@article {pmid41407993,
year = {2025},
author = {Cota Ortega, LE and Quiroz-Guzmán, E and Balcázar, JL},
title = {Ecological Drivers of Plasmid-Mediated Antimicrobial Resistance in Aquaculture.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02684-0},
pmid = {41407993},
issn = {1432-184X},
abstract = {Antimicrobial resistance (AMR) is a growing global challenge that compromises the effectiveness of disease control and increases risks for both human and animal health. Aquaculture systems are particularly vulnerable, as extensive and often inappropriate antimicrobial use has driven the emergence and persistence of multidrug-resistant bacteria. This mini-review summarizes the ecological and genetic mechanisms underlying AMR in aquaculture, with emphasis on plasmid-mediated resistance and its role in horizontal gene transfer. It also addresses the broader environmental and public health implications of these processes and calls for sustainable management, enhanced surveillance, and coordinated international policies to curb resistance dissemination and safeguard global food security.},
}

@article {pmid41407853,
year = {2025},
author = {Wolff, R and Garud, NR},
title = {Gene-specific selective sweeps are pervasive across human gut microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41407853},
issn = {1476-4687},
abstract = {The human gut microbiome is composed of a highly diverse consortia of species that are continually evolving within and across hosts[1,2]. The ability to identify adaptations common to many human gut microbiomes would show not only shared selection pressures across hosts but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, the extent to which adaptations have spread across human gut microbiomes is relatively unknown. Here we develop a new selection scan statistic named the integrated linkage disequilibrium score (iLDS) that can detect sweeps of adaptive alleles spreading across host microbiomes by migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with a beneficial variant. Application of the statistic to around 30 of the most prevalent commensal gut species from 24 human populations around the world showed more than 300 selective sweeps across species. We find an enrichment for selective sweeps at loci involved in carbohydrate metabolism, indicative of adaptation to host diet, and we find that the targets of selection differ significantly between industrialized populations and non-industrialized populations. One of these sweeps is at a locus known to be involved in the metabolism of maltodextrin-a synthetic starch that has recently become a widespread component of industrialized diets. In summary, our results indicate that recombination between strains fuels pervasive adaptive evolution among human gut commensal bacteria, and strongly implicate host diet and lifestyle as critical selection pressures.},
}

@article {pmid41407557,
year = {2025},
author = {Tyagi, E and Sachan, A and Bhuyan, R and Kumari, P and Prakash, A},
title = {Next-Gen Biofilm Control: Gene Editing and Computational Approaches.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {12},
pages = {e70122},
doi = {10.1111/apm.70122},
pmid = {41407557},
issn = {1600-0463},
mesh = {*Biofilms/drug effects/growth & development ; *Gene Editing/methods ; Humans ; *Computational Biology/methods ; CRISPR-Cas Systems ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Phage Therapy ; Bacteriophages ; },
abstract = {Biofilms are microbial communities enclosed in an extracellular polymeric substance (EPS), significantly contributing to antimicrobial resistance (AMR) in medical, industrial, and environmental settings. Their matrix enhances microbial survival, inhibits antibiotic penetration, and facilitates horizontal gene transfer, worsening the AMR crisis. Conventional antimicrobial treatments often fail against biofilms, necessitating novel therapeutic strategies. Emerging biofilm-targeted interventions, such as nanotechnology-based antimicrobials, bacteriophage therapy, and CRISPR-Cas9 gene editing, offer promising solutions. Nanoparticles improve drug delivery, bacteriophages selectively lyse resistant bacterial populations, and CRISPR-Cas9 disrupts AMR-related genes and biofilm virulence factors. Additionally, AI and ML are advancing biofilm prediction models and antimicrobial optimization, paving the way for precision-targeted interventions. This review explores biofilm biology and next-generation biofilm control strategies, with a focus on AI-driven bioinformatics. Future research should focus on clinical translation, regulatory standardization, and scalable implementation in healthcare and industrial settings to combat biofilm-associated AMR.},
}

*Biofilms/drug effects/growth & development
*Gene Editing/methods
Humans
*Computational Biology/methods
CRISPR-Cas Systems
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial
Phage Therapy
Bacteriophages

@article {pmid41406009,
year = {2025},
author = {Allen, F and McInnes, RS and van Schaik, W and Moran, RA},
title = {IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001598},
pmid = {41406009},
issn = {2057-5858},
mesh = {*Enterococcus faecium/genetics/drug effects/isolation & purification ; *Plasmids/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; *Evolution, Molecular ; *DNA Transposable Elements ; Anti-Bacterial Agents/pharmacology ; Humans ; Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {pRUM-like plasmids are commonly found in multidrug-resistant Enterococcus faecium, but the evolution of these plasmids has not been characterised in detail. When we analysed the genome sequences of two clinical E. faecium strains isolated in Birmingham, UK, we found two pRUM-like plasmids, pHHEf1 and pHHEf2. They were ~25 kb in size and shared the same 10 kb backbone but contained starkly different accessory regions that were bounded by and interspersed with the IS26 family insertion sequence IS1216. pHHEf1 contained a complete set of vancomycin resistance genes, while pHHEf2 contained aminoglycoside and erythromycin resistance genes along with an integrated small plasmid, pCOLA. It appeared that IS1216 had driven the diversification of these accessory regions. We sought to characterise the role of IS1216 in the broader evolution of pRUM-like plasmids by performing comparative analyses on 152 complete plasmid sequences from five continents. Extensive IS1216-mediated variation included backbone deletions, acquisition and loss of ten different antibiotic resistance genes, and the formation of cointegrates with plasmids of at least ten different replicon types. Cointegration events have introduced accessory segments with diverse functions, including horizontal transfer determinants and genes for bacteriocin T8. The derivations of these acquired segments highlight the impact of IS1216 in driving gene exchange between Enterococcus and Staphylococcus species. We traced the emergence of the pRUM-like lineage to a putative ancestor found in a vancomycin-sensitive ST17 E. faecium isolated in 1997. The ancestral plasmid, pCANE, includes the entire pRUM backbone with an additional 44.9 kb in place of the pRUM accessory region. The 44.9 kb segment includes putative conjugation determinants, suggesting that the emergence of the pRUM-like lineage coincided with a loss of transfer functions. We propose an IS1216-driven model for the evolution of pRUM-like plasmids, which appear to have arisen in E. faecium ST17 and contributed to the international success of CC17 as an opportunistic pathogen.},
}

*Enterococcus faecium/genetics/drug effects/isolation & purification
*Plasmids/genetics
*Drug Resistance, Multiple, Bacterial/genetics
*Evolution, Molecular
*DNA Transposable Elements
Anti-Bacterial Agents/pharmacology
Humans
Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid41405666,
year = {2025},
author = {Wenbin, T and Feng, D and Jing, L},
title = {The interplay between insect gut microbiota and host immunity in the development and dissemination of antibiotic resistance.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41405666},
issn = {1874-9356},
support = {25DF0314//China Higher Education Society Higher Education Science Research Planning Project/ ; },
abstract = {The escalating crisis of antibiotic resistance presents a formidable challenge to global public health and food security. Insects are increasingly recognized as significant reservoirs and vectors for antibiotic resistance genes (ARGs) which inhabit diverse ecosystems. This review explores how the insect gut microbiota contributes to the development and spread of antibiotic resistance, focusing on the mediating role of the host immune system. We outline the structural and functional dynamics of the insect gut microbiome and elaborate on direct mechanisms through which microbiota contribute to resistance, including ARG carriage, enzymatic inactivation of antibiotics, and modulation of host detoxification pathways. Special emphasis is placed on the bidirectional crosstalk between gut microbes and the host immune system: we discuss how immune effectors, particularly antimicrobial peptides (AMPs), exert selective pressures that may enrich resistant taxa, and how microbial metabolites reciprocally regulate immune activity. Key immune signaling pathways-Toll, Immune Deficiency(Imd), and Janus kinase-signal transducer and activator of transcription (JAK-STAT)-are explored for their roles in maintaining microbial homeostasis and modulating resistance phenotypes. We also highlight cutting-edge experimental approaches, including gnotobiotic models and multi-omics technologies, that are essential for elucidating causal relationships. We conclude by highlighting outstanding questions and outlining future research priorities that integrate microbiology, immunology, and computational biology. This review aims to establish a holistic framework for understanding the insect gut as a hotspot for antibiotic resistance evolution and to inspire innovative microbiome-based interventions.},
}

@article {pmid41405596,
year = {2025},
author = {Ste-Croix, DT and Vieira, P and Mimee, B},
title = {Comparative Genomics Analysis of Three Species of Root-Lesion Nematodes, Pratylenchus spp., Suggests an Intricate Evolutionary Origin of Effector Genes.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-05-25-0170-R},
pmid = {41405596},
issn = {0031-949X},
abstract = {Root-lesion nematodes of the genus Pratylenchus, which includes over 100 species, are among the most damaging plant-parasitic nematodes, affecting a wide range of crops globally. Their migration in and out of roots causes mechanical damage and necrosis, leading to significant yield losses worldwide. In this study, we generated high-quality genome assemblies for three Pratylenchus species, P. penetrans, P. crenatus, and P. neglectus, isolated from potato fields across Canada. Using in silico analyses, we performed comprehensive genome annotation, comparative gene family analysis, and life-stage-specific gene expression profiling to investigate candidate genes likely involved in host interactions. Horizontal gene transfer (HGT) events were also predicted using the Alienness vs Predictor tool, based on protein homology comparisons and phylogeny between metazoan and non-metazoan taxa. These analyses revealed unique genomic structures, expansions of effector genes, and putative HGT events that may contribute to parasite adaptability. Notably, in P. crenatus and P. penetrans, the diversification and expansion of effector repertoires, combined with species-specific HGT candidates, could suggests an evolutionary adaptations to support a broad host range. In contrast, the more compact effectorome of P. neglectus points to a parasitic strategy based on broad acting effectors. While these findings provide an initial genome-scale view of the molecular toolkit used by these nematodes, they are based on computational predictions and await functional validation. This study lays a foundation for future research into the molecular mechanisms underlying parasitism, host adaptation, and nematode evolution.},
}

@article {pmid41405436,
year = {2025},
author = {Lin, M and Ali, RAA and Khan, MN and Sultan, M and Bilal, H and Ahmad, S and Khurshid, M and Shafiq, M},
title = {Genomic Insights into mcr-Mediated Colistin Resistance in Escherichia coli, Aeromonas veronii, and Enterobacter kobei from Wastewater.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf307},
pmid = {41405436},
issn = {1365-2672},
abstract = {AIMS: This study investigated colistin resistance in Gram-negative bacteria isolated from wastewater. The research focuses on understanding the genetic mechanisms of mcr-mediated resistance and the role of wastewater as a reservoir for colistin-resistant bacterial pathogens.

METHODS AND RESULTS: The study utilized 16 sewage effluent samples collected from four discharge points (three hospitals and one municipal wastewater treatment plant), during May 2024. Bacterial isolates were obtained using the membrane filtration method, resulting in the recovery of 50 Gram-negative isolates, including Enterobacteriaceae and Aeromonas species. Identification was conducted using MALDI-TOF mass spectrometry. Whole-genome sequencing (WGS) and comprehensive bioinformatics analysis were performed to characterize resistance genes and phylogenetic relationships. Colistin resistance was found in E. coli (mcr-1), Aeromonas veronii (mcr-3), and Enterobacter kobei (mcr-9). E. coli was the predominant species, accounting for 50% of the isolates. WGS revealed predominant resistance profiles across isolates, with E. coli harboring 95 resistance genes, E. kobei 21, and A. veronii. 14. Genomic analysis identified mobile genetic elements (MGEs) like ISCR1 and tnpA, suggesting the potential for horizontal gene transfer. Comparative genomic analysis identified the genetic context of mcr genes, with the mcr-1 gene found on a plasmid in E. coli, mcr-3 on a conjugative plasmid in A. veronii, and mcr-9 on a plasmid in E. kobei.

CONCLUSIONS: These findings highlight the role of wastewater in the spread of colistin-resistant bacteria. The presence of mcr genes on mobile elements underscores the need for robust surveillance strategies to monitor the dissemination of these resistance traits in the environment.},
}

@article {pmid41404872,
year = {2025},
author = {Hariharan, J and Andam, CP and Buckley, DH},
title = {Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution in Streptomyces.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0295825},
doi = {10.1128/spectrum.02958-25},
pmid = {41404872},
issn = {2165-0497},
abstract = {UNLABELLED: The role of horizontal gene transfer (HGT) in shaping bacterial genomes is well recognized, but constraints on gene exchange and the degree to which these constraints shape genome evolution remain poorly described. In this study, we sought to determine whether geographic and phylogenetic distance constrains HGT within and between bacterial species. To address this question, we isolated strains (n = 17) of two closely related bacterial species, Streptomyces griseus and Streptomyces pratensis from two ecologically similar sites. We identified homologous recombination events within the core genomes of these species (557 recent and 457 ancient) and determined that patterns of recombination were constrained primarily by phylogeny rather than geography. Notably, shell accessory genes were over three times more likely to be shared between the same species than with non-related geographical neighbors. The richness of secondary metabolite gene clusters is highly variable with an average of 35-55 clusters per genome, depending on clade membership. The majority of secondary metabolite gene clusters (60%) are found in all strains, indicating that they were present in the most recent common ancestor of S. griseus and pratensis. We conclude that most HGT in the core and accessory genome is phylogenetically constrained, while HGT of shell genes is more likely influenced by geography. This outcome indicates that the predominant mechanisms of HGT favor high phylogenetic relatedness, and that rapid gene acquisition and loss in the accessory genome could aid with adaptation to contemporary environmental conditions.

IMPORTANCE: Horizontal gene transfer (HGT) is a vital ecological and evolutionary force in microbiology, but we still lack a precise understanding of how precisely HGT acts on the gene pool of a species or genus. While HGT can complicate phylogenetic analyses and assumptions of homology, its role in adaptation and acquiring secondary metabolites should not be overlooked. Microbial ecologists agree that the pangenome is a shifting collection of genes that can be influenced by both vertical inheritance and ecological factors. This study examines how the Streptomyces pangenome is shaped by these two forces and offers an important quantitative insight into how HGT shapes bacterial genome dynamics.},
}

@article {pmid41404316,
year = {2025},
author = {, and Papić, B and Fernández, PS and Garcia-Gutierrez, E},
title = {Training in metagenomics-integrated risk assessment for food-borne pathogens in the Slovenian and Spanish meat chain (METAMEAT).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {Suppl 1},
pages = {e231115},
pmid = {41404316},
issn = {1831-4732},
abstract = {Next-generation sequencing (NGS) has become an essential tool for antimicrobial resistance (AMR) surveillance, enabling comprehensive detection of AMR determinants in both bacterial isolates and complex microbial communities. Metagenomic sequencing enables culture-independent profiling of antimicrobial resistance genes (ARGs) in different environments, while whole-genome sequencing (WGS) is widely used in AMR surveillance laboratories to predict phenotypic resistance in major food-borne pathogens. AMR risk assessment usually considers factors such as the pathogenicity of the ARG-carrying bacterial host, the abundance of ARGs and their mobility potential inferred from association with plasmids or other mobile genetic elements that facilitate horizontal gene transfer. Clinical relevance of antimicrobials and the severity of clinical outcomes can further be implemented in AMR risk assessment. Exposure assessment contextualises hazards within real-world scenarios by estimating consumer exposure to AMR bacteria or their ARGs through food or other routes. Despite challenges in fully quantitative assessments, the integration of NGS-based surveillance with risk modelling represents a critical step towards proactive AMR risk management. In this study, broiler samples from different stages of a Slovenian and a Spanish slaughterhouse were analysed using conventional microbiology, shotgun metagenomic sequencing and WGS of isolates of selected pathogenic species. A modular, semi-quantitative risk assessment model was developed that combines (meta)genomic data with key risk factors and, where available, exposure assessment. This approach prioritises AMR risks in broiler meat processing and supports evidence-based decision-making in the areas of food safety and public health.},
}

@article {pmid41403704,
year = {2025},
author = {Yu, QY and Liu, X and Yao, H and Lü, PP and Yang, GJ and Lü, XT and Han, XG and Guo, LD and Huang, Y},
title = {The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf215},
pmid = {41403704},
issn = {2730-6151},
abstract = {Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.},
}

@article {pmid41379860,
year = {2025},
author = {Matthews, AC and Lehtinen, S and Dimitriu, T},
title = {Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission.},
journal = {PLoS biology},
volume = {23},
number = {12},
pages = {e3003564},
doi = {10.1371/journal.pbio.3003564},
pmid = {41379860},
issn = {1545-7885},
mesh = {*Plasmids/genetics ; *Escherichia coli/genetics/drug effects ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Selection, Genetic ; Evolution, Molecular ; },
abstract = {Conjugative plasmids carrying antimicrobial resistance (AMR) genes are critical for the spread of AMR, due to their ability to transmit horizontally between bacterial hosts. We previously observed that during experimental evolution in the presence of abundant susceptible Escherichia coli hosts, the AMR plasmid R1 rapidly evolves variants with increased horizontal transmission due to mutations causing increased plasmid copy number. Yet AMR was progressively lost from the evolving populations. Here, we show that AMR loss was associated with evolution of streamlined plasmids in which the AMR region is spontaneously deleted, making plasmid carriage undetectable by plating on selective antibiotic-containing media. These plasmids transmit both vertically and horizontally more efficiently than the ancestral AMR plasmid, driving AMR extinction in bacterial populations and effectively acting as an intrinsic defence against AMR plasmids. A simple model of plasmid competition further shows that any horizontal or vertical transmission advantage conferred by plasmid streamlining would be enough to drive the displacement of competing AMR plasmids, with a given horizontal transmission advantage leading to faster replacement in conditions favoring horizontal transmission. Our results suggest that within-host plasmid evolution or engineered streamlined plasmids could be exploited to limit the spread of AMR in natural populations of bacteria.},
}

*Plasmids/genetics
*Escherichia coli/genetics/drug effects
*Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Selection, Genetic
Evolution, Molecular

@article {pmid41402540,
year = {2025},
author = {Greige, S and Ramadan, L and Al-Alam, J and Harb, M and Wazne, M},
title = {A quantitative characterization of antibiotic resistance and its influencing factors in hospital wastewaters across Lebanon.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31879-1},
pmid = {41402540},
issn = {2045-2322},
support = {PIRF- I0065//President Intramural Research Fund (PIRF) of the Lebanese American University/ ; PIRF- I0065//President Intramural Research Fund (PIRF) of the Lebanese American University/ ; PIRF- I0065//President Intramural Research Fund (PIRF) of the Lebanese American University/ ; },
abstract = {Antimicrobial resistance poses global environmental and public health challenges, with hospital wastewater serving as a critical reservoir of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study evaluated the diversity and abundance of ARGs, mobile genetic elements (MGEs), and microbial communities in wastewaters of 13 hospitals across Lebanon. 16 S rRNA gene sequencing showed the microbial compositions of wastewaters to be widely variable. Procrustes analysis revealed that these differences influenced wastewater ARG/MGE profiles. High throughput qPCR showed that genes associated with integrons, transposons, plasmids, and insertion sequences were highly prevalent, with 14 genes detected at ≥ 0.01 copies per 16 S rRNA gene copy. Genes conferring resistance to β-lactams, aminoglycosides, tetracyclines, and sulfonamides were the most abundant. Network analysis identified significant co-occurrence patterns among microbial communities, MGEs, and ARGs, highlighting the potential for horizontal gene transfer (HGT) facilitated by specific transposons and integrons associated with particular microbial hosts. Several physicochemical parameters of the wastewaters also showed strong correlations with ARGs, MGEs, and microbes, suggesting that water quality may influence resistance dissemination. These findings underscore the critical need for monitoring of factors influencing ARG dynamics in hospital systems to limit the spread of antimicrobial resistance from clinical settings into the environment.},
}

@article {pmid41402260,
year = {2025},
author = {Lu, T and Li, Q and Hu, T and Li, W and Lu, Y and Huang, H and Zhao, Y},
title = {ABA-independent PP2C-binding in PYLs traces to bacterial origins and persists in land plants.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66141-9},
pmid = {41402260},
issn = {2041-1723},
abstract = {Land plants have evolved strategies to survive water deficiency. Among these adaptations, the "drying without dying" strategy evolved in early land plants and is maintained in the desiccated seeds of angiosperms. This process is regulated by a family of ABA receptors known as the PYR/PYL/RCAR (PYL) family, which can bind to clade A protein phosphatases 2Cs (PP2Cs) and suppress their inhibition of water stress responses. ABA-independent PYLs first emerged in an aquatic algal lineage; however, their evolutionary origins and the mechanistic basis of ABA-independent PYL variants in land plants remain poorly characterized. Here, we characterize ABA-independent PYL-like proteins from bacteria, algae, and land plants that retain constitutive PP2C binding but lack ABA-enhanced inhibitory activity, supporting their putative bacterial origin via horizontal gene transfer. We identified a bacterial PYL homolog (PrPYL) in Paraburkholderia rhynchosiae with PP2C-binding ability, three PP2C-inhibiting PYL homologs in Zygnematales algae, and ABA-independent PYL-like proteins in seed plants (e.g., AtPYL13 and AtPYL13-like proteins). AtPYL13-like genes in dicots exhibited high expression during seed maturation and in desiccated seeds, suggesting a functional shift from canonical ABA receptors to ABA-independent PYL-like proteins following gene family expansion. Two invariant residues underlie ABA dependence in canonical PYL receptors. Transcription factor ABI3 mediates AtPYL13 expression during the mature seed stage, thereby locally restricting constitutively activated stress signaling. Our findings indicate that ABA-independent PYL-like genes likely originated via horizontal transfer from bacteria and function in basal stress signaling in seed plants.},
}

@article {pmid41399813,
year = {2025},
author = {Li, P and Lin, Y and Sun, X and Huang, J and Huang, D and Xu, Y},
title = {Circulating Outer Membrane Vesicles from Gut-Colonized Carbapenem-Resistant Enterobacterales Degrade Antibiotics and Promote Bacterial Survival.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6509-6519},
pmid = {41399813},
issn = {1178-6973},
abstract = {PURPOSE: Gut colonization of carbapenem-resistant Enterobacterales (CRE) poses a significant risk for systemic infections, but the mechanisms driving resistance dissemination are poorly understood. This study aimed to investigate whether outer membrane vesicles (OMVs) secreted by gut-colonized CRE can enter the human circulatory system and mediate extracellular antibiotic resistance through functional carbapenemases and resistance genes.

