@article {pmid42938346,
year = {2026},
author = {Dos Santos, AMP and Portes, AB and Souza, HCA and Panzenhagen, P and Almeida, ACO and Ferrari, RG and Conte-Junior, CA},
title = {Tracking the Global Prevalence and Distribution of the AmpC-β-Lactamase-Carrying pESM Megaplasmid in Salmonella Minnesota.},
journal = {Genes},
volume = {17},
number = {10},
pages = {},
pmid = {42938346},
issn = {2073-4425},
support = {E-26/202.715/2026//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/205.688-2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/200.891/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 402215/2022-2//National Council for Scientific and Technological Development/ ; FinanceCode001//Brazilian Federal Agency for Support and Evaluation of Graduate Education/ ; },
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Salmonella/genetics/drug effects ; Animals ; Anti-Bacterial Agents/pharmacology ; Prevalence ; Saudi Arabia/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; Brazil/epidemiology ; },
abstract = {Background/Objectives: AmpC enzymes, encoded by the blaCMY-2 gene, confer resistance to a broad range of β-lactam antibiotics, including first-, second-, and third-generation cephalosporins, as well as β-lactam/β-lactamase inhibitor combinations. These genes can be located either on the chromosome or plasmids, with the plasmid-borne form posing a greater risk due to its potential for rapid dissemination via horizontal gene transfer. The pESM megaplasmid, identified in Salmonella Minnesota isolates, was characterized as carrying the blaCMY-2 gene, underscoring the urgent need for surveillance and control measures to address the threat of widespread resistance. Methods: In this in silico study, we analyzed the frequency and geographic distribution of pESM among publicly available S. Minnesota genomes over the last 20 years. Results: A total of 935 sequences were identified, of which 648 (69.3%) carried pESM. The countries with the highest number of positive isolates were Saudi Arabia (n = 303) and Brazil (n = 155), with a predominance of samples derived from poultry (n = 423; 65.27%). Genes involved in yersiniabactin synthesis and transport (ybtT, ybtU, ybtS, and ybtX) exhibited high proportion within the pESM-positive genomes, as did the merA gene, which is associated with mercury tolerance. Multi-locus sequence type (MLST) analysis showed that only ST548 and ST9594 carried the pESM. Forty distinct plasmid incompatibility groups were identified, with the most frequent being IncA/C2 (79.79%), followed by Col440I (74.97%), IncR (9.95%), IncI-1 (6.74%), ColpVC (8.02%), ColRNAI (5.45%), IncQ1 (4.71%), and IncFII(S) (4.28%. All pESM-positive genomes carried blaCMY-2, with high co-occurrence of sul2, tet(A), and the mer operon, indicating that putative pESM could mediate resistance to multiple antibiotics and heavy metals. Since 2015, the co-occurrence of these genes with pESM has increased, likely reflecting selection pressure and clonal expansion of successful lineages. Phylogenetic analysis revealed a recent clade primarily composed of poultry-derived isolates from Brazil and Saudi Arabia. Putative pESM is strongly associated with the IncA/C2 incompatibility group and the qnrB19 gene, reinforcing its role in disseminating antimicrobial resistance. Conclusions: These findings suggest putative pESM is central in spreading multidrug resistance and virulence traits in S. Minnesota, especially in poultry environments. The plasmid's prevalence in distinct sequence types and countries underscores its potential for horizontal transfer and global dissemination. Our results emphasize the need for enhanced surveillance of megaplasmids in foodborne pathogens and strategies to mitigate their spread.},
}

*beta-Lactamases/genetics
*Plasmids/genetics
*Bacterial Proteins/genetics
*Salmonella/genetics/drug effects
Animals
Anti-Bacterial Agents/pharmacology
Prevalence
Saudi Arabia/epidemiology
Drug Resistance, Multiple, Bacterial/genetics
Brazil/epidemiology

@article {pmid42938407,
year = {2026},
author = {Aljohani, WA},
title = {Anticipating the Next Recorded Bacterial Hosts of Plasmid-Borne Antimicrobial Resistance Genes: A Temporal Graph Analysis of Plasmid and Surveillance Data.},
journal = {Genes},
volume = {17},
number = {10},
pages = {},
pmid = {42938407},
issn = {2073-4425},
support = {QU-APC-2026//Qassim University/ ; },
mesh = {*Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Humans ; *Bacterial Infections/microbiology/genetics ; Genes, Bacterial ; },
abstract = {BACKGROUND/OBJECTIVES: Plasmid-mediated dissemination of antimicrobial resistance genes complicates the control of bacterial infections. Identifying bacterial hosts likely to harbour these genes could guide genomic surveillance before such associations enter public databases. We investigated whether existing plasmid and surveillance data could anticipate which resistance gene-host associations would next be recorded in those databases, and which genomic features inform that prediction.

METHODS: We integrated 72,556 complete plasmid records and 2,116,241 surveillance isolates, encompassing 458 resistance gene alleles, 574 replicon backbones and 222 bacterial species. A temporal graph model, MobiGraph, was trained on associations recorded before a fixed cutoff and evaluated on subsequently observed associations, using candidate hosts matched for sequencing effort and phylogenetic distance. Ranking within a candidate pool was the primary outcome; threshold-free summaries are reported as secondary.

