages. CRISPR spacer analysis showed a predominant targeting of phages, and genomes encoding CRISPR-Cas systems exhibited a lower abundance of MGEs and AMR genes, suggesting a trade-off between defense and gene acquisition. RNA-seq data from one reference strain indicate that only a fraction of the defensome is actively transcribed under standard conditions, hinting at environment-responsive regulation. Together, these findings provide new insights into the genomic strategies sustaining the persistence and adaptability of S. haemolyticus in clinical environments. The interplay between its immune systems and mobilome likely contributes not only to its evolutionary trajectory, but also to its role in the horizontal transfer of resistance determinants among pathogenic staphylococci. A deeper understanding of this immune-mobilome interface may help inform future strategies to limit the spread of resistance.},
}