PATIENTS AND METHODS: We conducted comparative proteomic analyses of OMVs isolated from parental CRE strains and patient plasma samples. Antibiotic degradation assays were performed to evaluate OMV-mediated hydrolysis of imipenem and meropenem. In vitro experiments assessed the protective effects of OMVs on carbapenem-susceptible Escherichia coli and Pseudomonas aeruginosa. Additionally, a Galleria mellonella infection model was used to examine OMV-mediated bacterial survival under carbapenem pressure.

RESULTS: Plasma-derived OMVs exhibited proteomic profiles similar to bacterial OMVs, including carbapenemase components, and demonstrated comparable antibiotic-degrading activity. These OMVs hydrolyzed 60-75% of imipenem and meropenem within 24 hours, protecting susceptible bacteria from growth inhibition in vitro. Although no horizontal gene transfer was observed, OMVs enhanced Klebsiella pneumoniae survival under carbapenem pressure in the G. mellonella model, increasing larval survival rates by 25%.

CONCLUSION: Our findings reveal a novel OMV-mediated extracellular resistance mechanism that operates independently of genetic transfer, promoting bacterial persistence in the bloodstream. This study provides key insights into the role of OMVs in clinical treatment failure and identifies potential therapeutic targets to combat antibiotic resistance dissemination.},
}

@article {pmid40856689,
year = {2025},
author = {Anton, BP and Blumenthal, R and Eaglesham, JB and Mruk, I and Roberts, RJ and Xu, S-y and Weigele, PR and Raleigh, EA},
title = {Biology of host-dependent restriction-modification in prokaryotes.},
journal = {EcoSal Plus},
volume = {13},
number = {1},
pages = {eesp00142022},
doi = {10.1128/ecosalplus.esp-0014-2022},
pmid = {40856689},
issn = {2324-6200},
mesh = {*DNA Restriction-Modification Enzymes/metabolism/genetics ; *Bacteria/genetics/enzymology ; *Gene Transfer, Horizontal ; *Prokaryotic Cells ; DNA Methylation ; Epigenesis, Genetic ; DNA, Bacterial/metabolism/genetics ; },
abstract = {Understanding the mechanisms that modulate horizontal genetic exchange in prokaryotes is a key problem in biology. DNA entry is limited by resident host-dependent restriction-modification (RM) systems (HDRM), which are present in most prokaryotic genomes. This review specifically focuses on the biological functions of HDRM, rather than detailed enzyme mechanisms. DNA in each cell carries epigenetic marks imposed by host-modifying enzymes (HDM), most often not only base methylation but also additions to the phosphodiester backbone. The pattern of base and backbone modifications is read by host-restriction enzymes (HDR). Broadly, HDRM systems read the pattern of chemical modifications to DNA at host-determined (HD) sites to regulate the fate of incoming mobile DNA. An inappropriate pattern may be restricted either due to the absence of protective modification or its presence; the latter activity is mediated by modification-dependent restriction enzymes (MDRE). Most often, restriction occurs via nuclease-mediated degradation, but it can also act via other mechanisms that prevent the initiation of replication. Like other genome-defense systems, HDRM systems are highly diverse and somewhat modular. The basic functions required for action in vivo and the protein domains responsible for each function are addressed here. Particularly under-studied among the latter are the interaction domains that control the launch of highly toxic activities such as HDR. These have been evolutionarily shuffled to build a variety of classical RM systems as well as more divergent systems.},
}

*DNA Restriction-Modification Enzymes/metabolism/genetics
*Bacteria/genetics/enzymology
*Gene Transfer, Horizontal
*Prokaryotic Cells
DNA Methylation
Epigenesis, Genetic
DNA, Bacterial/metabolism/genetics

@article {pmid41395940,
year = {2025},
author = {Karamycheva, S and Wolf, YI and Koonin, EV and Makarova, KS},
title = {Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0312725},
doi = {10.1128/mbio.03127-25},
pmid = {41395940},
issn = {2150-7511},
abstract = {Evolution of prokaryotic genomes is highly dynamic, including extensive gene gain via horizontal gene transfer and gene loss, as well as different types of genome rearrangements. Most quantitative analyses of prokaryotic genome evolution are based on single-gene events, although the distribution of genes is known to be non-random at the scales of operons and various genomic islands. Here, we present a spatial-temporal phylogenomic approach for detecting arrays of genes that are likely to have been acquired as a single block. It is shown that the acquisition of multi-gene blocks makes a major contribution to prokaryotic genome evolution and that these blocks consist primarily of co-directed, functionally coherent genes. A detailed analysis of the spatial-temporal data for the genomes of multiple groups of bacteria and archaea shows that the larger blocks of co-acquired genes represent primarily mobile genetic elements (MGEs), in many cases not identified previously. For example, this includes a new group of pleolipoviruses in Haloarchaea and a group of MGEs specific for Bacteroidota with hypervariable gene content and carrying a unique RNA polymerase enzyme. We also show that some ancestral phage-related large islands correspond to previously unnoticed R-type pyocins in Proteus and Morganella genomes. Many of the smaller gene blocks prone to high genome flux are expected to comprise antivirus defense systems and toxins-antitoxins. In a pilot analysis, eight novel toxin-antitoxin and seven novel defense systems were predicted in archaea of the phylum Thermococcaceae.IMPORTANCEWith many thousands of diverse bacterial and archaeal genomes made available by the fast advancing genomic and metagenomic sequencing, methods for in-depth analysis of genome organization and evolution are essential for extracting the maximum amount of information from this wealth of genomic data. We present a spatial-temporal approach for genome analysis that detects blocks of genes that were simultaneously acquired during genome evolution and shows that genes in such blocks are mostly transcribed in the same direction and have related functions, allowing for the prediction of previously unknown functional systems. The predictive power of the approach is demonstrated by detecting multiple novel mobile genetic elements and antivirus defense systems. Unlike most other functional prediction methods, the spatial-temporal approach does not require prior knowledge of the functions of any genes and has the potential to predict hundreds of novel functional systems amenable to further in-depth study, especially for poorly characterized groups of bacteria and archaea.},
}

@article {pmid41395494,
year = {2025},
author = {Monte, DFM and Sellera, FP},
title = {Editorial: Critical- and high-priority pathogens in the food chain.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1739491},
doi = {10.3389/fmicb.2025.1739491},
pmid = {41395494},
issn = {1664-302X},
}

@article {pmid41395485,
year = {2025},
author = {Jin, E and Gao, D and Zhou, Y and Wan, P and Chen, J and Gong, P and Li, P},
title = {Co-inoculation with Streptomyces thermovulgaris and commercial microbial agents enhances the reduction of antibiotic resistance genes in cattle manure composting: driving mechanisms involving microbial communities and mobile genetic elements.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1688304},
pmid = {41395485},
issn = {1664-302X},
abstract = {To investigate the mechanisms by which Streptomyces thermovulgaris a2 (Sta2) enhances the reduction of antibiotic resistance genes (ARGs) in cattle manure composting, this study compared the effects of commercial microbial inoculant (CK) and its combination with Sta2 (ST). The results showed that the ST treatment extended the thermophilic phase (≥55 °C) to 18 days (compared to 11 days with CK) and increased the removal rates of tetG, sul1, ermQ, aac(6')-Ib-cr, and intI1/intI2 (by 4.8%-48.4%), simultaneously inhibiting the enrichment of sul2 and ermX. During the thermophilic phase, ST treatment slowed the decline in the abundances of key genera (e.g., Bacillus, Thermobacillus, Brachybacterium) and effectively promoted the growth of Actinomadura and Longispora within Actinobacteria. Redundancy analysis revealed that bacterial community succession (56.3%) and mobile genetic elements (MGEs, 30.7%) were key drivers of ARG dynamics, with intI1 and Firmicutes positively regulating most ARGs. Co-occurrence network analysis identified Lysinibacillus (harboring 9 ARG-MGE associations), Luteimonas (9), Brachybacterium (8), and the pathogen Corynebacterium (6) as multidrug resistant hosts. In summary, ST treatment enhanced the reduction of certain genes and multidrug-resistant host control by prolonging the thermophilic duration, reconstructing the microbial community composition, and effectively inhibiting intI1- and intI2-mediated horizontal gene transfer.},
}

@article {pmid41394595,
year = {2025},
author = {Deka, N and Brauer, AL and Connerton, K and Hanson, B and Walker, JN and Armbruster, CE},
title = {Pangenome Analysis of Proteus mirabilis Reveals Lineage-Specific Antimicrobial Resistance Profiles and Discordant Genotype-Phenotype Correlations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689858},
pmid = {41394595},
issn = {2692-8205},
abstract = {UNLABELLED: Urinary tract infections (UTIs) impose a substantial health care burden with increasing antimicrobial resistance and treatment failure rates. Proteus mirabilis is a challenging UTI pathogen due to intrinsic resistances coupled with formation of crystalline biofilms. We combined pangenome analysis, antimicrobial resistance gene (AMR) predication, and antimicrobial susceptibility testing (AST) to determine whether highly multidrug-resistant (MDR) isolates of P. mirabilis arise from distinct lineages and explored the clinical utility of multilocus sequence typing (MLST). The pangenome of 1,001 P. mirabilis genomes from human urine revealed an open conformation driven by strain diversity and the accessory genome. A total of 213 sequence types (STs) were identified and only 7% had ≥11 genomes, highlighting strain diversity. 93% of the P. mirabilis genomes harbored resistance genes for ≥2 antibiotic subclasses, and 25% were predicted to be resistant to >6 subclasses, confirming a high MDR burden. By focusing on the 15 most prevalent STs, we observed that AMR subclasses were largely lineage-specific. However, isolates with very high resistance gene counts (>20) were distributed across multiple STs, indicating that extreme resistance gene accumulation is not restricted to ST. Comprehensive AST of 27 P. mirabilis clinical isolates further revealed variable genotype-phenotype concordance, indicating unresolved mechanisms of resistance not captured in current AMR prediction databases. In summary, our study emphasizes the critical need to expand genomic surveillance of P. mirabilis to fully understand the complex landscape of AMR in this species and translate these insights into improved diagnostic and therapeutic strategies.

IMPORTANCE: Proteus mirabilis is a clinically-challenging cause of urinary tract infections due to multidrug resistance and its ability to form crystalline biofilms that provide further antibiotic protection. In this study, we sought to determine how well sequence typing and antimicrobial resistance gene prediction correlate with laboratory-based antimicrobial susceptibility testing. By analyzing more than 1,000 P. mirabilis genomes from human urine samples, we found that some resistance patterns were sequence type-specific. However, the genome structure of this species suggests frequent horizontal gene transfer, and the most highly-resistant strains did not cluster by lineage. Importantly, many isolates that appeared "susceptible" based on their genomes were in fact resistant upon laboratory testing, revealing hidden or uncharacterized resistance mechanisms. These findings show that current gene-based prediction tools can miss clinically relevant resistance, underscoring the need for further study to guide effective treatment of P. mirabilis infections.},
}

@article {pmid41393790,
year = {2025},
author = {Saravanan, V and Kravetz, A and Battistuzzi, FU},
title = {Higher frequency of prokaryotic low complexity regions in core and orthologous genes.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1673480},
pmid = {41393790},
issn = {2673-7647},
abstract = {Prokaryotic genome evolution is shaped by mutation, gene duplication, and horizontal gene transfer, yet the interaction of these mechanisms, particularly in relation to low complexity regions (LCRs), remains poorly understood. LCRs are known to be mutation-prone and have been proposed to promote genetic innovation. However, the interaction between LCR-mediated and paralogy-mediated genetic innovation is still unclear. To clarify the interplay between these two evolutionary forces, we analyzed the distribution of LCRs in protein-coding genes from three closely related enterobacteria (Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae) at both species and population levels. Using pangenomic and orthology-based approaches, we categorized genes by duplication history and conservation status and assessed LCR frequencies across these groups. We found that LCRs were consistently enriched in core and orthologous genes rather than in accessory or paralogous ones. This pattern was stable across evolutionary timescales and particularly pronounced in genes involved in cell cycle control and defense. These results suggest that, contrary to prior assumptions, LCRs may serve conserved functional roles rather than acting primarily as agents of evolutionary plasticity even at population-level timescales.},
}

@article {pmid41391488,
year = {2025},
author = {Amodeo, S and Fischli, M and Oeljeklaus, S and Calderaro, S and Warscheid, B and Schneider, A},
title = {A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1327},
pmid = {41391488},
issn = {1362-4962},
support = {205601//NCCR/ ; 205200/WT_/Wellcome Trust/United Kingdom ; /SNSF_/Swiss National Science Foundation/Switzerland ; 541758684//Deutsche Forschungsgemeinschaft/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Trypanosoma brucei brucei/genetics/metabolism/growth & development ; *Protozoan Proteins/metabolism/genetics/chemistry ; Cytosol/metabolism ; *RNA Processing, Post-Transcriptional ; *RNA, Ribosomal/metabolism/genetics ; *RNA, Protozoan/metabolism/genetics ; Protein Domains ; },
abstract = {Unlike most eukaryotes, Trypanosoma brucei processes its cytosolic large subunit (LSU) RNA into six fragments. The factors responsible for these processing events were previously unknown. Here, we identify TbLrRP1 and TbLrRP2 as essential components of this trypanosome-specific LSU RNA processing pathway. Each contains a single transmembrane domain and localizes to the ER membrane and the nuclear envelope, forming a heterodimeric complex. Depletion of either protein disrupts LSU RNA processing, causing accumulation of unprocessed intermediates that are incorporated into translationally active cytosolic polysomes. This disruption impairs, but does not fully halt, growth of both procyclic and bloodstream form trypanosomes. The nuclease-related domain (NERD) of TbLrRP2 is essential for LSU RNA processing. Intriguingly, NERD-containing proteins were predicted to have DNase activity; however, our results suggest that the NERD of TbLrRP2 is a ribonuclease. In contrast, the DEDDh domain of TbLrRP1 is dispensable for LSU RNA processing, indicating it may have a scaffolding role. Both proteins require their transmembrane domains for full functionality. Our findings reveal a lineage-specific processing complex acting at a late stage of LSU RNA maturation, highlighting the unique adaptations of trypanosomal cytosolic ribosome biogenesis.},
}

*Trypanosoma brucei brucei/genetics/metabolism/growth & development
*Protozoan Proteins/metabolism/genetics/chemistry
Cytosol/metabolism
*RNA Processing, Post-Transcriptional
*RNA, Ribosomal/metabolism/genetics
*RNA, Protozoan/metabolism/genetics
Protein Domains

@article {pmid41391220,
year = {2025},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid41299812,
year = {2025},
author = {Wang, B and Li, Z and Chen, M and Wang, Y and Aimaiti, B and Fu, J and Li, K and Peng, Z and Zhang, R and Wang, T and Wang, H and Gu, B and Song, H and Ren, H and Hu, X},
title = {Epidemiology, genetic dynamics, and transmission of the mcr-1 gene in China.},
journal = {Emerging microbes & infections},
volume = {14},
number = {1},
pages = {2595798},
doi = {10.1080/22221751.2025.2595798},
pmid = {41299812},
issn = {2222-1751},
mesh = {China/epidemiology ; Humans ; Animals ; Colistin/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Escherichia coli Proteins/genetics ; Plasmids/genetics ; Poultry/microbiology ; Microbial Sensitivity Tests ; Gene Transfer, Horizontal ; },
abstract = {Colistin is a broad-spectrum antibiotic that kills bacteria through the disruption of the cell membrane, making it effective against various bacterial infections. Since the first global report of mobile colistin-resistant (mcr-1)-positive bacteria, which were discovered and described by Chinese scientists in 2015, monitoring and research on these bacteria have continuously been conducted. In this study, we analyzed 70 mcr-1-positive strains detected by surveillance hospitals across three different provinces of China, as well as 671 strains screened from the NCBI database that contain the mcr-1 gene. The epidemiological analysis indicated that the mcr-1 gene had circulated undetected in China for over three decades prior to its first report in 2015 and extensive agricultural use of polymyxins likely initiated the emergence of mcr-1 and blaNDM co-harbouring strains in poultry and livestock, with subsequent fecal-environmental transmission leading to human infections. The genetic dynamics and transmission analysis provides the first detailed elucidation of the adaptive evolutionary migration of mcr-1, which enhanced its dissemination across diverse bacterial hosts and facilitated the emergence of super-resistant Enterobacterales strains and IncHI2(A) super-plasmids co-harbouring mcr-1 and blaNDM.},
}

China/epidemiology
Humans
Animals
Colistin/pharmacology
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Escherichia coli Proteins/genetics
Plasmids/genetics
Poultry/microbiology
Microbial Sensitivity Tests
Gene Transfer, Horizontal

@article {pmid41390685,
year = {2025},
author = {Javaid, A and Tabassum, N and Karthikeyan, A and Kim, YM and Jung, WK and Khan, F},
title = {Prevalence and stable acquisition of biogenic amine-synthesizing genes in lactic acid bacteria across diverse niches: implications for food safety and human health.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00667-6},
pmid = {41390685},
issn = {2396-8370},
support = {RS-2023-00241461//Basic Science Research Program through the National Research Foundation of Korea, funded by the Ministry of Education/ ; },
abstract = {Biogenic amines (BAs) are metabolites produced by lactic acid bacteria (LAB) with implications for food safety and human health. Despite extensive phenotypic studies on individual BA biosynthesis genes, the distribution, evolutionary dynamics, ecological associations, and mobility mechanisms underpinning BA biosynthesis across LAB strains is unclear. Here, we conducted the first comprehensive genomic survey of 4880 LAB genomes to elucidate the prevalence and mobility of key BA genes. Ornithine decarboxylase (odc) showed a broader taxonomic distribution, while tyrosine decarboxylase (tdc), although predominant, was confined to Enterococcus. All BA genes exhibited strong ecological associations, suggesting niche-specific adaptation. Phylogenomic analysis highlighted complex evolutionary trajectories involving ancestral gains and extensive horizontal gene transfer (HGT), particularly for odc and tdc genes. Gene synteny and compositional signatures further supported lineage-specific retention and recurrent HGT events among phylogenetically related taxa. For example, the arginine decarboxylase (adc) gene and agmatinase were potentially co-acquired as an operon-level unit. Codon usage suggested translational assimilation, reflecting the functional integration of BA genes in LAB. Insertion sequences and composite transposons were predicted as putative vectors mediating BA gene mobility. Collectively, this study provides a framework linking BA gene distribution to niche and mobility, with implications for risk assessment in foods and probiotics.},
}

@article {pmid41389591,
year = {2025},
author = {Chen, J and Liu, Y and Fu, L and Song, X and Zhang, D and Duan, X and Li, Y and Zhao, Y and Guo, L},
title = {Exploring the molecular basis of serotyping and antibiotic resistance differences in Riemerella anatipestifer based on pan-genomics and machine learning.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110828},
doi = {10.1016/j.vetmic.2025.110828},
pmid = {41389591},
issn = {1873-2542},
abstract = {Riemerella anatipestifer (R. anatipestifer) is a major pathogen in poultry worldwide, with multidrug resistance (MDR) and diverse serotypes complicating disease control. This study systematically investigated the molecular basis of serotyping and MDR characteristics in 92 R. anatipestifer strains isolated from 13 provinces in China between 2008 and 2023 by integrating pan-genome analysis with machine learning approaches. In this study, serotypes 2 (29.4 %), 7 (25.0 %), and 1 (21.7 %) were predominant. All isolates exhibited MDR and strains of serotypes 2 and 7 had significantly higher MICs for tigecycline, doxycycline, polymyxin B, and florfenicol than serotype 1 (P < 0.05). Eleven resistance genes were identified, and some (e.g., floR, tetX) displayed serotype-specific distribution patterns. Phylogenetic analysis indicated close relatedness between serotypes 2 and 7, while serotype 1 strains were genetically diverse. The accessory genome was enriched in mobile elements and O-antigen-related genes, and multiple serotype-specific marker genes (e.g., pgIA, wbpI) were identified, revealing the molecular basis of serotype classification. Additionally, insertion sequences (IS1595) flanking CPS gene clusters implied that horizontal gene transfer and recombination events may play pivotal roles in serotype variation. This study provides the first integrative framework combining pan-genomics and machine learning to elucidate the genomic basis of serotype diversity and antimicrobial resistance in R. anatipestifer, offering new insights into its adaptive evolution and informing precision vaccine and diagnostic development.},
}

@article {pmid41390414,
year = {2025},
author = {Li, J and Xu, Y and Wu, Y and Luan, L and Wang, W and Chen, Q and Qin, S and Guo, H},
title = {The molecular characteristic of Neisseria meningtidis serogroup X strain emerging in Jiangsu province, China, 2022.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04555-7},
pmid = {41390414},
issn = {1471-2180},
support = {2023YFC2605105//National Key R&D Program of China/ ; },
abstract = {Invasive meningococcal disease (IMD) is always caused by Neisseria meningitidis, presents a significant clinical challenge with high mortality rates (up to 20%) and not only neurological sequelae, but also physical and psychological sequelae in survivors. While vaccination has effectively reduced the incidence of traditional serogroups like A and C in China, the emergence of serogroup replacement due to capsular switching-horizontal gene transfer of capsular genes-threatens ongoing public health efforts. This study reports firstly the identification of a ST-7 NmX strain (20220811) in Jiangsu Province, China, suspected to have arisen from an ST-7 NmA progenitor via capsular switching. Whole-genome comparison and phylogenetic analysis revealed a high degree of core genome similarity between the X strain and ST-7 serogroup A strains. However, a significant divergence was observed within the capsular gene cluster region spanning ctrC to rfbA (~ 10.6 kb), with recombination breakpoints identified near these genes. These findings strongly suggest the acquisition of NmX capsule through large fragment recombination. Meantime, virulence factor analysis indicated the absence of adhesion-related genes opa and pilC in the X strain, potentially reflecting a trade-off between reduced invasive capacity and enhanced immune evasion.},
}