RESULTS: The observed host ranked among the ten highest-priority candidates in 42.4% of test cases; the advantage over gradient boosting on mechanistic features was confined to the ranking metrics, the two being indistinguishable on area under the precision-recall curve. Plasmid incompatibility-group compatibility, previous gene-host associations and shared relaxase classes were prominent predictive features. Across five resistance determinants, including mcr-1, blaNDM and tet(X4), 43-62% of subsequent associations were ranked within the top ten. Among recovered events, the median interval from the prediction cutoff to first recorded observation was 22.5 months. In a separate evaluation of a fixed 500-entry watch list, 65 entries were subsequently recorded as gene-host pairs over 25 months, 13.0% against an 8.2% background rate (95% CI 10.3-16.2%); because the surveillance database does not resolve the replicon, this confirmation does not extend to the predicted backbone.

CONCLUSIONS: Existing plasmid and genomic surveillance records contain information that can help anticipate which resistance gene-host associations will next be recorded. Whether a newly recorded association reflects recent transfer or earlier under-sampling cannot be resolved from these data. These findings support prioritising bacterial hosts for targeted surveillance and experimental investigation of plasmid-mediated resistance dissemination.},
}

*Plasmids/genetics
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Phylogeny
Humans
*Bacterial Infections/microbiology/genetics
Genes, Bacterial

@article {pmid42938714,
year = {2026},
author = {Wang, X and Zhang, J and Lin, Z and Ru, P and Wang, C and Zhang, H},
title = {Sanguinarine Reduces Conjugative Transfer of mcr-1-Positive Plasmids in Escherichia coli.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938714},
issn = {2079-6382},
support = {262300422153//Natural Science Foundation of Henan Province/ ; 2026HYTP014//Henan Province Youth Talent Support Project/ ; 25A230011//The Key Research Project of Higher Education Institutions in Henan Province/ ; 2025HLTJ36//The Heluo Youth Talent Support Project/ ; },
abstract = {BACKGROUND/OBJECTIVES: IncI2 and IncX4 plasmids are important vehicles for dissemination of the mobile colistin resistance gene mcr-1. We evaluated whether sanguinarine (SA) reduces conjugative transfer of these two mcr-1-carrying plasmid types and examined biological changes accompanying the transfer phenotype.

METHODS: Conjugation was measured in Escherichia coli carrying pIncI2-mcr-1 or pIncX4-mcr-1 after exposure to 2-8 µg/mL SA. Growth-related measurements, intracellular ATP signal, glycogen content, enzyme activities, targeted energy metabolomics, RNA sequencing, reactive oxygen species (ROS), and membrane permeability were assessed, with biological profiling focused on the IncI2 system. pIncI2-mcr-1 transfer was also examined in a mouse-gut model.

RESULTS: SA caused no detectable reduction in the reported OD600-based growth curves or viable donor/recipient counts under the tested conditions. At 8 µg/mL, SA reduced IncI2-mcr-1 and IncX4-mcr-1 conjugation frequency by approximately 176-fold and 117-fold, respectively. In the IncI2 system, lower luciferase-based ATP signals, glycogen accumulation, altered GAPDH and G6PDH activities, and decreased abundance of transfer-related transcripts accompanied the reduction in transfer. Targeted LC-MS/MS independently confirmed a dose-associated decrease in ATP and identified lower pools of several glycolysis-associated metabolites. In mice, the mean IncI2 transfer-frequency estimate was 8.41 × 10[-3] in controls and 2.49 × 10[-3] with SA (n = 10 per group; p < 0.0001).

CONCLUSIONS: SA reduced transfer of the two tested mcr-1-carrying plasmids under the experimental conditions. The metabolic and transcriptional observations support an energy-associated explanatory model for the IncI2 system and highlight SA's potential as a conjugation inhibitor to curb the spread of colistin resistance.},
}