@article {pmid41388796,
year = {2025},
author = {Jian, J and Chen, C and Fang, X and Workman, CT and Ostenfeld Larsen, T and Li, Y and Sonnenschein, EC},
title = {The genome of Pleurosigma provides insights into the evolutionary adaptations of pelagic diatoms.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf037},
pmid = {41388796},
issn = {1756-1663},
abstract = {The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins facilitates the adaptation of P. pacificum to high light conditions in pelagic environments. The percentage of approximately 3.22% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms.},
}

@article {pmid41386129,
year = {2025},
author = {Bai, H and He, LY and Yadav, S and Gao, FZ and Liu, YS and Smidt, H and Ying, GG},
title = {Phages and plasmids mediate antibiotic resistance gene transfer in urban airborne bacteria.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140779},
doi = {10.1016/j.jhazmat.2025.140779},
pmid = {41386129},
issn = {1873-3336},
abstract = {Airborne antibiotic resistance genes (ARGs) pose emerging public health risks, particularly in urban settings, yet their dissemination mechanisms remain unclear. Here we cultured airborne bacteria from diverse urban environments and performed metagenomic sequencing to reconstruct 931 non-redundant metagenome-assembled genomes (MAGs), integrating horizontal gene transfer (HGT) detection, machine learning, and causal inference analyses. We identified hospitals, pharmaceutical factories, and railway stations as major sources of mobile ARGs. Both plasmids and phages actively mediate ARG transfer, promoting gene dissemination across broad phylogenetic distances. Machine learning revealed key phage functional modules related to structure, host attachment, lysis, DNA entry, and regulation that facilitate virus-mediated HGT, with synergistic interactions observed between plasmids and phages. These findings elucidate the dynamic resistome and mobility potential of metabolically active airborne bacteria, informing environmental surveillance and mitigation strategies to address airborne antimicrobial resistance within the One Health framework.},
}

@article {pmid41386783,
year = {2025},
author = {HuangFu, N and Zhu, X and Tang, Z and Wang, L and Zhang, K and Li, D and Ji, J and Cui, J and Guo, Z and Luo, J and Gao, X},
title = {Gut Microbe-Driven Resistance Mechanisms in Propylea Japonica: Insights from Horizontal Gene Transfer and Oxidative Phosphorylation.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e20326},
doi = {10.1002/advs.202520326},
pmid = {41386783},
issn = {2198-3844},
support = {CAAS-ZDRW202412//Agricultural Science and Technology Innovation Program/ ; 2022YFF1001400//National Key Research and Development Program of China/ ; Y2023QC23//Youth Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 2023ZD04062//Agricultural Science and Technology Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences and the Science and Technology Innovation 2030/ ; CARS-15-21//China Agriculture Research System/ ; },
abstract = {Insect-microbial symbiont relationships are widespread in nature and often involve lateral gene transfer. Although the evolutionary processes that allow insects to adapt to complex environments remain largely unknown, it is clear that symbiotic relationships have essential roles in these processes. Here, gut microbes-mediated regulation of Propylea japonica insecticide tolerance is found through modulation of a horizontally transferred gene (P. japonica Domain unknow funcation 1, PjDUF1) expression. However, this gene regulates the host capacity for dinotefuran tolerance by affecting the oxidative phosphorylation rate. This is confirmed by the RNAi-Mediated Silencing of PjDUF1. Importantly, evidence is found that PjDUF1 is donated from Acenitobacter via horizontal gene transfer (HGT). The findings provide the first experimental evidence that HGT events are important for pesticide tolerance in a prominent natural enemy species. Further study of the evolutionary origins of key natural enemy tolerance genes will shed additional light on how insects have developed resistance to adverse environments, suggesting strategies for protecting insect species that provide critical ecosystem services.},
}

@article {pmid41384994,
year = {2025},
author = {Zhang, J and Liu, J and Bayani, A},
title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.},
journal = {Journal of cancer research and clinical oncology},
volume = {152},
number = {1},
pages = {8},
pmid = {41384994},
issn = {1432-1335},
mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.},
}

Humans
*Hematologic Neoplasms/therapy/microbiology/immunology
*Phage Therapy/methods
Animals
*Bacteriophages
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41383826,
year = {2025},
author = {Wijaya, AJ and Anžel, A and Richard, H and Hattab, G},
title = {Genomic data representations for horizontal gene transfer detection.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf165},
pmid = {41383826},
issn = {2631-9268},
mesh = {*Gene Transfer, Horizontal ; *Genomics/methods ; Support Vector Machine ; Machine Learning ; },
abstract = {Horizontal gene transfer (HGT) accelerates the spread of antimicrobial resistance (AMR) via mobile genetic elements allowing pathogens to acquire resistance genes across species. This process drives the evolution of multidrug-resistant "superbugs" in clinical settings. Detection of HGT is critical to mitigating AMR, but traditional methods based on sequence assembly or comparative genomics lack resolution for complex transfer events. While machine learning (ML) promises improved detection, several studies in other domains have demonstrated that data representations will strongly influence its performance. There is, however, no clear recommendation on the best data representation for HGT detection. Here, we evaluated 44 genomic data representations using five ML models across four data sets. We demonstrate that ML performance is highly dependent on the genomic data representation. The RCKmer-based representation (k = 7) paired with a support vector machine is found to be optimal (F1: 0.959; MCC: 0.908), outperforming other approaches. Moreover, models trained on multi-species data sets are shown to generalize better. Our findings suggest that genomic surveillance benefits from task-specific genome data representations. This work provides state-of-the-art, fine-tuned models for identifying and annotating genomic islands that will enable proper detection of transfer of AMR-related genes between species.},
}

*Gene Transfer, Horizontal
*Genomics/methods
Support Vector Machine
Machine Learning

@article {pmid41383362,
year = {2025},
author = {Badshah, F and Rafiq, N and Kamal, M and Said, MB and Khan, S and Khattak, I and Khan, NU and Alabbad, AF and Usman, T},
title = {Prevalence, Antibiotic Resistance Pattern, and Molecular Characteristics of Staphylococcus epidermidis Isolated From Milk of Pure Breeds of Dairy Cattle With Subclinical Mastitis.},
journal = {Journal of tropical medicine},
volume = {2025},
number = {},
pages = {8893420},
pmid = {41383362},
issn = {1687-9686},
abstract = {Bovine mastitis, a widespread disease in dairy cattle characterized by udder inflammation triggered primarily by pathogenic micro-organisms, poses a considerable challenge to the dairy industry. Staphylococcus epidermidis (S. epidermidis) stands out as a significant etiological factor in the incidence of bovine subclinical mastitis (SCM), further exacerbated by the diminishing efficacy of antibiotics due to the increase in antibiotic-resistant strains. This study sets out to comprehensively investigate the landscape of S. epidermidis in dairy cattle afflicted with SCM. We examined the prevalence of S. epidermidis, assessed its antibiotic resistance patterns, and probed for the presence of antibiotic-resistant genes (mecA, tetK, and ermC) within S. epidermidis strains isolated from 305 milk samples across four distinct dairy cattle breeds: Holstein Friesian, Red Sindhi, Sahiwal, and Cholistani. Among the sampled cows, 56.39% (172 out of 305) were found to have SCM. Within this group, S. epidermidis was identified in 27.90% (48 out of 172) of the cases. Our breed-specific analysis revealed significant disparities, with Red Sindhi cows displaying the highest prevalence at 75%, followed by Holstein Friesian at 45.45%, and significantly lower levels in Sahiwal (5.19%) and Cholistani (3.44%) breeds. To assess the efficacy of antibiotics, we conducted sensitivity testing using nine commonly prescribed antibiotics. Alarmingly, 18 out of the 48 isolates (37.5%) exhibited multidrug resistance (MDR). Our antibiogram results underscored a high resistance of S. epidermidis isolates, particularly against cefoxitin (56.25%) and penicillin (43.75%), while demonstrating remarkable susceptibility to amikacin (2.08%), clindamycin (0%), ciprofloxacin (0%), and chloramphenicol (0%). Furthermore, we employed PCR to ascertain the presence of resistant genes in all S. epidermidis isolates. mecA was detected in 38 isolates (79.16%), while tetK was identified in 33 isolates (68.75%). Notably, the study did not detect the presence of the ermC gene. Our investigation highlights the efficacy of chloramphenicol, clindamycin, and ciprofloxacin against S. epidermidis. However, the prevalence of multidrug-resistant strains calls for careful antibiotic use in veterinary practices. Further research is needed to examine geographic and farm-specific factors affecting S. epidermidis prevalence, and genetic techniques like multilocus sequence typing should be employed to study clonal spread and horizontal gene transfer. Routine antimicrobial sensitivity assessments and continuous monitoring of medication use are essential to develop sustainable strategies against antibiotic resistance in the dairy industry.},
}

@article {pmid41381821,
year = {2025},
author = {Denysenko-Bennett, M and Kwolek, D and Góralski, G and Szklarczyk, M and Piwowarczyk, R and Stefanović, S and Schneider, AC and Joachimiak, AJ},
title = {Horizontal gene transfer of the Pytheas sequence from Cuscuta to Orobanche via a host-mediated pathway.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31853-x},
pmid = {41381821},
issn = {2045-2322},
support = {K/DSC/003923//Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland/ ; 326439//NSERC of Canada Discovery/ ; },
abstract = {Horizontal Gene Transfer (HGT) is a phenomenon of DNA transfer between organisms that does not involve a parent-offspring relationship. HGT is believed to play an important role in all groups of organisms, including plants, and especially in parasites. Here we describe a chain of transfers from Cuscuta (Convolvulaceae) to Orobanche rigens (Orobanchaceae)-both parasitic plants-via a host belonging to tribe Genisteae (Fabaceae). During its "journey" between genomes, the transferred sequence, which we named Pytheas, was altered by deletions, additions of new segments from the current genome, substitutions, and rearrangements. This is the first robustly documented case of a multi-step transfer pathway-involving one IGT and two HGTs-connecting three plant species. Specifically, this system involves a host plant mediated gene flow between two distinct parasites without involvement of transposable elements, the cox1 intron, or other vectors. This case also demonstrates how host-parasite interactions can facilitate the spread of genetic material between evolutionarily distant lineages.},
}

@article {pmid41381568,
year = {2025},
author = {Cabral, V and Oliveira, RA and Correia, MB and Pedro, MF and García-Garcerá, M and Ubeda, C and Xavier, KB},
title = {Klebsiella ARO112 promotes microbiota recovery, pathobiont clearance and prevents inflammation in IBD mice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10911},
pmid = {41381568},
issn = {2041-1723},
support = {MSCA-IF-2018-843183//European Commission (EC)/ ; PCIN-2015-094//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella/physiology/genetics ; *Inflammatory Bowel Diseases/microbiology/therapy/chemically induced ; Mice ; Disease Models, Animal ; *Probiotics/pharmacology ; Inflammation/prevention & control/microbiology ; Mice, Inbred C57BL ; Colitis/microbiology/chemically induced ; Anti-Bacterial Agents/pharmacology ; Female ; Butyrates/metabolism ; Male ; },
abstract = {Precise microbiota modulation towards improving immune function and metabolic homeostasis is a major goal in clinical research. It is also critical for reducing pathogen invasion or pathobiont expansion, contributors to epidemic Inflammatory Bowel Diseases (IBD), where recurrent antibiotic treatments often exacerbate microbiota imbalances. Within the thousands of strains of a natural gut microbiota, we previously identified a specific Klebsiella strain, ARO112, capable of promoting resistance to, and clearance of, pathogenic Enterobacteriaceae. Here, we assess its therapeutic potential using a comprehensive genomic and phenotypic analysis and experiments in mouse models of IBD. We demonstrate that ARO112 not only exhibits a safety profile comparable to the widely used probiotic Escherichia coli Nissle 1917, but also has a reduced capacity to acquire antibiotic resistance, via horizontal gene transfer, and to capture iron, thereby bypassing major concerns associated with pathogenic Enterobacteriaceae strains. In antibiotic-treated, genetically predisposed IBD mice, ARO112 accelerates pathobiont clearance, promotes the recovery of microbiota diversity, elevates intestinal butyrate concentration, and prevents mild inflammation. Moreover, even in the absence of pathogen infection, ARO112 prevents severe inflammation-driven pathology in a chemically-induced colitis model. Our findings highlight ARO112 as a potential biotherapeutic agent that disrupts inflammation-treatment-infection cycles characteristic of chronic gut inflammatory diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Klebsiella/physiology/genetics
*Inflammatory Bowel Diseases/microbiology/therapy/chemically induced
Mice
Disease Models, Animal
*Probiotics/pharmacology
Inflammation/prevention & control/microbiology
Mice, Inbred C57BL
Colitis/microbiology/chemically induced
Anti-Bacterial Agents/pharmacology
Female
Butyrates/metabolism
Male

@article {pmid41380974,
year = {2025},
author = {Li, B and Liang, J and Baniasadi, HR and Phillips, MA and Michael, AJ},
title = {Spermine and thermospermine synthases emerged multiple times during eukaryote evolution.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111028},
doi = {10.1016/j.jbc.2025.111028},
pmid = {41380974},
issn = {1083-351X},
abstract = {The polyamines spermine and thermospermine are differentially distributed throughout eukaryotic phyla. It is unlikely that they were present in the Last Eukaryotic Common Ancestor, thus their biosynthetic enzymes, spermine synthase (SpmSyn) and thermospermine synthase (TspmSyn) emerged during eukaryotic evolution. Herein, we show the different evolutionary mechanisms by which functionally validated SpmSyns and TspmSyns evolved, and their phylogenetic distribution in eukaryotes. Animal lineage SpmSyn was horizontally acquired as a bacterial S-adenosylmethionine decarboxylase-SpmSyn fusion protein before the emergence of the single-celled closest relatives of animals, the Choanoflagellata. SpmSyn has been lost from comb jellies, some sponge species, and was lost from most free-living and parasitic worms. Corals encode two SpmSyn homologs, one of which has evolved into a TspmSyn. In fungi, SpmSyn evolved by gene duplication of spermidine synthase and subsequent neofunctionalization early in the budding yeast Saccharomycotina subphylum. Similarly, the plant SpmSyn evolved by gene duplication of spermidine synthase and then neofunctionalization in lycophytes, coincident with the emergence of vascularization. TspmSyn is found throughout plants and green algae, but lost from wild and domesticated barley. It was likely acquired by endosymbiotic gene transfer from the cyanobacterial ancestor of the chloroplast, although the closest homolog of plant TspmSyn is from the Chloroflexota. TspmSyn homologs evolved into SpmSyns in red algae and into spermidine synthase in glaucophyte algae. Chloroflexota-type TspmSyns are found in many protist phyla, often correlated with secondary endosymbiosis of red or green algae, but were acquired by horizontal gene transfer in phyla that have not possessed algal plastids.},
}

@article {pmid41378915,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf275},
pmid = {41378915},
issn = {1751-7370},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.},
}

@article {pmid41377425,
year = {2025},
author = {Nawaz, S and Nadeem, IA and Talha, M and Irshad, NUN and Imran, SB},
title = {Engineered microbes over immunosuppression: MAGIC as a transformative strategy for vasculitides.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {12},
pages = {9131-9132},
pmid = {41377425},
issn = {2049-0801},
}

@article {pmid41371426,
year = {2025},
author = {Gambushe, SM and Idowu, PA and Zishiri, OT},
title = {Comparative genomics of diverse Escherichia coli O157:H7 strains to characterize plasmids, prophages, virulence, and antimicrobial resistance genes.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102771},
doi = {10.1016/j.plasmid.2025.102771},
pmid = {41371426},
issn = {1095-9890},
abstract = {Plasmids play a critical role in bacterial evolution and represent major drivers of the emergence and dissemination of antimicrobial resistance. As primary mobile genetic elements (MGEs), plasmids facilitate the horizontal transfer of resistance determinants alongside genes associated with virulence, metabolic functions, and broader adaptive advantages. Recent studies have further highlighted the importance of conjugative plasmids, such as IncI1-like elements, in mediating the spread of extended-spectrum β-lactamase (ESBL) genes and other clinically relevant traits across diverse bacterial populations. Whether the recurrent detection of these plasmids is coincidental or reflects unique genetic features that enhance their capacity for transmission remains an important question in microbial genomics. In this context, the present study analyses complete genome sequences and whole-genome maps of Escherichia coli O157:H7 strains to characterize their antimicrobial resistance genes, virulence-associated loci, prophage content, and plasmid profiles. Publicly available sequences from the NCBI GenBank repository were examined using comparative genomic tools, including BRIG, VirulenceFinder, ResFinder, PlasmidFinder, and PHASTEST. This work also underscores the limited availability of whole-genome data for E. coli O157:H7 and O157:H7NM in developing regions, particularly within African countries, highlighting the need for expanded genomic surveillance. Comparative analyses revealed that most strains displayed high genomic similarity to the reference Sakai strain, with relatively few missing regions, although a subset exhibited reduced homology marked by numerous gaps. Prophages, bacteriophages integrated into the bacterial genome, were found to contribute substantially to genomic diversity, influencing virulence potential, antimicrobial resistance, and patterns of horizontal gene transfer. These findings emphasize the complex role of mobile genetic elements in shaping the evolution of E. coli O157:H7 and reinforce the importance of continued genomic sequencing to further elucidate the pathogen's diversity and adaptive mechanisms.},
}

@article {pmid41371128,
year = {2025},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}

@article {pmid41370983,
year = {2025},
author = {Ahmad, N and Joji, RM and Saeed, NK and Shahid, M},
title = {Genomic insights and molecular epidemiology through whole genome sequencing in clinical Serratia marcescens ST-367 isolated from the Kingdom of Bahrain.},
journal = {Journal of infection and public health},
volume = {19},
number = {2},
pages = {103087},
doi = {10.1016/j.jiph.2025.103087},
pmid = {41370983},
issn = {1876-035X},
abstract = {BACKGROUND: Serratia marcescens may cause rare central nervous system infections. The growing antibiotic resistance in these isolates makes treatment challenging. S. marcescens (MIID-C14) was isolated from the cerebrospinal fluid of a 56-year-old female patient admitted to Salmaniya Medical Complex, Bahrain. Due to the virulence and multidrug resistance exhibited by this bacterium, we aimed to analyse the genetic makeup of this isolate.

METHODS: The isolate was identified via MALDI-TOF mass spectrometry, antimicrobial susceptibility was performed by VITEK-2 system, and whole-genome sequencing (WGS) was conducted on the Illumina Novoseq 6000 S4 platform. The genome was annotated using the Prokaryotic Genome Annotation Pipeline (NCBI). In-silico predictions of antibiotic resistance genes, virulence genes, and multilocus sequence typing were performed using curated bioinformatics tools.

RESULTS: MIID-C14 showed resistance to cefotaxime, ceftazidime, cefepime, and ertapenem, and was sensitive to gentamicin, ciprofloxacin, and trimethoprim/sulfamethoxazole. The complete genome of MIID-C14 was 4983,593 bp with 60.2 % GC content, and a Benchmarking Universal Single-Copy Orthologs score of 100. Molecular analysis identified antibiotic resistance genes for aminoglycosides (aac(6')), fluoroquinolones (oqxB), Diaminopyrimidine/Sulfonamides (sul), and a chromosomal beta-lactamase (SRT-2). Multilocus sequence typing identified the sequence type as ST-367. Additionally, the genome harbored 218 mobile genetic elements, including 98 instances of horizontal gene transfer, and two virulence genes (fliM and rcsB). WGS data of this strain are available in the NCBI database under the BioProject: PRJNA1113219, BioSample: SAMN41450192, GenBank Accession: JBDXSY000000000.

CONCLUSION: To our knowledge, this is the first report of S. marcescens ST-367 in the Gulf Cooperation Council. The genetic diversity and mechanisms of virulence and antibiotic resistance in this isolate shed light on the evolution of high-risk isolates. Additionally, this will serve as a foundation for future extensively drug-resistant isolates.},
}

@article {pmid41370957,
year = {2025},
author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G},
title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.},
journal = {Environment international},
volume = {207},
number = {},
pages = {109971},
doi = {10.1016/j.envint.2025.109971},
pmid = {41370957},
issn = {1873-6750},
abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.},
}

@article {pmid41370391,
year = {2025},
author = {Wendt, GR and Collins, JJ},
title = {Unusual inheritance of a functional cki homolog in the human pathogen Schistosoma mansoni.},
journal = {Science advances},
volume = {11},
number = {50},
pages = {eaea4905},
doi = {10.1126/sciadv.aea4905},
pmid = {41370391},
issn = {2375-2548},
mesh = {*Schistosoma mansoni/genetics/pathogenicity/metabolism ; Animals ; Humans ; Schistosomiasis mansoni/parasitology/genetics ; Tumor Suppressor Protein p53/genetics/metabolism ; *Helminth Proteins/genetics/metabolism ; Phylogeny ; },
abstract = {Schistosomes, parasitic flatworms responsible for the neglected tropical disease schistosomiasis, are protected by a skin-like tegument, and tegument maintenance is controlled by a schistosome ortholog (p53-1) of the tumor suppressor TP53. To understand p53-1 function, we characterized a schistosome cyclin-dependent kinase inhibitor homolog (cki). Knockdown of cki resulted in hyperproliferation that, combined with p53-1 knockdown, yielded tumor-like growths, indicating that cki and p53-1 are tumor suppressors in Schistosoma mansoni. cki homologs are ubiquitous in parasitic flatworms but are absent from their free-living ancestors, suggesting that cki may have come from horizontal gene transfer. This suggests that the evolution of parasitism in flatworms was aided by an unusual means of metazoan genetic inheritance.},
}

*Schistosoma mansoni/genetics/pathogenicity/metabolism
Animals
Humans
Schistosomiasis mansoni/parasitology/genetics
Tumor Suppressor Protein p53/genetics/metabolism
*Helminth Proteins/genetics/metabolism
Phylogeny

@article {pmid41370031,
year = {2025},
author = {Cai, X and Kang, C and Li, G and Zhang, M and Chen, X and Li, B and Li, B and Zhu, L and Wu, K and Chen, W},
title = {Poultry pathogenicity, antimicrobial resistance, and one health genomic characterization of ST83 Escherichia coli.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {4},
pmid = {41370031},
issn = {1678-4405},
support = {CARS-40-S02//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Escherichia coli/genetics/pathogenicity/drug effects/isolation & purification/classification ; *Escherichia coli Infections/veterinary/microbiology ; *Poultry Diseases/microbiology ; Chickens/microbiology ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Genome, Bacterial ; Virulence ; China ; Humans ; One Health ; *Drug Resistance, Bacterial ; Plasmids/genetics ; Escherichia coli Proteins/genetics ; Genomics ; Microbial Sensitivity Tests ; },
abstract = {Escherichia coli is a clinically relevant zoonotic pathogen with significant impacts on both food safety and animal/human health. This study characterized the pathogenicity and genomic features of sequence type (ST) 83 E. coli isolated from liver samples of deceased chicken in China, along with its potential for zoonotic transmission. A total of eight ST83 E. coli isolates were obtained from liver samples. Pathogenicity tests demonstrated the isolates' virulence in chickens, inducing significant pathological lesions indicative of poultry health risks. Genomic analysis indicated an alarming antimicrobial resistance gene (ARG) profile, including tet(X4) and blaNDM-5, among ST83 E. coli strains in China. The ARGs were strongly associated with mobile genetic elements (MGEs) such as IncQ1 plasmids and insertion sequences (ISs) IS903, highlighting their co-transmission potential through horizontal gene transfer. In addition, core genome phylogeny and pangenome analysis identified minimal genetic divergence between human- and animal-derived strains. This close relationship, evidenced by shared accessory genes and small SNP differences, suggests potential zoonotic transmission. Collectively, these findings indicate that ST83 E. coli is a dual-threat pathogen, being not only a virulent pathogen in poultry but also a One Health concern due to its potential for zoonotic transmission and antimicrobial resistance dissemination.},
}

Animals
*Escherichia coli/genetics/pathogenicity/drug effects/isolation & purification/classification
*Escherichia coli Infections/veterinary/microbiology
*Poultry Diseases/microbiology
Chickens/microbiology
Anti-Bacterial Agents/pharmacology
Phylogeny
Genome, Bacterial
Virulence
China
Humans
One Health
*Drug Resistance, Bacterial
Plasmids/genetics
Escherichia coli Proteins/genetics
Genomics
Microbial Sensitivity Tests

@article {pmid41369518,
year = {2025},
author = {Thomas, M and Schlüter, A and Fjodorova, J and Rückert, C and Busche, T and Niehaus, K},
title = {Genomic and proteomic characterization of a newly isolated Paenarthrobacter ilicis strain and its plasmid-mediated xanthan degradation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0169025},
doi = {10.1128/spectrum.01690-25},
pmid = {41369518},
issn = {2165-0497},
abstract = {Environmental soil samples enriched with xanthan gum led to the discovery and isolation of a novel strain of motile Paenarthrobacter ilicis in Bielefeld, Germany, which possesses a previously uncharacterized xanthan utilization gene region on its sole plasmid. This bacterium is the first member of the Paenarthrobacter genus to feature the ability to degrade xanthan. Growth experiments elucidated the optimal growth conditions with regard to pH (7.0) and temperature (28°C-30°C). The genome of Paenarthrobacter ilicis strain 6C consists of two replicons, namely a chromosome with 4,049,144 nucleotides (62.8% GC content) and a plasmid of 147,742 base pairs (61.8% GC content). This novel Paenarthrobacter ilicis strain carries 3,806 predicted coding regions, approximately half (51%) of which were verified with proteome analysis. Cultures grown with either glucose or xanthan as a carbon source were compared in relation to protein abundances at four growth stages and time points with regard to both intracellular and extracellular protein fractions. The proteome analysis (data are available via ProteomeXchange with identifier PXD063987) was undertaken using an LC-ESI-MS-MS shotgun proteomics approach, and the proteins were identified and quantified via label-free quantification using MaxQuant 2.6.6. This proteomics investigation exposed significant differences in protein abundances with regard to time and condition. Among the most highly enriched proteins seen when feeding exclusively on xanthan as a carbon source were enzymes encoded on a xanthan degradation plasmid (pPANIL_6C) with a xanthan utilization region coding for the PL8 xanthan lyase, GH38-, GH3-, GH9-family proteins, and several sugar transporters. These proteins constitute key components of a prospective xanthan degradation pathway.IMPORTANCEA novel Paenarthrobacter isolate was sequenced and characterized by proteome analysis to provide the first clear look at a novel genus in the realm of xanthan-degrading microorganisms. This research provides additional groundwork for the ongoing characterization of Paenarthrobacter, as well as widening the understanding of xanthan-degrading microorganisms. For the first time, a xanthan degradation region was identified on a plasmid 1 kb directly downstream from a mobilization gene (mobF), posing the question of whether this metabolic capacity can be shared through horizontal gene transfer. Overall, this research expands the current knowledge base regarding Paenarthrobacter biology, as well as microbial xanthan degradation and utilization.},
}

@article {pmid41369271,
year = {2025},
author = {Fraga-Pampín, S and Osorio, CR and Vences, A},
title = {Replicon Family of Vibrionaceae Plasmids as a Reservoir of Antimicrobial and Phage Resistance Genes in Marine Ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf274},
pmid = {41369271},
issn = {1751-7370},
abstract = {Plasmids are mobile genetic elements that drive horizontal gene transfer among bacteria, influencing microbial community composition and functional traits in marine ecosystems. However, many marine plasmids remain unclassified due to unknown replication mechanisms. Here, we describe VBR1, a novel plasmid replicon family, widespread among species of the family Vibrionaceae. The minimal VBR1 replicon comprises a 570-bp AT-rich origin of replication (oriV) and two genes, vrp1AB, sufficient for autonomous replication in Escherichia coli and Photobacterium damselae. A comprehensive GenBank search revealed 158 previously untyped plasmids from Vibrionaceae species worldwide harboring this replicon, including relevant pathogens for animals and humans as well as environmental species. VBR1 plasmids share a syntenic set of backbone genes, are predominantly conjugative, and frequently encode antimicrobial resistance (AMR) genes, conferring resistance to multiple antibiotic classes. Most VBR1 plasmids also carry phage defense and anti-defense systems, underscoring their ecological and evolutionary significance. AMR and defense/antidefense gene repertoires are highly variable across VBR1 plasmids, suggesting frequent gene acquisition, recombination events, and rapid replacement and diversification of resistance and defense determinants. The co-localization of AMR and phage defense systems on many VBR1 plasmids highlights their role in shaping virus-host interactions and microbial community dynamics. Our findings establish VBR1 as a widespread, clinically and ecologically relevant replicon family, providing a framework for the classification and surveillance of previously orphan plasmids, and advancing our understanding of AMR and phage resistance dynamics in marine ecosystems.},
}

@article {pmid41368032,
year = {2025},
author = {Gao, W and Zhang, X and Sun, M and Han, D and Wang, J and Li, Y and Sanren, and Yu, L and Gui, F and Guo, L and Nimalaxi, and Wang, Z and Liu, K},
title = {Research of antimicrobial resistance and its associated genes distribution in Escherichia coli from diarrheic calves in the Ulagai region of China.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1685829},
pmid = {41368032},
issn = {2297-1769},
abstract = {As a conditional pathogenic bacterium, Escherichia coli is a major contributor to infect calf diarrhea. It has attracted extensive attention due to antimicrobial resistance (AMR) and pathogenicity. To elucidate the AMR profiles and resistance-related genes in E. coli isolated from calf diarrhea samples in the Ulagai region E. coli was isolated and identified from samples of calf feces using E. coli chromogenic medium, Gram staining, and 16S rRNA sequencing. The antimicrobial susceptibility was tested using the Kirby-Bauer disk diffusion method. Resistance genes were analyzed using PCR. Additionally, strains showing severe multidrug resistance were selected for whole-genome sequencing. Multidrug resistance was observed in all 50 isolated E. coli strains. They were resistant to bacitracin, and 82% were resistant to gentamicin. Strains 24, 27, 36, and 15 exhibited particularly high levels of resistance. Analysis of resistance-related genes detected over 90% resistance associated with TEM-1 and tetR and over 80% for CTXM-55, QacH, strB, and floR, sul2 was observed in 100% of the isolates. Four strains indicated genome sizes of 5,144,828 bp, 4,798,224 bp, 4,813,249 bp, and 5,450,201 bp, respectively, harboring 5, 3, 6, and 2 plasmids. Prediction of antibiotic resistance genes revealed that the isolates contained numerous resistance genes, strain 27 carried the highest number (148 in total). All strains isolated from diarrheic calves exhibited multidrug resistance and carried numerous resistance genes. Furthermore, the observation of abundant mobile genetic elements in the strains increases the risk of horizontal gene transfer of resistance genes, indicating the severity of issues faced by clinical prevention and control measures.},
}

@article {pmid41366877,
year = {2025},
author = {de Souza, HCA and Panzenhagen, P and Dos Santos, AMP and Portes, AB and Almeida, ACO and Conte Junior, CA},
title = {Understanding the Association of Plasmid Incompatibility Groups With Variable Antimicrobial Resistance Genotypes in Bacteria.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70187},
doi = {10.1002/mbo3.70187},
pmid = {41366877},
issn = {2045-8827},
support = {E26/202.227/2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Brazil/ ; E26/204.078/2022//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) Brazil/ ; 313119/2020-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Brazil-FinanceCode001./ ; },
mesh = {*Plasmids/genetics ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Genotype ; *Drug Resistance, Bacterial/genetics ; Replicon ; Whole Genome Sequencing ; },
abstract = {Plasmids play an essential role in the spread of antimicrobial resistance (AMR) by facilitating the horizontal transfer of resistance genes between bacterial environments. However, large-scale investigations into the association between plasmid incompatibility groups (Inc groups) and specific resistance profiles remain limited. In this study, we analyzed 28,047 plasmid sequences from publicly available whole-genome sequencing data sets, identifying incompatibility groups in 11,288 plasmids using in silico replicon typing. Our results revealed that the majority of plasmids harbored a single replicon, while a substantial fraction carried multiple replicons, predominantly two. We evaluated the relationship between plasmid replicon spillovers and their role in the spread of resistance genes. Our results revealed that plasmids with five replicons have a significantly higher resistance potential (60%) compared to plasmids with fewer replicons, decreasing their adaptability and propensity for cointegration, which facilitates horizontal gene transfer. Among the resistance-associated plasmids, the IncF, IncI, and IncH families were predominant and acted as effective carriers of resistance genes. Comparative analyses between resistant and non-resistant plasmids did not reveal a clear visual pattern of association between the most prevalent Inc groups and specific antimicrobial classes, indicating that such relationships are shaped by contextual factors, including selective instructions, bacterial host diversity, and distribution. These findings highlight the complexity of the spread of plasmid-mediated AMR and highlight the need for integrated genomic and epidemiological approaches to better understand the ecological and evolutionary dynamics that influence the spread of resistance genes.},
}

*Plasmids/genetics
*Bacteria/genetics/drug effects
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Genotype
*Drug Resistance, Bacterial/genetics
Replicon
Whole Genome Sequencing

@article {pmid41218129,
year = {2025},
author = {Beh, JQ and Wick, RR and Howden, BP and Connor, CH and Webb, JR},
title = {Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.},
journal = {Antimicrobial agents and chemotherapy},
volume = {69},
number = {12},
pages = {e0109725},
doi = {10.1128/aac.01097-25},
pmid = {41218129},
issn = {1098-6596},
support = {GNT1196103//National Health and Medical Research Council, Australia/ ; },
mesh = {*Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; Genome, Bacterial/genetics ; Humans ; Computational Biology ; beta-Lactamases/genetics ; Gene Transfer, Horizontal ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Plasmids are self-replicating, extrachromosomal genetic elements that serve as vehicles for antimicrobial resistance (AMR) genes. In bacteria, plasmids frequently carry critical AMR genes such as extended spectrum beta-lactamases (blaCTX-M) in gram-negative and glycopeptide resistance gene (vanA) in gram-positive species. Plasmid sequences are genetically diverse within and across taxa, with the PLSDB database recording up to 72,360 non-redundant sequences in May 2024. Horizontal transfer of plasmids continues to threaten the effectiveness of last-resort antibiotics, especially as plasmids can disseminate horizontally crossing taxonomic boundaries. Whole-genome sequencing is a powerful approach for investigating AMR plasmids, yet there are several challenges facing bioinformatic tools and databases. Here, we review those challenges and their implications for AMR plasmid research as well as summarizing key bioinformatic analyses and tools used in AMR plasmid investigations. The review highlights how genomics has revolutionized AMR plasmid studies in drug-resistant pathogens and provides insights on the current limitations and future challenges to leverage plasmid genomics in public health research.},
}

*Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing/methods
*Drug Resistance, Bacterial/genetics
Genome, Bacterial/genetics
Humans
Computational Biology
beta-Lactamases/genetics
Gene Transfer, Horizontal
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid41366207,
year = {2025},
author = {Vezina, B and Morampalli, BR and Nguyen, HA and Gomez-Simmonds, A and Peleg, AY and Macesic, N},
title = {The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66874-7},
pmid = {41366207},
issn = {2041-1723},
support = {APP1176324//Department of Health | National Health and Medical Research Council (NHMRC)/ ; APP1117940//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {Infections caused by carbapenemase-producing organisms are a global health threat. IMP carbapenemases are one of the key drivers of these infections but little is known regarding their global epidemiology. We analyse three decades of blaIMP gene spread using sequence data from 4556 genomes collected between 1996-2023. A total of 52 blaIMP variants were identified across 93 bacterial species. We reconstruct the historical emergence and variant-specific epidemiologies of blaIMP genes and showed how key variants (blaIMP-1, blaIMP-4, blaIMP-7, blaIMP-8 and blaIMP-13) achieved global endemicity, while blaIMP-26 and blaIMP-27 became regionally endemic in Southeast Asia and North America, respectively. Dissemination was driven predominantly by horizontal gene transfer facilitated by mobile genetic elements such as class 1 integrons and insertion sequences. These elements mobilised blaIMP genes into 52 distinct plasmid clusters (predominantly IncHI2A, IncN, IncL/M, and IncC), enabling broad inter-species transmission. Despite limited overall cross-source transmission, spillover primarily occurred between human and environmental reservoirs. Structural analysis revealed conserved IMP carbapenemase structure (mean lDDT 0.977) with convergent missense mutations at seven catalytically relevant sites. Our analysis provides a framework for understanding blaIMP dissemination, highlighting their emergence as an important, yet under-recognised, public health threat.},
}

@article {pmid41364990,
year = {2025},
author = {Shen, S and Shimotori, K and Tsuchiya, K and Shigeta, S and Sueyoshi, M and Matsuda, T and Shimizu, Y},
title = {Carrier-resolved metagenomics suggests the dual "filter-hub" function of a large freshwater lake toward incoming antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {1010},
number = {},
pages = {181145},
doi = {10.1016/j.scitotenv.2025.181145},
pmid = {41364990},
issn = {1879-1026},
abstract = {Rivers and wastewater-treatment plants (WWTPs) convey antibiotic resistance genes (ARGs) to lakes. Studies simultaneously profiling ARGs and their carriers and tracking their persistence in lakes remain scarce. We collected cell- and virus-size fractions from Lake Biwa, Japan, 11 in-flowing rivers, and one WWTP for shotgun metagenomic sequencing. We reconstructed 326 bacterial metagenome-assembled genomes, 7917 plasmid contigs (472 harboring conjugation genes), and 32,375 viral contigs. The chromosomes contained 1502 ARGs (predominantly fluoroquinolone and glycopeptide resistance). The plasmids encoded efflux- and target-alteration determinants spanning 25 drug classes. Only 3.6 % of the viral genomes carried ARGs, chiefly qnr and dfr. ARG class composition differed among carriers, forming a spatial mosaic unrelated to land use or livestock density. Of the ARG-carrying cells and viruses, 85-97 % were undetectable in the lake, suggesting dilution and adaptation failure. Chromosome comparison identified 1809 putative horizontal gene transfer events, 2.1 % of which bridged lake-resident and external taxa. ARG profiles differed according to carrier type. Thus, Lake Biwa might function simultaneously as a filter, removing incoming ARG-carrying cells and viral particles, and as a "silent hub," potentially integrating external ARGs into lake-resident bacteria through horizontal gene transfer. These data provide a foundation for assessing and managing antimicrobial resistance in large freshwater ecosystems.},
}

@article {pmid41364024,
year = {2025},
author = {Nandini, SS and Jagdish, S and Rana, S and Nandi, D},
title = {Involvement of Escherichia coli-encoded Lon protease and its substrates in phenotypic antibiotic resistance elicited by 4-amino-2-nitrophenol.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0160325},
doi = {10.1128/aem.01603-25},
pmid = {41364024},
issn = {1098-5336},
abstract = {UNLABELLED: In prokaryotes, the energy-dependent protein degradation is controlled, primarily, by two ATP-dependent proteases, Lon and Clp. This study investigates the roles of Escherichia coli (E. coli)-encoded Lon protease in the metabolism of 2,4-dinitrophenol (2,4-DNP), a toxic industrial compound. Enhanced conversion of yellow-colored 2,4-DNP to a reddish-brown product was observed in a strain lacking Lon protease (Δlon). This observation led us to characterize and understand the mechanisms of 2,4-DNP metabolism. UV-visible and LC-MS analyses revealed differences in the conversion products between the wild-type and Δlon. One of the substrates of Lon protease is MarA, a transcription factor, and studies with different mutants followed by trans complementation demonstrated MarA-dependent conversion. The bathochromic shift of spectral peaks suggested reduction processes and possible involvement of nitroreductase enzymes. Indeed, the expression of two genes encoding nitroreductases, nfsA and nfsB, increased with 2,4-DNP and was dependent on MarA. Importantly, the production of the reddish-brown product was lower in strains lacking nfsA or nfsB. Finally, LC-MS analysis identified one of the conversion products of 2,4-DNP to be 4-amino-2-nitrophenol (4,2-ANP). Dose studies with purified 4,2-ANP demonstrated that it did not lower the growth of E. coli (unlike 2,4-DNP) and induced phenotypic antibiotic resistance in an acrB-dependent (like 2,4-DNP) but in a marA-independent (unlike 2,4-DNP) manner. This study revealed how E. coli in the environment converts a toxic compound (2,4-DNP) into a lesser toxic compound (4,2-ANP) and helps survive in the presence of antibiotics. Overall, this study contributes to our understanding of biological responses to nitroaromatics.

IMPORTANCE: E. coli is one of the common microorganisms in feces-contaminated sewage and often interacts with several pollutants. This study identifies the roles of Lon protease and its substrate MarA in inducing nitroreductases, NfsA and NfsB, in reducing toxic 2,4-DNP to less toxic 4,2-ANP, a novel inducer of phenotypic antibiotic resistance in E. coli. This study sheds light on the roles of E. coli-encoded Lon protease upon exposure to harmful nitroaromatics. Common environmental pollutants can act as a selective pressure, favoring the survival as well as proliferation of bacteria containing antibiotic-resistant genes, which can easily be transferred to other bacteria through horizontal gene transfer. This study offers insights into mitigation methods in E. coli, a well-characterized model. It is possible that such environmental pollution strategies may be translated to other models, such as Pseudomonas, which are commonly used in bioremediation studies.},
}

@article {pmid41362948,
year = {2025},
author = {Carmona-Salido, H and Salvador-Clavell, R and Jäckel, C and Schulze, I and Satchell, KJF and Hammerl, JA and Amaro, C},
title = {Emergence, climate-driven expansion, and diversification of a European Vibrio vulnificus lineage (L4) with multi-host pathogenic potential.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2601370},
doi = {10.1080/22221751.2025.2601370},
pmid = {41362948},
issn = {2222-1751},
abstract = {Climate-driven changes are reshaping the ecology of Vibrio vulnificus in European waters. Here, we present a retrospective genomic and phenotypic analysis of pre-2018 isolates belonging to lineage 4 (L4), a phylogenetic group historically confined to the Mediterranean Sea and now detected in northern Europe. Using a lineage-specific multiplex PCR combined with whole-genome sequencing, we identified 49 clinical and environmental L4 isolates from German coastal waters. Comparative genomics revealed extensive genetic plasticity in L4, indicative of frequent recombination and horizontal gene transfer, including three MARTX toxin architectures, fourteen distinct capsular genotypes, two type VI secretion systems, and multiple prophages. Notably, nearly half of the L4 isolates encoded a previously undescribed MARTX variant (type H), apparently derived from recombination within a type C toxin and containing a novel calmodulin-dependent NADase (CdN) domain with potential functional implications for virulence. One strain also harboured the plasmid-borne genes ftbp and fpcrp, which confer resistance to fish innate immunity and the ability to cause sepsis, thereby extending the distribution of the piscis pathovar to all five V. vulnificus lineages. Functional assays showed that most L4 strains withstood the bactericidal activity of iron-overloaded human serum, consistent with a capacity to cause sepsis in susceptible individuals. Collectively, these findings redefine V. vulnificus as a multi-host climate-responsive marine pathogen and establish L4 as a newly adapted European lineage whose northward expansion exemplifies how genomic diversification and ocean warming jointly drive the evolution of high-risk marine pathogens within a One Health framework.},
}

@article {pmid41360524,
year = {2026},
author = {Chawla, K and Saxena, SS and Agre, VC and Sharma, A and Piveteau, P and Sharma, S},
title = {Prevalence and dissemination of bacterial human pathogens in agricultural environments: A food safety and health concern.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117806},
doi = {10.1016/j.foodres.2025.117806},
pmid = {41360524},
issn = {1873-7145},
mesh = {Humans ; *Agriculture ; *Food Safety ; *Foodborne Diseases/microbiology/epidemiology/prevention & control ; Animals ; Soil Microbiology ; *Bacteria/genetics/pathogenicity ; Food Microbiology ; Prevalence ; Manure/microbiology ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; },
abstract = {Human pathogens have caused several worldwide outbreaks of foodborne diseases over the years, posing a serious threat to food security and human health. While their presence in agricultural environments is increasingly recognized, the factors driving their persistence and dissemination remain insufficiently understood. This review addresses this knowledge gap by synthesizing current understanding of how human pathogens enter and survive in agroecosystems. The focus has been on major contamination routes-including soil, irrigation water, and raw animal manure-and highlight adaptive mechanisms such as horizontal gene transfer that enhance pathogen persistence. Furthermore, the role of farming practices in shaping pathogen load and the spread of antibiotic resistance genes (ARGs) in arable land has been examined. Mitigation strategies applicable at both pre- and post-harvest stages are critically evaluated, and emerging research directions are discussed. By integrating these insights, this review contributes to a deeper understanding of the ecological dynamics of human pathogens in agricultural environments, and provides future directions for developing improved control measures to ensure safer food production systems.},
}

Humans
*Agriculture
*Food Safety
*Foodborne Diseases/microbiology/epidemiology/prevention & control
Animals
Soil Microbiology
*Bacteria/genetics/pathogenicity
Food Microbiology
Prevalence
Manure/microbiology
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics

@article {pmid41359680,
year = {2025},
author = {Liu, R and Velasco-Amo, MP and Arias-Giraldo, LF and Donegan, MA and Potnis, N and Hardy, NB and Almeida, RPP and Landa, BB and De La Fuente, L},
title = {Natural competence in the bacterial pathogen Xylella fastidiosa varies across genotypes and is associated with adhesins.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013757},
doi = {10.1371/journal.ppat.1013757},
pmid = {41359680},
issn = {1553-7374},
abstract = {Natural competence is one of the mechanisms of horizontal gene transfer, an important process that contributes to host-use evolution and other types of environmental adaptation in bacteria. Recently, the plant pathogen Xylella fastidiosa has undergone expansion of its host and geographic ranges. Natural competence has been empirically documented for a few strains of X. fastidiosa, but its prevalence across genotypes and populations is largely unknown. In this study, we characterized the natural competence in vitro of 142 X. fastidiosa strains from diverse hosts and geographic origins, and revealed substantial variability among strains, particularly across subspecies. X. fastidiosa subsp. fastidiosa strains were largely naturally competent, while only 15% of studied subsp. multiplex strains showed recombination, and none of the strains classified in other subspecies were competent. While recombination rates in vitro were associated with subspecies classification, host and climatic variables from the area of isolation did not explain differences in recombination across strains. A genome-wide association study identified several genes linked to variation in natural competence, including a heretofore unknown role for xadA2, which codes for a surface afimbrial adhesin, and the already known fimbrial adhesin type IV pili genes pilY1-1 and pilY1-3. Overall, this study highlights the variability of natural competence among X. fastidiosa strains, that could have an impact on their potential for adaptation to the environment.},
}

@article {pmid41357778,
year = {2025},
author = {Miyamoto, Y and Katsuhiro, N and Okumura, K and Takase, R and Watanabe, D and Ogura, K and Hashimoto, W},
title = {A Horizontally Transferred Alginate Metabolism Gene Cluster in the Human Gut Genus Bacteroides.},
journal = {Journal of applied glycoscience},
volume = {72},
number = {4},
pages = {7204106},
pmid = {41357778},
issn = {1880-7291},
abstract = {Alginate, a heteropolysaccharide composed of α-L-guluronic acid (G) and β-D-mannuronic acid (M), comprises poly-G, poly-M, and mixed poly-MG regions. Alginate lyases, classified within the polysaccharide lyase (PL) family, degrade alginate into unsaturated saccharides via β-elimination. Due to the abundance of alginate in brown algae, various marine bacteria produce alginate lyases for its assimilation. Recently, alginate lyases have also been identified in gut bacteria such as those of the genus Bacteroides. In this study, we purified an alginate lyase from enrichment culture supernatants containing alginate, using a human fecal sample, and isolated B. xylanisolvens strain MK6803, which can grow on alginate as a sole carbon source-unlike the type strain B. xylanisolvens XB1A. Draft genome sequencing of strain MK6803 revealed an alginate-metabolizing gene cluster encoding three alginate lyases belonging to PL6_1, PL17_2, and PL38, along with a putative oxidoreductase. This gene cluster was shared with B. ovatus CP926 and B. xylanisolvens CL11T00C41, but not with the type strain XB1A. Bacteroides species lacking this gene cluster exhibited no alginate assimilation, even if they possessed genes encoding one or more of the three alginate lyases. This suggests that the presence of the putative oxidoreductase, alongside the lyases, is essential for alginate assimilation in Bacteroides species. Phylogenetic analysis indicated horizontal gene transfer within the genus Bacteroides. These findings highlight the role of alginate metabolism in the adaptation of human gut microbiota.},
}

@article {pmid41353563,
year = {2025},
author = {Huang, Y and Zhang, S and Lin, H and Liu, C and Li, Z and Yang, K and Liu, Y and Jin, L and Lu, C and Cheng, Y and Hu, C and Zhao, H and Zhang, G and Qian, Q and Fan, L and Wu, D},
title = {RIFinder reveals widespread adaptive remote introgression in grass genomes.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101658},
doi = {10.1016/j.xplc.2025.101658},
pmid = {41353563},
issn = {2590-3462},
abstract = {Genetic transfers are pervasive across both prokaryotes and eukaryotes, primarily encompassing canonical genomic introgression between species or genera, and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between phylogenetically distant species, which differs from canonical introgression and HGT in certain aspects of its temporal scale and mechanistic features, here defined as remote introgression (RI), has remained poorly explored in evolutionary genomics. In this study, we present RIFinder, a novel phylogeny-based method for RI event detection, and apply it to a comprehensive dataset of 122 grass genomes. Our analysis identifies 622 RI events originating from 543 distinct homologous genes, revealing distinct characteristics among grass subfamilies. Specifically, the subfamily Pooideae exhibits the highest number of introgressed genes while Bambusoideae contains the lowest. Comparisons among accepted genes, their donor copies and native homologs demonstrate that introgressed genes undergo post-transfer localized adaptation, with significant functional enrichment in stress-response pathways. Notably, we identify a large Triticeae-derived segment in a Chloridoideae species Cleistogenes songorica, which is potentially associated with its exceptional drought tolerance. Furthermore, we provide compelling evidence that RI has contributed to the origin and diversification of biosynthetic gene clusters of gramine, a defensive alkaloid chemical, across grass species. Collectively, our study establishes a robust method for RI detection and highlights its critical role in adaptive evolution. The Python implementation of RIFinder is publicly available at https://github.com/Ne0tea/RIFinder.},
}

@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}

*Soil Microbiology
Manure/microbiology
Fertilizers
*Soil/chemistry
Animals
Agriculture/methods
Poultry
Microbiota
Metagenomics
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal

@article {pmid41349311,
year = {2025},
author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A},
title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110820},
doi = {10.1016/j.vetmic.2025.110820},
pmid = {41349311},
issn = {1873-2542},
abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.},
}

@article {pmid41348595,
year = {2025},
author = {Jiang, L and Li, Y and Xie, B and Wang, L and Chen, S},
title = {In silico approaches for discovering microbial antiviral defense systems.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf619},
pmid = {41348595},
issn = {1477-4054},
support = {2022YFA0912200//National Key Research and Development Program of China/ ; 32125001//National Natural Science Foundation of China/ ; 32220103001//National Natural Science Foundation of China/ ; 32430006//National Natural Science Foundation of China/ ; ZDSYS20230626090759006//Shenzhen Science and Technology Program/ ; },
mesh = {*Computational Biology/methods ; *Computer Simulation ; Bacteriophages/genetics ; *Bacteria/virology/genetics ; },
abstract = {Prokaryotes possess a remarkably diverse and dynamic repertoire of antiviral defense systems, enabling them to withstand phage predation. However, their frequent horizontal gene transfer, extensive sequence diversity, modular genomic organization, and rapid evolution make purely experimental discovery challenging. Coupled with the massive influx of microbial genomes from high-throughput sequencing, computational strategies have become indispensable complementary tools that can enhance the efficiency and scope of defense systems discovery. In this review, we categorize computational approaches into four major strategies: (i) Sequence homology-based methods, which reliably annotate known defense systems through protein sequence similarity but are limited in detecting highly divergent or novel systems; (ii) Structure-guided approaches, which leverage conserved protein folds to uncover remote homologs and single-gene defense proteins, providing sensitivity beyond sequence-based identification, albeit at high computational cost; (iii) Genomic context-based strategies, which exploit gene co-localization and defense islands to uncover multi-gene defense clusters and previously uncharacterized defense modules; and (iv) Artificial intelligence-powered methods, which integrate sequence-derived embeddings with genomic context information to predict low-homology proteins and reconstruct candidate defense systems at scale, enabling discovery of novel systems beyond the reach of conventional approaches. We further discuss emerging tools and frameworks, such as the conserved gene cluster discovery tool and genomic foundation models, which hold strong potential to extend conventional approaches for identifying novel defense systems and supporting the generative design of synthetic modules. By comparing methodological principles, strengths, and limitations, this review provides a practical framework for the systematic exploration of microbial immune systems, guiding applications such as rational phage therapy, microbiome engineering, and synthetic biology.},
}

*Computational Biology/methods
*Computer Simulation
Bacteriophages/genetics
*Bacteria/virology/genetics

@article {pmid41347242,
year = {2025},
author = {Li, T and Li, J and Tang, Z and Liu, X and Yao, S and Zhu, J and Wang, W and Huo, L and Chen, S and Zhang, G and Liu, Z},
title = {Genomic evolution of enteric pathogens: mechanisms of pathogenicity and diagnostic innovations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1647437},
pmid = {41347242},
issn = {1664-302X},
abstract = {Genomic evolution serves as a pivotal driver of pathogenicity and host adaptation in intestinal pathogens. This review systematically dissects, from a phylogenetic perspective, the key genomic evolutionary mechanisms underpinning pathogenesis across five major classes of intestinal pathogens and their significance. Bacteria (e.g., Escherichia coli) acquire virulence- and antibiotic resistance-enhancing genes via horizontal gene transfer and genomic recombination, equipping them to disrupt the intestinal mucosal barrier and evade host immune defenses. Fungi (e.g., Candida albicans and Cryptococcus spp.) significantly augment their pathogenic potential through chromosomal rearrangements and dynamic expansions or losses within gene families. Parasites (e.g., Giardia lamblia) successfully evade host immune recognition and clearance through complex life cycles and stage-specific gene expression regulation. Viruses (e.g., rotaviruses and noroviruses) rapidly adapt to host cellular environments via genomic mutation and recombination, triggering acute gastroenteritis. Although prions primarily propagate via the nervous system, the pronounced cellular stress response they elicit in intestinal tissues suggests the gut may serve as a potential secondary transmission or amplification site. Collectively, these diverse evolutionary mechanisms confer unique colonization, survival, and competitive advantages upon distinct pathogen classes within the complex gut microenvironment. Employing Escherichia coli as a paradigm, systematic bioinformatic analysis of 335 key virulence factors revealed evolutionarily stable functional clusters (e.g., effector/toxin systems, 21.0%) with core contributions to pathogenicity. These conserved genomic signatures provide a robust foundation for developing novel high-precision diagnostics. For instance, CRISPR-based platforms achieve 100% clinical concordance in detecting the Shiga toxin gene (stx2), while loop-mediated isothermal amplification coupled with lateral flow assay (LAMP-LFA) enables rapid (< 40 min) and accurate detection of bla NDM - 1-mediated carbapenem resistance. The deep integration of multi-omics data (genomics, transcriptomics, proteomics, etc.) with artificial intelligence (AI) is substantially accelerating the discovery of novel biomarkers. Looking forward, innovative technologies such as real-time nanopore sequencing and nanomaterial-enhanced high-sensitivity biosensors hold promise for achieving rapid, broad-spectrum pathogen detection, thereby robustly supporting the World Health Organization (WHO)'s "One Health" strategic goals. In conclusion, the "Genomic Evolution-Biomarker Discovery-Diagnostic Development" integrated triad framework presented herein offers crucial insights and actionable pathways for advancing next-generation precision diagnostics and formulating effective global infection control strategies.},
}

@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}

Fermentation
*Capsicum/microbiology/virology
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/virology
*Fermented Foods/microbiology/virology
Gene Transfer, Horizontal
*Viruses/genetics/classification/isolation & purification
Bacteriophages/genetics/classification/isolation & purification
*Microbiota
Food Microbiology

@article {pmid41342568,
year = {2025},
author = {Gardiner, AT and Jin, Y and Bína, D and Joosten, M and Kaftan, D and Mujakić, I and Gardian, Z and Castro-Hartmann, P and Qian, P and Koblížek, M},
title = {Two solutions for efficient light-harvesting in phototrophic Gemmatimonadota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0109425},
doi = {10.1128/msystems.01094-25},
pmid = {41342568},
issn = {2379-5077},
abstract = {Phototrophic Gemmatimonadota represent a unique group of phototrophic bacteria that acquired a complete set of photosynthetic genes via horizontal gene transfer and later evolved independently. Gemmatimonas (Gem.) phototrophica contains photosynthetic complexes with two concentric light-harvesting antenna rings that absorb at 816 and 868 nm, allowing it to better exploit the light conditions found deeper in the water column. The closely related species Gem. groenlandica, with highly similar photosynthetic genes, harvests infrared light using a single 860 nm absorption band. The cryo-electron microscopy structure of the Gem. groenlandica photosynthetic complex reveals that the outer antenna lacks monomeric bacteriochlorophylls, resulting in a smaller optical antenna cross-section. The Gem. groenlandica spectrum is red-shifted relative to Gem. phototrophica due to the formation of a H-bond enabled by a different rotamer conformation of αTrp[31] in the outer ring. This H-bond forms with a neighboring bacteriochlorophyll and increases the intra-dimer exciton coupling, affecting the exciton localization probability within the rings and increasing exciton cooperativity between the complexes. The functional consequences of the spectral shift, caused solely by a subtle conformational change of a single residue, represent a novel mechanism in which phototrophic organisms adjust their antennae for particular light conditions and enable Gem. groenlandica to grow higher in the water column where more photons are available.IMPORTANCEThe photoheterotrophic species of the phylum Gemmatimonadota employ unique photosynthetic complexes with two concentric antenna rings around a central reaction center. In contrast to other phototrophic species, these organisms have not evolved any regulatory systems to control the expression of their photosynthetic apparatus under different light conditions. Despite the overall similarity, the complexes present in Gemmatimonas phototrophica and Gemmatimonas groenlandica have different absorption properties in the near-infrared region of the spectrum that make them more suitable for low or medium light, respectively. The main difference in absorption depends on the conformation of a single tryptophan residue that can form an H-bond with a neighboring bacteriochlorophyll. The presence or absence of this H-bond affects how the protein scaffold interacts with the bacteriochlorophylls, which in turn determines how light energy is transferred within and between the photosynthetic complexes.},
}

@article {pmid41342538,
year = {2025},
author = {Wang, X-Y and Ye, T and Ma, J-G and Ni, H-B and Xue, L-G and Zhao, Q and Guo, L and Zhang, X-X},
title = {Genomic epidemiology and plasmid characterization of antimicrobial resistance and virulence in cattle Escherichia coli from China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0325625},
doi = {10.1128/spectrum.03256-25},
pmid = {41342538},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) in Escherichia coli from livestock poses a growing public health threat, yet genomic data on cattle-derived strains in China remain limited. This study investigated AMR, virulence, and plasmid profiles of E. coli from diarrheic cattle in four provinces: Anhui (AH), Ningxia (NX), Shandong, and Shanxi (SX). Ninety-one isolates were characterized using antimicrobial susceptibility testing and whole-genome sequencing. Resistance to ampicillin (49.5%), cefotaxime (37.4%), and tetracycline (36.3%) was common, with NX showing the highest resistance rate. Twenty-one multidrug-resistant strains were identified, mainly from NX and SX. Genomic analysis revealed 53 distinct antibiotic resistance genes (ARGs), predominantly mdf(A), aph(6)-Id, and tet(A), with the highest burdens in NX and SX. Among 196 virulence genes, adherence (fim and csg) and secretion systems (espX, espR) predominated, with AH showing the greatest diversity. Plasmid profiling detected 37 replicon types, with incompatibility FIB (IncFIB) being the most abundant. A strong correlation between plasmids and ARGs was found (r = 0.626, P < 0.001), with key ARGs [blaCTX-M-55, tet(A)] located on IncI1 and IncX1 plasmids, while most virulence genes were chromosomal. Molecular typing identified 45 sequence types (STs) and 59 serotypes, with ST29 (O26:H11) unique to AH and ST1011 (O86:H51) to NX. Phylogenetic analysis revealed clustering by phylogroup, with shared STs and serotypes across regions, indicating clonal and geographic dissemination. These findings underscore the genomic diversity and dissemination risk of AMR E. coli in Chinese cattle, highlighting the need for region-specific surveillance.IMPORTANCEThe growing threat of antimicrobial resistance (AMR) in Escherichia coli from livestock raises serious concerns for both animal and public health, especially under the One Health framework. Genomic information on cattle-derived E. coli in multi-regions of China has been limited, hindering our understanding of regional AMR patterns. This study addresses that gap by analyzing isolates from diarrheic cattle across four provinces, uncovering clear geographic variation in resistance profiles, virulence traits, and plasmid content. The identification of clinically relevant resistance genes such as blaCTX-M-55 and tet(A) on plasmids indicates a high potential for horizontal gene transfer. The strong association between plasmid types and resistance gene burden highlights key targets for surveillance. These findings offer valuable insights into the molecular epidemiology of bovine E. coli and support more effective, region-specific strategies to monitor and control the spread of AMR in livestock.},
}

@article {pmid41341957,
year = {2025},
author = {Ben, H and Agarwal, H and Gurnani, B and Pradhan, AA and Khan, AA and Jain, N},
title = {Breaking the barrier: disruption of bacterial biofilms using microwave radiation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1670237},
pmid = {41341957},
issn = {2235-2988},
mesh = {*Biofilms/radiation effects/growth & development ; *Microwaves ; *Escherichia coli/radiation effects/physiology ; Microbial Viability/radiation effects ; *Disinfection/methods ; *Sterilization/methods ; Humans ; },
abstract = {Biofilms are microbial consortia encased in the extracellular matrix that pose severe threats in healthcare and environmental settings due to their resistance to antimicrobials and their role in persistent infections. These structured communities colonize medical devices (e.g., catheters, implants) and contribute to nosocomial infections. Critically, biofilm-laden medical waste acts as a reservoir for multidrug-resistant pathogens and facilitates horizontal gene transfer, perpetuating antimicrobial resistance (AMR). Improper disposal risks environmental contamination, enabling pathogens to infiltrate water systems, soil, and food chains, exacerbating public health crises. Conventional methods like chemical disinfection or UV treatment often fail to dismantle biofilms, leaving viable pathogens to disseminate. In the present work, we have established the use of microwave radiation as an effective alternative strategy for pre-disposal sterilization of Escherichia coli UTI89 biofilm on different surfaces. In our results, 15 minutes of microwave exposure significantly reduced cell viability by up to 95% and regrowth potential by up to 25% of E. coli UTI89 biofilms formed on coverslips and catheter-mimicking surfaces. Microwave-treated biofilms showed marked structural disruption and increased membrane permeabilization, as confirmed by FE-SEM and CLSM analyses. These findings highlight microwave radiation as a promising strategy for efficient pre-disposal sterilization and mitigating environmental risks associated with biofilm-derived pathogens in healthcare waste. These findings support the use of microwave exposure as an innovative approach for sterilizing medical waste and controlling biofilm-associated pathogens, aligning with current global efforts to identify sustainable alternatives for infection control. Overall, our results indicate that microwave radiation could be implemented as an innovative strategy for effective pre-disposal sterilization, reducing the risks of environmental AMR dissemination from medical waste, and curbing biofilm-derived pathogens in landfills and water systems. We firmly believe that implementing our approach in conjunction with current modalities in clinical workflows could reduce device-related infections and help alleviate the burden of AMR.},
}

*Biofilms/radiation effects/growth & development
*Microwaves
*Escherichia coli/radiation effects/physiology
Microbial Viability/radiation effects
*Disinfection/methods
*Sterilization/methods
Humans

@article {pmid41341030,
year = {2025},
author = {Cui, Z and Lin, C and Zhao, H and Wang, X},
title = {Radioprotection redefined: drug discovery at the intersection of tardigrade biology and translational pharmacology.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1713914},
pmid = {41341030},
issn = {1663-9812},
abstract = {Ionizing radiation inflicts lethal double-strand DNA breaks and oxidative stress that underlie acute radiation syndrome, secondary malignancies, and dose-limiting toxicity in radiotherapy; yet the conventional armamentarium of radioprotectants-aminothiols, broad-spectrum antioxidants, cytokines, and superoxide-dismutase mimetics-yields only modest benefit because of narrow therapeutic windows, systemic toxicity, and inadequate protection of radiosensitive tissues. In striking contrast, tardigrades (phylum Tardigrada) routinely endure exposures beyond 5 kGy by deploying a multifaceted defense repertoire that includes genome-shielding proteins such as damage suppressor (Dsup) and Tardigrade DNA-Repair protein 1 (TDR1), families of intrinsically disordered proteins that vitrify cytoplasm and scavenge radicals, antioxidant pigments acquired via horizontal gene transfer, and exceptionally efficient DNA-repair and redox networks. Viewing radioprotection through a translational pharmacology lens reveals a pipeline of emerging modalities-including recombinant or cell-penetrating proteins, mRNA therapeutics, peptidomimetics, and biomimetic nanomaterials-while also spotlighting critical hurdles of scalable bioprocessing, macromolecule stability, immunogenicity, and targeted delivery. By integrating insights from extremophile biology with cutting-edge drug-discovery platforms, tardigrade-inspired interventions promise to safeguard healthy tissue during cancer treatment, reduce casualties in nuclear accidents, and shield astronauts on deep-space missions, thereby redefining the future landscape of radioprotection and transforming an evolutionary curiosity into a potent arsenal of medical countermeasures.},
}

@article {pmid41325432,
year = {2025},
author = {Müller, NF and Wick, RR and Judd, LM and Williamson, DA and Bedford, T and Howden, BP and Duchêne, S and Ingle, DJ},
title = {Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013621},
doi = {10.1371/journal.ppat.1013621},
pmid = {41325432},
issn = {1553-7374},
mesh = {*Plasmids/genetics ; Phylogeny ; *Shigella/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; Dysentery, Bacillary/microbiology ; Bayes Theorem ; },
abstract = {The 'silent pandemic' of antimicrobial resistance (AMR) represents a significant global public health threat. AMR genes in bacteria are often carried on mobile elements, such as plasmids. The horizontal movement of plasmids allows AMR genes and resistance to key therapeutics to disseminate in a population. However, the quantification of the movement of plasmids remains challenging with existing computational approaches. Here, we introduce a novel method that allows us to reconstruct and quantify the movement of plasmids in bacterial populations over time. To do so, we model chromosomal and plasmid DNA co-evolution using a joint coalescent and plasmid transfer process in a Bayesian phylogenetic network approach. This approach reconstructs differences in the evolutionary history of plasmids and chromosomes to reconstruct instances where plasmids likely move between bacterial lineages while accounting for parameter uncertainty. We apply this new approach to a five-year dataset of Shigella, exploring the plasmid transfer rates of five different plasmids with different AMR and virulence profiles. In doing so, we reconstruct the co-evolution of the large Shigella virulence plasmid with the chromosome DNA. We quantify higher plasmid transfer rates of three small plasmids that move between lineages of Shigella sonnei. Finally, we determine the recent dissemination of a multidrug-resistant plasmid between S. sonnei and S. flexneri lineages in multiple independent events and through steady growth in prevalence since 2010. This approach has a strong potential to improve our understanding of the evolutionary dynamics of AMR-carrying plasmids as they are introduced, circulate, and are maintained in bacterial populations.},
}

*Plasmids/genetics
Phylogeny
*Shigella/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal
Evolution, Molecular
Anti-Bacterial Agents/pharmacology
Dysentery, Bacillary/microbiology
Bayes Theorem

@article {pmid41339380,
year = {2025},
author = {Mabeo, OR and van Niekerk, B and Olanrewaju, OS and Bezuidenhout, CC and Molale-Tom, LG},
title = {Comprehensive genome analysis of MDR Klebsiella pneumoniae in influent and effluent of a selected wastewater treatment plant.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43061},
pmid = {41339380},
issn = {2045-2322},
support = {UID 121615//National Research Foundation (NRF)/ ; UID 118755//National Research Foundation (NRF)/ ; Contract - 2019/2020-00224//Water Research Commission/ ; },
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/pathogenicity ; *Wastewater/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Water Purification ; Plasmids/genetics ; },
abstract = {This study investigates the antibiotic resistance profiles, virulence factors and genomic characteristics, of Klebsiella pneumoniae isolates obtained from influent and effluent samples of a wastewater treatment plant. Data generated sheds light on the dissemination and persistence of antibiotic resistance in compartments in a wastewater treatment plant (WWTP). Given the increasing concern regarding the role of wastewater in the dissemination of antibiotic-resistant bacteria, this research focused on K. pneumoniae populations using culture-based and genomics approaches. The culture-based approach showed that antibiotic resistance to β-lactam antibiotics was corroborated by PCR detection of the genes. Whole Genome Sequencing (WGS) analysis revealed a diverse array of Antibiotic-Resistant Genes (ARGs), including those encoding extended-spectrum β-lactamases (ESBLs) and resistance to other clinically relevant ˙antibiotics. Plasmid analysis unveiled various replicon types indicative of horizontal gene transfer mechanisms. Moreover, the identification of virulence genes implicated in adhesion, biofilm formation, and iron acquisition underscores the pathogenic potential of K. pneumoniae isolates in wastewater. In addition, the genomics comparison between K. pneumoniae strains from the influent and effluent of the WWTPs ecosystem reveal that "core" genome is shared. However, unique genomic clusters in the environmental strains suggests niche-specific adaptations, shedding light on the genomic plasticity of K. pneumoniae in response to environmental cues. This may have implications for antibiotic resistance dissemination and ecological interactions within wastewater ecosystems. Data presented here highlights the urgent need for enhanced surveillance and management strategies to mitigate the spread of antibiotic resistance through wastewater treatment plants ecosystems.},
}

*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/pathogenicity
*Wastewater/microbiology
*Genome, Bacterial
*Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Water Purification
Plasmids/genetics

@article {pmid41338429,
year = {2025},
author = {Trost, K and Gennis, RB and Allen, JF and Mills, DB and Martin, WF},
title = {Oxygen reductase origin followed the great oxidation event and terminated the Lomagundi excursion.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {},
number = {},
pages = {149575},
doi = {10.1016/j.bbabio.2025.149575},
pmid = {41338429},
issn = {1879-2650},
abstract = {The history of Earth's atmospheric oxygen is a cornerstone of evolutionary biology. While unequivocal evidence for an increase in atmospheric O2 marks the Great Oxidation Event (GOE) roughly 2.4 billion years ago, evidence underlying proposals for pre-GOE O2 accumulation is debated. Here we have investigated the distribution of genes for oxygen reductases, the enzymes that consume O2 in respiratory chains, across independently generated molecular timescales of prokaryotic evolution. The data indicate that cytochrome bd-oxidases, heme copper oxidases and alternative oxidases arose in the wake of the GOE ca. 2.4 billion years ago, after which the genes were subjected to abundant lateral gene transfer, a reflection of their utility in redox balance and membrane bioenergetics. The data lead us to propose a straightforward four-stage model for O2 accumulation surrounding the GOE: (i) Negligible O2 existed prior to the GOE. (ii) Cyanobacterial O2 production started at the GOE, yet was capped at 2 % [v/v] atmospheric O2, the threshold at which cyanobacterial nitrogenase is inhibited by O2. (iii) Production of 0.02 atm of O2 (2 % [v/v]) at the GOE buried roughly the entire atmospheric CO2 inventory, causing sudden enrichment of [13]C in dissolved inorganic carbon (the Lomagundi [13]C anomaly), through RuBisCO isotope discrimination, without atmospheric O2 exceeding 2 % [v/v]. (iv) High atmospheric [12]C at the end of the Lomagundi excursion marks the origin of oxygen reductases, their rapid spread via function in respiratory CO2 liberation, and the onset of equilibrium between photosynthetic O2 production and respiratory O2 consumption at 2 % atmospheric O2.},
}

@article {pmid41334652,
year = {2025},
author = {Shafer, N and Dubrule, BE and De Buck, J},
title = {Mycobacteriophage Mcgavigan Uses Noncanonical Bxb1-Like Repressor for Heterotypic Superinfection Immunity.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70133},
doi = {10.1002/jobm.70133},
pmid = {41334652},
issn = {1521-4028},
support = {//This study was supported by a grant from Agriculture Funding Consortium (2024F2352R), supported by Research Driven Agricultural Research (RDAR), Sustainable Canadian Agricultural Partnership (SCAP) and Alberta Milk./ ; },
abstract = {Mycobacteriophage Mcgavigan could be a promising candidate for use as a preventative agent against infections with Mycobacterium avium subsp. paratuberculosis. Bioinformatic analysis of the Mcgavigan genome revealed the presence of an operon containing a "Bxb1-like" repressor. The operon may have been acquired by the phage through horizontal gene transfer with a Bxb1-like mycobacteriophage in its evolutionary past. We sought to investigate the function of the acquired repressor as a potential regulator of lysogeny or as a source of heterotypic superinfection immunity. Recombineering with CRISPR counter-selection was employed to achieve a clean deletion of the Bxb1-like repressor from Mcgavigan's genome. Integrase was also deleted as a means of creating a lytic-only phage for comparison purposes and the elimination of lysogeny with this edit was confirmed. To test phenotypic changes which resulted from these deletions, several parameters such as burst size, latency period, and killing efficiency were measured for each knockout mutant and lysogeny was tested. The integrase deletion mutant had complete lysogeny abolishment and performed similarly to wild-type phage on all measured parameters. The deletion of the Bxb1-like repressor did not affect the lysogenic capability of the phage. Whereas Mcgavigan lysogens are typically immune to superinfection from Terelak, a mycobacteriophage related to Bxb1, lysogens created from Mcgavigan with the Bxb1-like repressor deletion were completely resensitized to heterotypic superinfection by Terelak. This suggested that this repressor was acquired by Mcgavigan through horizontal gene transfer for the purposes of superinfection immunity against cluster A1 mycobacteriophages and was not used for maintenance of lysogeny.},
}

@article {pmid41334162,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Abalkhail, A},
title = {Antimicrobial resistance at a turning point: microbial drivers, one health, and global futures.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698809},
pmid = {41334162},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a major health threat of the 21st century, undermining the effectiveness of modern medical interventions and reversing decades of progress in infection control. Its drivers include microbial evolution, horizontal gene transfer, inappropriate use in human and veterinary medicine, agricultural practices, environmental reservoirs, and uneven regulation. This review integrates microbial, clinical, and environmental perspectives within a One Health framework. At the microbial level, resistance arises through mutation, gene transfer, and biofilm-associated tolerance, with soil, wastewater, and wildlife serving as conduits for spreading resistance elements. Advances in diagnostics-including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), digital PCR, and CRISPR-based assays are transforming detection and surveillance, but deployment remains uneven, particularly in low- and middle-income countries. Antimicrobial stewardship now extends beyond hospitals, supported by decision support systems, artificial intelligence (AI), and community programs; however, gaps in surveillance capacity and policy implementation continue to limit impact. One Health linkages connect agricultural use, wastewater, and wildlife exposure with human risk, embedding clinical decisions within ecological and veterinary contexts. Persistent gaps include fragmented regulation, limited involvement of microbiologists in policy development, and weak incentives for antibiotic innovation. Priority directions include biomarker-guided prescribing, CRISPR-directed antimicrobials, microbiome-sparing therapeutics, and genomics-informed surveillance that integrates clinical and environmental data. Positioning the clinical microbiology laboratory as an operational hub can align rapid diagnostics, interpretive reporting, antimicrobial stewardship, and integrated surveillance (GLASS, EARS-Net, NARMS, and wastewater/wildlife monitoring) on a common platform. Clear reporting triggers and concise case vignettes can translate laboratory results into actionable bedside decisions and policy measures across diverse resource settings, with measurable benefits for patient outcomes and public health.},
}

@article {pmid41333139,
year = {2025},
author = {Kleinbub, S and Braymer, JJ and Pfeiffer, F and Dyall-Smith, M and Spirgath, K and Alfaro-Espinoza, G and Koerdt, A},
title = {From genes to Black Rust: genomic insights into corrosive methanogens.},
journal = {FEMS microbes},
volume = {6},
number = {},
pages = {xtaf018},
pmid = {41333139},
issn = {2633-6685},
abstract = {Within the past ten years, genetic evidence has been increasing for the direct role that microbes play in microbiologically influenced corrosion (MIC), also known as biocorrosion or biodeterioration. One prominent example is the correlation between the corrosion of metal and the presence of genes encoding an extracellular [NiFe]-hydrogenase (MIC hydrogenase) in the methanogenic archaeon, Methanococcus maripaludis. In this study, DNA sequencing and bioinformatic analysis were used to classify the MIC hydrogenase as belonging to a core set of genes, the MIC core, found so far in Methanococci and Methanobacteria classes of methanogens. Genetic evidence is provided for the mobilization of the MIC core via multiple mechanisms, including a horizontal gene transfer event from Methanobacteria to Methanococci and a newly described MIC-transposon. A detailed comparison of M. maripaludis genomes further pointed to the relevance that cell wall modifications involving N-glycosylation of S-layer proteins and the MIC hydrogenase likely play in methanogen-induced MIC (Mi-MIC). Microscopic analysis of corrosive methanogens encoding the MIC core indicated that Methanobacterium-affiliated strain IM1 can form extensive biofilms on the surface of corrosion products whereas individual cells of M. maripaludis Mic1c10 were only found localized to crevices in the corrosion layer. An updated model of Mi-MIC involving two modes of action is presented, which predicts that the propensity of cells to adhere to iron surfaces directly influences the rate of corrosion due to the localization of the MIC hydrogenase at the metal-microbe interface.},
}

@article {pmid41332517,
year = {2025},
author = {Mueller, J and Krishnan, KJ and Wei, Q and Hefner, Y and Monk, JM and Verkler, H and Tibocha-Bonilla, JD and Ayala, A and Palsson, BO and Feist, AM and Niu, W},
title = {Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.17.688870},
pmid = {41332517},
issn = {2692-8205},
abstract = {Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains. We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ∼8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes such as PcaI and PcaJ revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.},
}

@article {pmid41332095,
year = {2025},
author = {Xie, M and Jiang, J and Xiong, Z and Zhang, D and Chen, H and Shen, S and Okoh, AI and Gao, M and Zheng, H and Li, R},
title = {Impacts of Environmental Pollutants on Antimicrobial Resistance Gene Transfer: A Comparative Analysis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05585},
pmid = {41332095},
issn = {1520-5851},
abstract = {Horizontal gene transfer is a major driver of antimicrobial resistance gene (ARG) dissemination in the environment. Although the influence of individual environmental pollutants on ARG transfer has been widely studied, comprehensive comparisons across different pollutants remain limited due to the absence of high-throughput detection methods. Herein, we developed a high-throughput screening (HTS) platform to systematically evaluate the effects of environmental pollutants on ARG transfer. We established a transfer-responsive fluorescence reporter system by genetically engineering an Escherichia coli strain as a donor, incorporating a conjugative RP4 plasmid carrying three ARGs. Following the horizontal transfer of the RP4 plasmid into the recipient bacterium, the nonfluorescent recipient will emit green fluorescence. The HTS platform provided faster, more efficient, and reproducible analysis than traditional colony-forming unit assays. Of the 136 environmental pollutants tested, only four antibiotics significantly enhanced ARG transfer, while others showed negligible effects at environmentally relevant concentrations. A mechanistic analysis revealed that these antibiotics induced asymmetric pressure, activating the type IV secretion system in donor cells, and thereby facilitating conjugation transfer. Overall, the HTS platform provides a robust and efficient method for evaluating the impact of pollutants on ARG transfer, thereby enhancing our comprehension of environmental risks and facilitating targeted regulatory interventions.},
}

@article {pmid41331974,
year = {2025},
author = {Chu, J and Chen, Y and Farhan, MHR and Guo, Y and Sui, Y and Wang, B and Yang, X and Li, Y and Cheng, G},
title = {Role of Trace Elements in Antimicrobial Resistance Dynamics.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70108},
pmid = {41331974},
issn = {1097-0290},
support = {//This study was supported by the National Key Research and Development Program of China (No. 2022YFD1800400) and the National Natural Science Foundation of China (No. 32072921)./ ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a major threat to global public health and food safety, particularly in agricultural systems where nonantibiotic agents such as metals derived from fertilizers, pesticides, and livestock waste accumulate through intensive farming practices. As trace elements, these nondegradable pollutants, including specific metals (copper, zinc), metalloids (arsenic), and nonmetallic components like nanoparticles (NPs) from agrochemicals, exert long-term selective pressure on soil and aquatic microbiomes in farmland and aquaculture environments. We reviewed how such pressures alter microbial community composition and enhance horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through conjugation, transformation, transduction, and membrane vesicle transport. Critically, sub-lethal concentrations of engineered nanoparticles (NPs), increasingly used as antimicrobial agents in agriculture, may paradoxically promote nano-resistance and co-select for AMR. By synthesizing mechanisms driving AMR spread under these stressors, this study highlights the urgency of re-evaluating agricultural pollution management strategies such as optimizing metal thresholds in irrigation water and regulating nano-agrochemicals to mitigate resistance evolution. Our analysis bridges the gap between environmental AMR drivers and sustainable agricultural practices, providing actionable insights for policymakers and stakeholders.},
}

@article {pmid41326987,
year = {2025},
author = {Siddique, N and Arafat, KY and Gilman, MAA and Rahman, MM and Das, ZC and Islam, T and Hoque, MN},
title = {Genomic insights into multidrug resistant Escherichia coli from bovine mastitis in Bangladesh.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {788},
pmid = {41326987},
issn = {1471-2180},
support = {LS20221764, duration 2023-2025//Ministry of Education (BANBEIS), Government of the People's Republic of Bangladesh/ ; },
abstract = {BACKGROUND: Mastitis poses a significant threat to dairy industry and public health due to the emergence of multidrug-resistant (MDR) Escherichia coli. This study provides a genomic characterization of two MDR E. coli strains, MBBL4 and MBBL5, from bovine mastitis in Bangladesh, highlighting their evolutionary relationships, resistome, and virulome.

METHODS: Species-level identification of MBBL4 and MBBL5 was confirmed using biochemical assays, VITEK-2 system, and 16S rRNA gene sequencing. Antimicrobial susceptibility profiling was conducted to determine their resistance patterns. Whole genome sequencing (WGS) and comprehensive genomic analysis were performed for phylogenetic, comparative genomics, mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and virulence factor genes (VFGs) analyses.

RESULTS: Both isolates exhibited extensive MDR patterns, showing resistance to ten antibiotics. Phylogenetic and ANI analyses showed that MBBL4 clustered with mastitis-associated and human bacteremia strains of E. coli, while MBBL5 was closely related to wildlife-associated strains, reflecting divergent evolutionary lineages. Pangenome analysis revealed an open pangenome structure, indicating high genetic diversity, with MBBL4 harboring 21 unique genes and MBBL5 possessing nine unique genes. Both genomes harbored numerous ARGs spanning over 11 antibiotic classes, and VFGs, predominantly associated with adherence and secretion systems, underscoring their extensive resistome, virulome, and adaptive potentials. Abundant MGEs (plasmids, prophages, insertion sequence elements and genomic islands) further underscored the role of horizontal gene transfer in driving resistance and virulence in these strains.

CONCLUSION: This study highlights the zoonotic potential and adaptive capacity of MDR E. coli from bovine mastitis in Bangladesh driven by resistome, virulome, and mobile genetic elements. These findings highlight the urgent need for One Health-based genomic surveillance to mitigate MDR E. coli transmission from dairy farms to humans and the environment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04514-2.},
}

@article {pmid41327428,
year = {2025},
author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I},
title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02238-z},
pmid = {41327428},
issn = {2049-2618},
support = {ISF 1947/19//Israel Science Foundation/ ; ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; },
abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.

RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.

CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.},
}

@article {pmid41325976,
year = {2025},
author = {Kim, JS and Jin, YH and Park, SY and Jeong, HW and Kim, J and Park, SH and Kim, CK and Yoo, Y and Yoon, YK and Lee, JI and Jung, J and Park, JS},
title = {Clonal diversity and plasmid-mediated emergence of NDM-1-producing Raoultella ornithinolytica in clinical isolates.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.11.018},
pmid = {41325976},
issn = {2213-7173},
abstract = {OBJECTIVES: Raoultella ornithinolytica is recognized as an emerging opportunistic pathogen, with sporadic reports of multidrug resistance. However, comprehensive analyses of carbapenem-resistant isolates remain limited. This study investigated the molecular features and plasmid-mediated transmission of blaNDM-1 among clonally distinct clinical isolates of R. ornithinolytica in Seoul, South Korea.

METHODS: All 13 carbapenem-resistant R. ornithinolytica isolates referred to the central reference laboratory in Seoul from seven hospitals between 2018 and 2020 were analyzed. Isolates were characterized using antimicrobial susceptibility testing, resistance gene detection, plasmid replicon typing, pulsed-field gel electrophoresis, conjugation assays, and whole-genome sequencing.

RESULTS: Among the 13 isolates, 10 harbored blaNDM-1, seven of which carried the gene on IncX3 plasmids. Despite clonal diversity, six of the 13 isolates shared nearly identical transferable IncX3 plasmids of approximately 45 kb, indicating horizontal plasmid dissemination among non-clonal strains. A novel blaNDM-1 configuration, IS3000-∆ISAba125-IS1A-blaNDM-1-bleMBL-trpF, was found in both R. ornithinolytica and Enterobacter cloacae from a single hospital, including two patients with co-infection. These findings highlighting the key role of IncX3 plasmids in rapid dissemination of blaNDM-1 across species boundaries.

CONCLUSIONS: This study demonstrates the contribution of IncX3 plasmids to the intra- and interspecies spread of blaNDM-1, underscoring the need for enhanced genomic surveillance of emerging pathogens such as R. ornithinolytica to limit carbapenem resistance transmission in clinical settings.},
}

@article {pmid41324333,
year = {2025},
author = {Sun, H and Chang, W and Xiong, PC and Zhou, ZJ and Tang, Q and Yu, HQ},
title = {Unveiling the Impact of Extracellular Polymeric Substances (EPS) on the Conjugative Transfer of Antibiotic Resistance Genes (ARGs).},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11421},
pmid = {41324333},
issn = {1520-5851},
abstract = {The spread of antibiotic resistance genes (ARGs) via horizontal gene transfer (HGT) in wastewater treatment processes presents a critical One-Health challenge. While extracellular polymeric substances (EPS) are known to envelop microbial cells and mediate intercellular interactions, their role in conjugation, the predominant HGT mode, remains unclear. Herein, we developed an in vivo framework to investigate the impacts of EPS on conjugation. Simulating the generation of antibiotic-resistant Pseudomonas aeruginosa, a critical ESKAPE pathogen, we found that EPS significantly shaped conjugative behaviors with their depletion consistently reducing conjugation occurrences. Mechanistic investigations revealed that while EPS removal increased the cell membrane permeability, community-level reactive oxygen species (ROS), and virulence gene expression, it also led to decreased intracellular energy production and diminished transcription of key conjugation components. Furthermore, EPS depletion compromised the physical integrity of microbial community structures such as biofilms, weakened cell-to-cell contact, and reduced biomass of microbes involved in conjugation. These factors collectively determine the fate of conjugation events. To further validate the regulatory role of EPS, we engineered a CRISPR-ddCas12a system to repress EPS biosynthesis, significantly suppressing the conjugation of ARGs. This work provides critical insights into conjugation mechanisms and underscores the potential of targeting EPS to limit conjugation in wastewater treatment.},
}

@article {pmid41321254,
year = {2025},
author = {Stevens, MJA and Buvoli, GN and Kelbert, L and Cernela, N and Stephan, R},
title = {Campylobacter Species Isolated From Wild Birds in Switzerland and Comparison to Isolates From Food and Human Origin.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70176},
doi = {10.1002/mbo3.70176},
pmid = {41321254},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Animals ; Switzerland/epidemiology ; *Birds/microbiology ; Humans ; *Animals, Wild/microbiology ; *Campylobacter Infections/microbiology/veterinary/epidemiology ; *Campylobacter/isolation & purification/genetics/classification/drug effects ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Genome, Bacterial ; *Food Microbiology ; Gene Transfer, Horizontal ; Plasmids/genetics/analysis ; beta-Lactamases/genetics ; Campylobacter jejuni/isolation & purification/genetics/drug effects ; *Bird Diseases/microbiology/epidemiology ; Prevalence ; Microbial Sensitivity Tests ; },
abstract = {Campylobacter species, a major cause of gastroenteritis, have been frequently isolated from wild birds. Here we determined the prevalence of Campylobacter in wild birds from Switzerland. Campylobacter isolates were then further characterized by whole genome sequencing. A total of 154 samples from 27 different wild bird species were analyzed and Campylobacter was detected in 23 samples (14.9%). Twenty-one isolates were identified as C. jejuni, one as C. coli and one isolate likely belongs to a novel species. Whole genome analyses revealed that the strains were diverse, belonging to 17 different sequence types. Antimicrobial resistances of the C. jejuni strains included class D ß-lactamase blaOXA genes in all isolates, T86I mutations in GyrA conferring resistance to quinolones in 7 isolates, and tet(O) in 3 isolates. A comparison to 787 Campylobacter from various sources in Switzerland showed that strains spread between humans, poultry and wild birds. Moreover, plasmid analyses and genome comparison provided a strong indication of horizontal gene transfer between Campylobacter strains. Our results strongly support a One-Health approach that includes wild animals to understand and control epidemiology of Campylobacter.},
}

Animals
Switzerland/epidemiology
*Birds/microbiology
Humans
*Animals, Wild/microbiology
*Campylobacter Infections/microbiology/veterinary/epidemiology
*Campylobacter/isolation & purification/genetics/classification/drug effects
Whole Genome Sequencing
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial
Genome, Bacterial
*Food Microbiology
Gene Transfer, Horizontal
Plasmids/genetics/analysis
beta-Lactamases/genetics
Campylobacter jejuni/isolation & purification/genetics/drug effects
*Bird Diseases/microbiology/epidemiology
Prevalence
Microbial Sensitivity Tests

@article {pmid41319644,
year = {2025},
author = {Liu, Y and He, R and Feng, M and Yuan, D and Li, Z},
title = {Temperature modulation by bacterial communities may shape the MGE-mediated spread of ARGs during composting of gentamicin fermentation residue.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128138},
doi = {10.1016/j.jenvman.2025.128138},
pmid = {41319644},
issn = {1095-8630},
abstract = {This study investigated the co-composting of press-dehydrated gentamicin fermentation residue (GFR) with swine manure to address the challenges posed by antibiotic fermentation residues, such as high residual antibiotic concentrations and the spread of antibiotic resistance genes (ARGs). The results demonstrated that composting could effectively remove gentamicin residues with removal rates up to 96.89 %. However, The absolute abundance of ARGs increased by 5.8- and 6.2-fold in the GPS and GS treatments, respectively, by the end of composting, suggesting their high persistence in composting environments. Swine manure, which had higher bacterial abundance and diversity than GFR, substantially shaped the initial ARG profiles in the composting treatments. Furthermore, partial least squares path model (PLS-PM) indicated that the sharp increase of ARGs after composting was significantly influenced by horizontal gene transfer mediated by MGEs, with integrons and plasmids playing a crucial role in their dissemination. Temperature was identified as a key factor affecting ARGs abundance by regulating the abundance or activity of MGEs. These results, in conjunction with the bacteria and ARG relationship, indicate that temperature dynamics shaped by microbial community succession may be a stronger driver of ARG dissemination than the role of bacteria as passive hosts, particularly for MGE-associated genes. This study highlights the significance of future research into strategies aimed at curbing the dissemination of ARGs across diverse settings, particularly by examining the expression patterns of MGEs under varying temperature conditions.},
}

@article {pmid41317516,
year = {2025},
author = {Liu, Y and Wan, L and Li, X and Zhou, Y and Hu, R},
title = {Emergence of KL57 hypervirulent Klebsiella pneumoniae in Wuxi, China: Genomic insights into virulence plasmid evolution and blaKPC-2-bearing IncFIIK34 plasmid transmission.},
journal = {International journal of medical microbiology : IJMM},
volume = {321},
number = {},
pages = {151687},
doi = {10.1016/j.ijmm.2025.151687},
pmid = {41317516},
issn = {1618-0607},
abstract = {OBJECTIVE: KL57 Klebsiella pneumoniae (K. pneumoniae) is an emerging serotype with epidemiological characteristics and pathogenic mechanisms that remain incompletely understood. This study comprehensively analyzed the genomic features of KL57 K. pneumoniae strains isolated in Wuxi from 2016 to 2023, and investigated the global molecular epidemiology and population dynamics of KL57 K. pneumoniae.

METHODS: From January 2016 to December 2023, 17 KL57 K. pneumoniae isolates were collected from various clinical specimens at the Wuxi No.2 People's Hospital, Jiangsu Province, China. Antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and bioinformatics analysis including evaluation of virulence genes, resistance genes, and plasmid replicon types were performed on these strains. To elucidate the genetic relationships and global distribution of the KL57 K. pneumoniae, phylogenetic trees were constructed through comparative analyses of our KL57 strains alongside those obtained from public databases. Additionally, the distribution patterns of serotypes and carbapenemase genes among these strains were examined.

RESULTS: Seventeen KL57 K. pneumoniae strains were categorized into four distinct sequence types (STs), with ST412 being the most prevalent in Wuxi, and ST2846, which was identified for the first time. Analysis of virulence genes indicated KL57 K. pneumoniae isolates often express multiple virulence factors. Antimicrobial resistance profiling revealed that only one ST218 isolate contained the blaKPC-2 gene, which was located on an IncFIIK34 plasmid. Geographically, ST412, ST218, and ST592 were the main predominant epidemic sequence types of the KL57 K. pneumoniae. A global analysis indicated that KL57 carbapenem-resistant K. pneumoniae (CRKp) strains predominantly harbored the blaNDM-1, blaOXA-48, blaKPC-2, and blaOXA-181 genes. Furthermore, phylogenetic analysis demonstrated significant diversity in the sequence types of KL57 K. pneumoniae strains across continents, with notable variations even between countries.

CONCLUSION: Our study corroborates the widespread occurrence of the ST412 KL57 K. pneumoniae in China and identifies a specific strain harboring the IncFIIK34 resistance plasmid. Additionally, the KL57 CRKp strain carries a variety of carbapenemase genes, and some of these strains simultaneously harbor multiple such genes. Our findings suggest that this subtype demonstrates enhanced resistance adaptability and may facilitate the dissemination of drug resistance through horizontal gene transfer. Consequently, it is necessary to develop more targeted surveillance strategies that focus on resistance gene characteristics and prevalent subtypes.},
}

@article {pmid41316946,
year = {2025},
author = {Zhang, S and Wu, F and Zhao, H and Zhao, L and Li, D and Yang, F and Liu, L},
title = {Type IV Secretion Systems and Conjugation in Gram-Negative Pathogens.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71116},
doi = {10.1096/fj.202502286R},
pmid = {41316946},
issn = {1530-6860},
support = {252102310367//| Henan Provincial Science and Technology Research Project ()/ ; XYBSKYZZ202137//Doctoral Scientific Research Foundation of Xinxiang Medical University/ ; xskjzzd202306//College students& science and technology innovation project of Xinxiang Medical University (Key Project)/ ; },
mesh = {*Gram-Negative Bacteria/genetics/metabolism ; *Type IV Secretion Systems/metabolism/genetics ; *Conjugation, Genetic ; Humans ; Drug Resistance, Bacterial ; Acinetobacter baumannii/genetics ; Gram-Negative Bacterial Infections/microbiology ; Pseudomonas aeruginosa/genetics ; Klebsiella pneumoniae/genetics ; },
abstract = {Gram-negative pathogens such as Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa are the leading causes of hospital-acquired infections worldwide. A commonality among these pathogens is their widespread antibiotic resistance, posing a significant challenge to public health. Bacterial conjugation, as a mechanism of horizontal gene transfer, plays a crucial role in the spread of antibiotic resistance. Among these pathogens, the presence of type IV secretion systems (T4SSs) is particularly notable, as they are involved in the DNA conjugation process. In this review, we first describe the structure and conjugation process of T4SSs, aiming to introduce the current understanding of the involvement of T4SSs in the dissemination of antibiotic resistance in these four pathogens. We further attempt to address questions regarding the role of T4SSs in antibiotic resistance. We will also briefly discuss how T4SSs can be potential therapeutic targets.},
}

*Gram-Negative Bacteria/genetics/metabolism
*Type IV Secretion Systems/metabolism/genetics
*Conjugation, Genetic
Humans
Drug Resistance, Bacterial
Acinetobacter baumannii/genetics
Gram-Negative Bacterial Infections/microbiology
Pseudomonas aeruginosa/genetics
Klebsiella pneumoniae/genetics

@article {pmid41129321,
year = {2025},
author = {Sabnis, A and Figueroa, W and Santos-López, A and Bradshaw, J and Chu Yuan Kee, MJ and Chen, J and San Millán, Á and Penadés, JR},
title = {Non-conjugative plasmids limit their mobility to persist in nature.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116456},
doi = {10.1016/j.celrep.2025.116456},
pmid = {41129321},
issn = {2211-1247},
mesh = {*Plasmids/genetics ; *Staphylococcus aureus/genetics/virology ; Bacteriophages/genetics ; Gene Transfer, Horizontal ; },
abstract = {Plasmids are mobile genetic elements that disseminate beneficial genes, such as those conferring antibiotic resistance, but the evolutionary forces shaping their distribution remain unclear. This study challenges the idea that non-conjugative plasmids evolved for high-frequency spread. Using Staphylococcus aureus as a model, we found these plasmids lack key DNA sequences ("pac" or "cos" sites) essential for efficient phage-mediated transduction, despite such sequences not being costly. While S. aureus plasmids can evolve to enhance phage-mediated mobility by incorporating phage DNA, this strategy proves detrimental. In mixed populations, low plasmid transfer enables plasmids to co-exist and protect host bacteria and neighbors from threats. However, increased movement reduces plasmid diversity, eroding protective benefits and leaving populations vulnerable. Our findings indicate plasmids evolve to restrict movement, maintaining diversity and ensuring survival against threats like antibiotics and phages. This balance explains why plasmid mobility remains low in nature, despite their potential for rapid gene transfer.},
}

*Plasmids/genetics
*Staphylococcus aureus/genetics/virology
Bacteriophages/genetics
Gene Transfer, Horizontal

@article {pmid41313384,
year = {2025},
author = {Pal, R and Poddar, BJ and D Pandit, P and Purohit, HJ and Warke, R and Warke, GM},
title = {Pan-genome analysis of Morganella morganii reveals niche-specific selection of functional traits: friend or foe?.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {40},
pmid = {41313384},
issn = {1432-072X},
mesh = {*Genome, Bacterial ; *Morganella morganii/genetics/isolation & purification/drug effects/classification ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Multigene Family ; Drug Resistance, Bacterial/genetics ; Phylogeny ; Wastewater/microbiology ; Animals ; },
abstract = {Morganella morganii exemplifies a typical case of an open pangenome, where genes move intra- and interspecies via horizontal gene transfer. Through pangenome analysis, the study maps three agriculture isolates; M. morganii with strong plant growth promoting (PGP) activity, along with 78 publicly available genomes from clinical, food, wastewater, and animal sources. The analysis showed 20,860 gene clusters with only 9.99% core genes and a discriminating distribution of 75.20% cloud genes across different niches. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed 33, 36, and 38 genes related to nutrient solubilization in M. morganii isolates HM01, HM02, and HM03, respectively. Chemotaxis genes, crucial for stress response, were most abundant in HM03 (30), followed by HM01 (17) and HM02 (27). Additionally, numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites were identified. Clinical and wastewater isolates harboured a higher number of mobile genetic element (MGE) linked antimicrobial resistance (AMR) genes that confer resistance to 15 antibiotic classes. These AMR genes were predominantly plasmid-borne and found to transfer in M. morganii from clinical pathogens such as E. coli and A. baumannii. This study indicates that habitat pressure creates the scenario for selection of functional traits which enables the ecosystem specific survival of M. morganii. Together, the present investigation provides important insight into the genomic diversity and remarkable PGP potential of M. morganii strains for sustainable agriculture. The pangenome analysis proposes that detailed investigation is needed to confirm their efficacy as PGP bacteria and to distinguish them from pathogenic strains.},
}

*Genome, Bacterial
*Morganella morganii/genetics/isolation & purification/drug effects/classification
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Multigene Family
Drug Resistance, Bacterial/genetics
Phylogeny
Wastewater/microbiology
Animals

@article {pmid41313000,
year = {2025},
author = {Zhang, R and Liu, P and Bai, J and Zhu, K and Liu, Y and Roberts, AP and Pan, Y and Li, J},
title = {Phylogenetic and genomic insights into magnetosome biomineralization in magnetotactic Alphaproteobacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212125},
doi = {10.1128/aem.02121-25},
pmid = {41313000},
issn = {1098-5336},
abstract = {Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-enclosed magnetite or greigite nanocrystals (magnetosomes). How magnetosome gene clusters (MGCs) control magnetosome morphology and evolve across lineages remains central to reconstructing the history of magnetotaxis. Here, we report five uncultured MTB strains from Yuyuantan Lake (Beijing, China), all within Rhodospirillales order (Alphaproteobacteria class). Using phylogenetics, fluorescence in situ hybridization-scanning electron microscopy, and transmission electron microscopy, we show that magnetosome morphology is more strongly constrained by phylogeny than by cell morphology. Whole-genome comparisons and MGC phylogenies indicate that vertical inheritance predominates at the genus level, whereas topological incongruences reveal additional processes, notably horizontal transfer and gene duplication. In particular, the presence of a canonical mamAB operon together with a duplicated mamAB-2 cluster supports inter-genus horizontal gene transfer between Magnetospirillum and Paramagnetospirillum. These findings refine evolutionary models by showing that conserved MGC architectures provide a stable scaffold for magnetosome biomineralization while permitting diversification within the Alphaproteobacteria class.IMPORTANCEMagnetotactic bacteria (MTB) build intracellular magnetic nanoparticles (magnetosomes) that guide navigation and influence biogeochemical cycling. Yet how the underlying genes map onto ancestry and crystal shape remains unclear. Pairing quantitative crystal-morphology statistics with phylogenomic analysis for MTB from the Rhodospirillales order, we show that magnetosome traits carry a stronger phylogenetic signal than cell shape. Newly recovered uncultured strains broaden Paramagnetospirillum diversity, and a high-quality genome (YYTV-2) represents a novel species within the rarely studied Candidatus Magneticavibrio. Analyses of both the canonical mamAB operon and a duplicated mamAB-2 cluster indicate predominantly vertical inheritance, with horizontal transfer and gene duplication introducing modular variation. These results tighten genotype-mineral phenotype links, improving the interpretation of magnetofossils and MTB as indicators of environmental change.},
}

@article {pmid41312414,
year = {2025},
author = {Temesgen, AB and Shiferaw, SA},
title = {Antimicrobial Multidrug Resistance and Mechanisms of Action: An Overview.},
journal = {BioMed research international},
volume = {2025},
number = {},
pages = {8847267},
pmid = {41312414},
issn = {2314-6141},
mesh = {Humans ; *Anti-Infective Agents/therapeutic use/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics/drug effects ; *Drug Resistance, Multiple/genetics/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity/genetics ; Animals ; },
abstract = {Antimicrobial multidrug resistance is the ability of microorganisms to withstand the effects of several antimicrobial agents, presenting a major challenge to modern healthcare systems worldwide. Although considerable research has been conducted, the molecular and evolutionary mechanisms underlying resistance are still not completely understood. This review brings together current knowledge to explain how resistance originates, spreads, and persists in different pathogens. Microorganisms may show primary resistance, which arises naturally without prior exposure to drugs, or acquired resistance, which develops after contact with antimicrobial agents. Intrinsic resistance is related to structural or functional traits that are naturally present in specific species. Strains that are extensively resistant demonstrate survival against a wide range of important drugs, while clinical resistance becomes evident when standard treatments fail to control infections effectively. Pathogens employ several mechanisms, including enzymatic inactivation of drugs, modification of target sites, reduced drug uptake, and active efflux systems. Parasitic and fungal pathogens often rely on impaired drug transport and altered molecular targets, whereas viruses adopt multiple strategies to escape the activity of antiviral drugs. The appearance of highly resistant organisms such as methicillin-resistant Staphylococcus aureus reflects the growing threat of so-called superbugs. The rapid spread of resistance, driven by genetic mutations and horizontal gene transfer, highlights its ability to disseminate quickly within microbial populations. A clear understanding of these molecular processes is essential to guide the development of new therapeutic strategies, improve clinical management, and strengthen global efforts to control antimicrobial resistance.},
}

Humans
*Anti-Infective Agents/therapeutic use/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics/drug effects
*Drug Resistance, Multiple/genetics/drug effects
Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity/genetics
Animals

@article {pmid41312397,
year = {2025},
author = {Shawa, M and Kamboyi, HK and Chambaro, H and Hayashida, K and Nao, N and Chizimu, J and Nundwe, M and Zorigt, T and Kawai, N and Ogata, S and Ndebe, J and Nsofwa, M and Sinjani, M and Nasilele, SJ and Samutela, M and Simbotwe, M and Changula, K and Sawa, H and Hang'ombe, BM and Suzuki, Y and Kajihara, M and Higashi, H},
title = {Genomic characterization of cefotaxime-resistant Proteobacteria isolated from a bat-harboring cave in Zambia.},
journal = {New microbes and new infections},
volume = {68},
number = {},
pages = {101661},
pmid = {41312397},
issn = {2052-2975},
abstract = {Bats are widely recognized as reservoirs of emerging and re-emerging pathogens, and their ecological interactions with humans and livestock present important opportunities for the transmission of infectious agents and antimicrobial resistance (AMR). However, little is known about the occurrence of resistant bacteria in bat-associated environments in Zambia or their potential role in the maintenance of AMR outside clinical and agricultural settings. This study investigated the genomic characteristics of cefotaxime-resistant Proteobacteria isolated from bat fecal droppings collected at Leopards Hill Cave, an established hotspot for zoonotic pathogens. Four hundred bat fecal samples were cultured on cefotaxime-supplemented MacConkey agar, and those exhibiting bacterial growth were subjected to antimicrobial susceptibility testing and whole-genome analysis. Of the 400 samples processed, four (1 %) yielded growth, resulting in three bacterial species: Pseudomonas aeruginosa (n = 1), Enterobacter mori (n = 1), and Brucella intermedia (formerly Ochrobactrum intermedium) (n = 2). Genomic screening revealed that P. aeruginosa strain CB_234 harbored bla OXA-50, aph(3')-IIb, and catB7, which confer resistance to β-lactams, aminoglycosides, and chloramphenicol, respectively. It also possessed multiple virulence determinants involved in adherence, motility, and secretion systems that enhance host colonization and environmental persistence. Core genome phylogenetic analysis placed CB_234 within a clade exclusively composed of clinical isolates from Nigeria, Thailand, Russia, Kenya, and Ghana, indicating a shared evolutionary lineage among globally dispersed hospital-associated strains. Conversely, environmental isolates from plant and aquatic sources, along with a dog-associated isolate, were phylogenetically distant, highlighting the distinct evolutionary origins. The E. mori isolate carried bla ACT and qnrE resistance genes and plasmid replicons, suggesting potential mobility of resistance traits through horizontal gene transfer. In contrast, the two B. intermedia isolates did not harbor any known AMR genes or plasmid replicons. However, this species is increasingly recognized as an opportunistic pathogen. The detection of AMR-associated bacterial species in a natural bat habitat supports the evidence of resistance determinants circulating in wildlife environments in Zambia. Given that bats are unlikely to encounter clinical antibiotics directly, the persistence of such genes in their environment suggests that natural ecosystems may play an underappreciated role in maintaining AMR reservoirs independent of direct antimicrobial pressure. These findings underscore the importance of incorporating wildlife and environmental niches into national and global AMR surveillance frameworks under a One Health approach to better understand the ecological dimensions of AMR emergence and dissemination.},
}

@article {pmid41309349,
year = {2025},
author = {Yount, TA and Shukla, N and Chang, YW and St Geme, JW},
title = {PilY proteins: bimodular drivers of type IV pilus versatility.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.016},
pmid = {41309349},
issn = {1878-4380},
abstract = {Type IV pili (T4P) are dynamic surface fibers that mediate diverse bacterial activities, including adhesion, twitching motility, horizontal gene transfer, biofilm formation, and virulence. The PilY family of T4P-associated proteins are found across a wide range of bacterial species and are critical for key T4P functions. PilY proteins are characterized by a shared domain architecture which consists of a variable N-terminal region that mediates adhesion and a conserved C-terminal beta-propeller domain that facilitates pilus biogenesis. Given their surface exposure and roles in virulence, PilY family proteins represent an attractive target for novel therapeutic interventions, including small-molecule antivirulence therapies against pathogenic bacteria and potential as vaccine antigens. This review synthesizes our current understanding of PilY structure, localization, function, and evolutionary relationships across T4P systems.},
}

@article {pmid41308287,
year = {2025},
author = {Díaz-Martínez, C and Bolívar, A and Pérez-Rodríguez, F},
title = {Influence of product type and ripening time on the antibiotic resistance profile of lactic acid bacteria isolated from Spanish fermented pork products.},
journal = {Meat science},
volume = {232},
number = {},
pages = {109998},
doi = {10.1016/j.meatsci.2025.109998},
pmid = {41308287},
issn = {1873-4138},
abstract = {Antibiotic resistance (AR) poses a significant public health threat, particularly in the food chain where lactic acid bacteria (LAB) may act as reservoirs for resistance genes. This study aimed to evaluate the AR profiles of LAB isolated from Spanish fermented pork products, focusing on the effects of product type and ripening time on the AR patterns. A total of 150 samples of various fermented pork products were collected and analyzed for LAB isolates. Antibiotic susceptibility testing was conducted using the Kirby-Bauer method, revealing that most isolates exhibited resistance to multiple antibiotics, with enterococci showing higher resistance levels, particularly to cefotaxime, tetracycline, and erythromycin. Notably, factors such as product type and ripening duration influenced resistance profiles, with long-ripened products demonstrating higher resistance to tetracycline and erythromycin, while short-ripened products showed increased resistance to vancomycin and ciprofloxacin. The findings suggest that Spanish fermented pork products could serve as potential reservoirs of multidrug-resistant LAB, underscoring the importance of continued surveillance of AR dynamics in food products to better understand any potential implications for human health.},
}

@article {pmid41308173,
year = {2025},
author = {Vijayanathan, M and Faryad, A and Abeywickrama, TD and Christensen, JM and Jakobsen Neilson, EH},
title = {The auxin gatekeepers: Evolution and diversification of the YUCCA family.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {4},
pages = {e70563},
doi = {10.1111/tpj.70563},
pmid = {41308173},
issn = {1365-313X},
support = {0054890//Novo Nordisk Fonden/ ; 101110417//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant/ ; 1051-00083B//Danmarks Frie Forskningsfond/ ; 1131-0002B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Indoleacetic Acids/metabolism ; Phylogeny ; Evolution, Molecular ; *Plant Proteins/genetics/metabolism ; *Plant Growth Regulators/metabolism ; *Yucca/genetics/metabolism ; Multigene Family ; Gene Expression Regulation, Plant ; },
abstract = {The critically important YUCCA (YUC) gene family is highly conserved and specific to the plant kingdom, primarily responsible for the final and rate-limiting step for indole-3-acetic acid (IAA) biosynthesis. IAA is an essential phytohormone, involved in virtually all aspects of plant growth and development. In addition, IAA is involved in fine-tuning plant responses to biotic and abiotic interactions and stresses. While the YUC gene family has significantly expanded throughout the plant kingdom, a detailed analysis of the evolutionary patterns driving this diversification has not been performed. Here, we present a comprehensive phylogenetic analysis of the YUC family, combining YUCs from species representing key evolutionary plant lineages. The evolutionary history of YUCs is complex and suggests multiple recruitment events via horizontal gene transfer from bacteria. We identify and hierarchically classify the YUC family into an early diverging grade, five distinct classes and 41 subclasses. Angiosperm YUC diversity and expansion are explained in the context of protein sequence conservation, as well as spatial and gene expression patterns. The presented YUC gene landscape offers new perspectives on the distribution and evolutionary trends of this crucial family, which facilitates further YUC characterization within plant development and response to environmental change.},
}

*Indoleacetic Acids/metabolism
Phylogeny
Evolution, Molecular
*Plant Proteins/genetics/metabolism
*Plant Growth Regulators/metabolism
*Yucca/genetics/metabolism
Multigene Family
Gene Expression Regulation, Plant

@article {pmid41305496,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111474},
pmid = {41305496},
issn = {1999-4915},
support = {1736030//U.S. National Science Foundation/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; 1S10OD028725-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bradyrhizobium/virology ; *Glycine max/microbiology ; *Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity ; Host Specificity ; Symbiosis ; Phylogeny ; Genome, Viral ; },
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

*Bradyrhizobium/virology
*Glycine max/microbiology
*Bacteriophages/genetics/isolation & purification/classification/physiology/pathogenicity
Host Specificity
Symbiosis
Phylogeny
Genome, Viral

@article {pmid41305371,
year = {2025},
author = {Zhang, Q and Zwe, YH and Sano, D and Li, D},
title = {Antimicrobial Resistance Transmission of Multidrug-Resistant Bacteria in Hydroponic Farming Components.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111134},
pmid = {41305371},
issn = {2076-0817},
support = {W22W3D0001//Singapore Food Agency/ ; A-8000216-00-00 and JPJSBP120229002//JSPS-NUS Joint Research Grant/ ; },
mesh = {*Drug Resistance, Multiple, Bacterial ; *Hydroponics/methods ; Plasmids/genetics ; *Escherichia coli/drug effects/genetics ; *Salmonella/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Gene Transfer, Horizontal ; Humans ; },
abstract = {Hydroponic farming offers sustainability benefits, but its microbial safety remains a concern, particularly regarding antimicrobial resistance (AMR) transmission. This study evaluated the potential for conjugative plasmid transfer of multidrug-resistant bacteria in hydroponic systems, using Salmonella Saintpaul B23 as a donor and various Escherichia coli strains and a self-isolated Salmonella strain from a hydroponic system as recipients. The tested bacteria are human enteric bacteria and may have a chance of being introduced into hydroponic systems. The transconjugation assay was conducted in hydroponic solutions and on different hydroponic components. Results revealed that hydroponic solutions and plant substrates could support significant transconjugation (>4 log CFU transconjugants detected in per mL hydroponic solution and >4 log CFU transconjugants detected in per g plant substrates), while facility surfaces showed minimal transfer (<1 log CFU transconjugants detected on per cm[2] surface). UV irradiation reduced plasmid transfer rates significantly (p < 0.05), suggesting its potential as a mitigation strategy, though proper implementation is critical. Antibiotic residues at sub-minimum inhibitory concentrations exhibited varying effects on AMR propagation, with gentamicin and chloramphenicol unexpectedly reducing transconjugants. These findings highlight the complex dynamics of AMR transmission in hydroponics and underscore the importance of monitoring, UV application, and cautious use of recycled waste to ensure microbial safety and mitigate AMR risks in agricultural production.},
}

*Drug Resistance, Multiple, Bacterial
*Hydroponics/methods
Plasmids/genetics
*Escherichia coli/drug effects/genetics
*Salmonella/drug effects/genetics
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
*Gene Transfer, Horizontal
Humans

@article {pmid41304237,
year = {2025},
author = {Zhang, L and Wang, M and Sheng, J and Yu, L and Zhao, Y and Liao, W and Liu, Z and Yu, J and Zhang, X},
title = {Analysis of Antimicrobial Resistance and Virulence Factors in Multidrug-Resistant Streptococcus suis Serotype 2 Isolates Using Whole-Genome Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112552},
pmid = {41304237},
issn = {2076-2607},
support = {ZR2022QC118//Natural Science Foundation of Shandong Province/ ; 32202810//National Natural Science Foundation of China/ ; },
abstract = {Multidrug-resistant (MDR) Streptococcus suis (S. suis) is a zoonotic pathogen capable of infecting pigs across all age groups, leading to conditions such as meningitis, arthritis, and endocarditis. In humans, infections can result in septic arthritis, meningitis, necrotizing fasciitis, and septicemia, which may be fatal. The absence of a complete genome sequence hinders comprehensive bioinformatic studies of MDR S. suis derived from pigs. In this study, we present the whole-genome sequence of MDR S. suis serotype 2 ST01 isolated from joint fluid samples obtained from pigs. Whole-genome analysis revealed that the ST01 chromosome carries 19 antibiotic resistance genes that confer resistance to major classes of antibiotic including aminoglycosides, tetracyclines, fluoroquinolones, lincosamides, polypeptide, and nitrofurans. Additionally, it contains 15 virulence factors associated with immune modulation, bacterial adherence, and stress survival. Whole-genome analysis identified 84 horizontal gene transfer elements in ST01 (comprising 28 genomic islands, 52 transposons, and 4 prophages), alongside mutations resulting in reduced virulence (302 instances) and loss of pathogenicity (34 instances). Furthermore, 18 antibiotic targets along with 21 lethal mutations were identified as potential targets for preventing, controlling, and treating infection caused by MDR S. suis serotype 2 ST01. In vivo infection experiments demonstrated that intraperitoneal inoculation with ST01 resulted in mortality among Kunming mice, with a median lethal dose (LD50) of 5.62 × 10[9] CFU/mL. Histopathological analysis revealed varying degrees of lesions in the infected organs of the mice. This study thus provides valuable insights into strategies aimed at combating S. suis infections and their transmission within swine populations.},
}

@article {pmid41304231,
year = {2025},
author = {Fadiji, AE and Adeniji, A and Lanrewaju, AA and Adedayo, AA and Chukwuneme, CF and Nwachukwu, BC and Aderibigbe, J and Omomowo, IO},
title = {Key Challenges in Plant Microbiome Research in the Next Decade.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112546},
pmid = {41304231},
issn = {2076-2607},
abstract = {The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant-microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed.},
}

@article {pmid41304121,
year = {2025},
author = {Ramirez-Plascencia, HHF and Colima-Fausto, AG and Licona-Lasteros, KC and Díaz-Zaragoza, M and Cazarez-Navarro, G and Macias-Barragan, JG and Rodriguez-Preciado, SY},
title = {Presence of Microorganisms in the Environment: One Health Approach.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112435},
pmid = {41304121},
issn = {2076-2607},
abstract = {The One Health approach offers an integrative framework to understand infectious threats, environmental factors, antimicrobial resistance (AMR) and how their interactions affect the human-animal-environment interface. This review examines the epidemiology, transmission pathways, and mechanisms of microorganisms of public health importance (bacteria, fungi, parasites, and viruses). It highlights the interconnectedness of ecosystems, where the environment plays a central role in the dissemination of pathogens, driven by climate change, globalization, agricultural intensification, and habitat degradation. AMR is a major concern, driven by the indiscriminate use of pharmaceuticals in human, veterinary, and agricultural settings, horizontal gene transfer through mobile genetic elements, and microbial evolution. The study of different pathogens is of great importance due to their high prevalence in different ecosystems, their virulence, clinical interest, and mortality rates produced. Some of them are ESKAPE bacteria, Candida auris, Plasmodium falciparum, and emerging viruses such as SARS-CoV-2, which present complex transmission dynamics influenced by ecological and health determinants. The review also addresses the effects of climate change on the persistence and geographic spread of pathogens. Successful implementation of the One Health program requires intersectoral policies, integrated surveillance systems, prudent use of antimicrobials and investment in translational science. Coordinating these strategies is essential to limit the spread of pathogens, protect biodiversity, and save global health in the face of the growing threat of infectious diseases.},
}

@article {pmid41303648,
year = {2025},
author = {Hammerl, JA and Hertwig, S},
title = {The Gene Ail for the Attachment-Invasion Locus Protein of Yersinia enterocolitica Biotype 1A Strains Is Located on the Genomes of Novel Prophages.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211166},
pmid = {41303648},
issn = {1422-0067},
mesh = {*Yersinia enterocolitica/genetics/virology/classification/isolation & purification/pathogenicity ; *Prophages/genetics ; Phylogeny ; *Bacterial Outer Membrane Proteins/genetics ; Animals ; Genome, Bacterial ; *Virulence Factors/genetics ; *Genome, Viral ; },
abstract = {The attachment-invasion locus protein Ail of pathogenic Yersinia strains is an important virulence factor, both for invasion of eucaryotic cells and for serum resistance. In other Yersinia strains, e.g., those belonging to biotype (BT) 1A of Yersinia enterocolitica, ail has only occasionally been described. Sequence analysis of 370 BT 1A isolates in our laboratory revealed 41 (11.1%) which were ail-positive. Most of these isolates were recovered from minced meat and tonsils of wild boars, and belonged to 17 MLST allele profiles. A closer look at DNA sequences surrounding ail disclosed that the gene in most isolates is embedded in DNA regions encoding phage proteins. The genomes of four prophages belonging to four different phylogenetic clusters were determined and analyzed by in silico studies. These have sizes of 34.9 and 50.7 kb, and are closely related to each other but not to known phages. Unlike other regions of the prophages, the integrases and attachment sites of some of them diverge, leading to different integration sites in the isolates. In a fifth cluster, ail is relocated at a position on the Y. enterocolitica chromosome that is several hundred kilobases apart from those of the other clusters, but surrounded by prophage-related sequences. In addition, highly pathogenic 1B/O:8 strains contain a DNA segment which includes ail and is 65 to 94% identical to the prophage sequences determined in this study.},
}

*Yersinia enterocolitica/genetics/virology/classification/isolation & purification/pathogenicity
*Prophages/genetics
Phylogeny
*Bacterial Outer Membrane Proteins/genetics
Animals
Genome, Bacterial
*Virulence Factors/genetics
*Genome, Viral

@article {pmid41301669,
year = {2025},
author = {Mlynarcik, P and Zdarska, V and Kolar, M},
title = {Are Putative Beta-Lactamases Posing a Potential Future Threat?.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111174},
pmid = {41301669},
issn = {2079-6382},
support = {LX22NPO5103//Ministry of Education, Youth and Sports of the Czech Republic (MŠMT)/ ; IGA_LF_2025_022//Palacký University Olomouc/ ; },
abstract = {BACKGROUND: Antimicrobial resistance is a growing global health threat, with beta-lactamases playing a central role in resistance to beta-lactam antibiotics. Building on our previous survey of 2340 putative beta-lactamases, we conducted an in-depth analysis of 129 prioritized candidates (70-98.5% amino acid identity to characterized enzymes) detected in 102 bacterial genera across 13 phylogenetic classes from environmental, animal, and human sources worldwide.

METHODS: We applied a motif-centric assessment of class-defining catalytic residues, evaluated the genomic context using a heuristic Index of Proximal Mobility (IPM) derived from the two immediately adjacent open reading frames, and examined the phylogenetic placement. AI-based substrate predictions were generated at a restricted scope as exploratory evidence.

RESULTS: Candidates spanned all Ambler classes (A-D); preservation of catalytic motifs was common and consistent with potential catalytic activity. Twelve of 129 (9.3%) loci had nearby mobile-element types (e.g., insertion sequences, integrases, transposases) and scored High IPM, indicating genomic contexts compatible with horizontal gene transfer. We also observed near-identical class A enzymes across multiple genera and continents, frequently adjacent to mobilization proteins.

CONCLUSIONS: We propose a reproducible, bias-aware, early warning framework that prioritizes candidates based on motif integrity and mobility context. The framework complements existing surveillance (GLASS/EARS-Net) and aligns with a One Health approach integrating human, animal, and environmental reservoirs. Identity thresholds and IPM are used for inclusion and contextual prioritization, rather than as proof of function or mobility; AI-based predictions serve as hypothesis-generating tools. Experimental studies will be essential to confirm enzymatic activity, mobility, and clinical relevance.},
}

@article {pmid41301664,
year = {2025},
author = {Osei Duah Junior, I and Ampong, J and Danquah, CA},
title = {Mechanisms and Evolution of Antimicrobial Resistance in Ophthalmology: Surveillance, Clinical Implications, and Future Therapies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111167},
pmid = {41301664},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is a growing global health concern with profound implications for ophthalmology, where it compromises the management of ocular infections such as bacterial keratitis, conjunctivitis, endophthalmitis, and postoperative complications. Resistance in common ocular pathogens, including Staphylococcus aureus (S. aureus), Streptococcus pneumoniae (S. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), and coagulase-negative staphylococci (CoNS) emerge through genetic mutations, horizontal gene transfer, and biochemical mechanisms such as enzymatic degradation, target modification, efflux pumps, and reduced membrane permeability. Biofilm formation further complicates eradication on the ocular surface and interior. The key drivers of resistance include inappropriate or prolonged topical antibiotic use, routine prophylaxis in ocular surgery, subtherapeutic dosing, and cross-resistance with systemic antimicrobials. The rise in multidrug-resistant strains, particularly methicillin-resistant S. aureus, fluoroquinolone-resistant P. aeruginosa, and drug-resistant S. pneumoniae has been linked to delayed treatment response, increased healthcare costs, and sight-threatening outcomes. Recent advances in rapid diagnostics, molecular assays, and point-of-care testing support earlier and more precise detection of resistance, enabling timely therapeutic decisions. Promising strategies to address AMR in ophthalmology include antimicrobial stewardship, novel drug delivery platforms, and alternative approaches such as bacteriophage therapy and antimicrobial peptides. Emerging tools, including genomic surveillance, artificial intelligence (AI)-driven resistance prediction, and personalized antimicrobial regimens, further expand opportunities for innovation. Collectively, this review synthesizes current evidence on AMR in ocular disease, summarizing patterns of resistance, underlying mechanisms, and clinical consequences, while highlighting strategies for mitigation and underscoring the need for global awareness and collaboration among clinicians, researchers, and policymakers to safeguard vision.},
}

@article {pmid41301640,
year = {2025},
author = {Akhwale, JK and Mutai, IJ and Nale, JY},
title = {The Potential Roles of Prophages in the Pathogenicity of Klebsiella pneumoniae Strains from Kenya.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111145},
pmid = {41301640},
issn = {2079-6382},
abstract = {Background/Objectives: Antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in K. pneumoniae pathogenicity. Methods: Prophages were extracted from 89 Kenyan K. pneumoniae genomes. The intact prophages were examined for virulence genes carriage, and their phylogenetic relationships were established. Results: Eighty-eight (~99%) of the genomes encode at least a single prophage, and there is an average of four prophages and 2.8% contributory genomes per bacterial strain. From the 364 prophages identified, 250 (68.7%) were intact, while 58 (15.9%) and 57 (15.7%) were questionable and incomplete, respectively. Approximately, 30% of the intact prophages encode 38 virulence genes that are linked to iron uptake (8), regulation (6), adherence (5), secretion system (4), antiphagocytosis (4), autotransporter (4), immune modulation (3), invasion (2), toxin (1) and cell surface/capsule (1). Phylogenetic analyses revealed three distinct clades of the intact prophages irrespective of their hosts, sources and locations, which support the plasticity of the genomes and potential to mediate horizontal gene transfer. Conclusions: This study provides first evidence showing the diverse prophages that are encoded in K. pneumoniae from SSA with particular focus on Kenyan strains. This also shows the potential roles these prophages play in the pathogenicity and success of K. pneumoniae and could improve knowledge and complement control strategies in the region and across the globe. Further work is needed to show the expression of these genes through lysogenisation.},
}

@article {pmid41301601,
year = {2025},
author = {Rossi, F and Santonicola, S and Colavita, G},
title = {Enrichment of Antibiotic Resistance Genes on Plastic Waste in Aquatic Ecosystems, Aquatic Animals, and Fishery Products.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111106},
pmid = {41301601},
issn = {2079-6382},
abstract = {This comprehensive review compiles current knowledge about the connection between plastic waste and the selection and transmission of antibiotic resistance genes (ARGs) in aquatic ecosystems, which can result in ARG contamination of fishery products-a significant source of microplastic (MP) introduction into the food chain. Plastic debris in aquatic environments is covered by a biofilm (the plastisphere) in which antibiotic-resistant bacteria (ARB) are selected and horizontal gene transfer (HGT) of ARGs is facilitated. The types of plastic waste considered in this study for their role in ARG enrichment are mainly microplastics (MPs), and also nanoplastics (NPs) and macroplastics. Studies regarding freshwaters, seawaters, aquaculture farms, and ARG accumulation favored by MPs in aquatic animals were considered. Most studies focused on the identification of the microbiota and its correlation with ARGs in plastic biofilms, while a few evaluated the effect of MPs on ARG selection in aquatic animals. A higher abundance of ARGs in the plastisphere than in the surrounding water or natural solid substrates such as sand, rocks, and wood was repeatedly reported. Studies regarding aquatic animals showed that MPs alone, or in association with antibiotics, favored the increase in ARGs in exposed organisms, with the risk of their introduction into the food chain. Therefore, reducing plastic pollution in water bodies and aquaculture waters could mitigate the ARG threat. Further investigations focused on ARG selection in aquatic animals should be conducted to better assess health risks and increase awareness of this ARG transmission route, enabling the adoption of appropriate countermeasures.},
}