@article {pmid42938780,
year = {2026},
author = {Ennaciri, H and Regragui, A and Bengoumi, D and Rahmatallah, N and El Bahraouy, R and Sbiti, M and El Rhaffouli, MR and El Berbri, I and El Rhaffouli, H and Fassi Fihri, O},
title = {Comparative Antimicrobial Resistance Patterns in Extraintestinal Escherichia coli Isolates from Humans and Broiler Chickens in the Meknes Region, Morocco: A One Health Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938780},
issn = {2079-6382},
abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a major One Health challenge affecting both human and animal health. Comparative studies investigating resistance patterns across reservoirs remain limited in Morocco. This study compared antimicrobial resistance profiles and presumptive β-lactam resistance phenotypes of extraintestinal Escherichia coli isolates from humans and broiler chickens. Methods: A comparative cross-sectional study was conducted using 874 non-duplicate human-derived E. coli isolates and 142 broiler-derived E. coli isolates. Antimicrobial susceptibility testing was performed using the disk diffusion method according to CA-SFM/EUCAST 2024 guidelines. Resistance rates and presumptive β-lactam resistance phenotypes were compared between reservoirs. Results: Broiler isolates exhibited significantly higher resistance to amoxicillin (93.0% vs. 65.5%), ticarcillin (92.9% vs. 64.1%), amoxicillin-clavulanic acid (75.2% vs. 48.1%), fluoroquinolones, trimethoprim-sulfamethoxazole, fosfomycin, and gentamicin (all p < 0.05). In contrast, resistance to cephalosporins was significantly higher among human isolates, whereas resistance to cefoxitin and carbapenems was detected exclusively among human isolates. The presumptive IRT-like phenotype was markedly more prevalent in broiler isolates (66.9% vs. 26.9%; OR = 5.50; p < 0.001), while the presumptive AmpC and carbapenem-resistant phenotypes were identified only in human isolates. Conversely, the wild-type phenotype was significantly more frequent among human isolates (33.1% vs. 5.6%; OR = 0.12; p < 0.001). The prevalence of the presumptive ESBL phenotype was comparable between reservoirs (12.1% vs. 8.5%; p = 0.258). Conclusions: Human-derived and broiler-derived E. coli isolates exhibited distinct antimicrobial resistance patterns and β-lactam resistance profiles. Resistance levels were significantly higher among broiler isolates for most antimicrobial agents tested, whereas resistance to cephalosporins was significantly higher among human isolates, with cefoxitin and carbapenem resistance detected exclusively in the latter. Human isolates displayed a greater diversity of presumptive β-lactam resistance phenotypes, whereas broiler isolates were largely dominated by the presumptive IRT-like phenotype. The detection of isolates with a presumptive ESBL phenotype among broilers despite the absence of documented routine use of extended-spectrum cephalosporins highlights the potential contribution of horizontal gene transfer and co-selection. Further molecular and antimicrobial consumption studies are warranted to clarify the drivers of resistance dissemination within a One Health framework.},
}

@article {pmid42925030,
year = {2026},
author = {Coste, M and Breusing, C and Travis, BA and Girguis, PR},
title = {Transposable element content is associated with total genome size and host taxonomy in sulfur-oxidizing bacterial endosymbionts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114826},
doi = {10.1128/msystems.01148-26},
pmid = {42925030},
issn = {2379-5077},
abstract = {UNLABELLED: Transposable elements (TEs) are mobile genetic sequences that can disrupt, relocate, or create genes and regulatory elements, thereby contributing to genome evolution. Their potential role in shaping adaptation, including symbiotic relationships, has drawn increasing attention. Most research on TEs to date has focused on terrestrial environments, while less is known about TE function and prevalence in marine habitats. This study investigates the presence and distribution of TEs in marine chemosynthetic symbioses, specifically among the genomes of sulfur-oxidizing Gammaproteobacteria associated with animals living in a diversity of chemically reducing environments. Our data reveal that factors such as phylogenetic relationship and habitat type have no demonstrated association with TE abundance, while factors such as genome size, host family, and lifestyle are significantly correlated. Almost all vesicomyid clam symbionts lacked TEs likely because of reductive genome evolution, while mytilid symbionts had the highest TE abundance possibly due to increased rates of homologous recombination or TE proliferation related to adaptive genome streamlining. Transposase family diversity varied considerably among symbiont groups but was not associated with genome size, indicating that other factors influence transposase composition. Notably, a large fraction of transposase genes was flanked by genes involved in DNA replication and repair, membrane transport, and prokaryotic defense systems, implying a possible role in environmental or host adaptation. This study highlights the dynamic nature of TE content in symbiotic bacteria and allows for the formulation of hypotheses on TE function for the evolution of bacteria in diverse, chemically reducing environments.

IMPORTANCE: Transposable elements are key drivers of bacterial genome evolution and environmental adaptation by creating new gene functions and altering existing ones, yet they remain comparatively understudied in marine microbes. In this study, we assessed TE content and the function of flanking genes in symbiotic and free-living sulfur-oxidizing bacteria from a variety of aquatic environments. Our analyses show that genome size, bacterial lifestyle, and host association have a significant impact on TE abundance, but not necessarily transposase diversity. Transposases were often flanked by DNA replication and repair genes, membrane transporters, and prokaryotic defense systems, which likely represent transposition cargo that might be relevant for habitat adaptation. The patterns observed within these data further our understanding of the distribution and function of transposases and lay a foundation for future studies investigating the role of transposases in bacterial genome evolution.},
}

@article {pmid42925031,
year = {2026},
author = {Liu, P and Wang, Y and Roberts, AP and Meng, F and Zhang, R and Zhang, C and Zhu, K and Cao, Z and Pan, Y and Li, J},
title = {Evolutionary histories of microbial calcification-associated genes across the tree of life.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0091126},
doi = {10.1128/msystems.00911-26},
pmid = {42925031},
issn = {2379-5077},
abstract = {UNLABELLED: Biocalcification, a widespread process by which animals and algae form hard tissues and cellular structures, has played a major role in the global carbon cycle over the past 541 Ma. Extracellular or intracellular carbonates are formed by diverse bacteria, yet the genetic basis and evolutionary history of this process remain poorly resolved. Here, we present a large-scale survey of an intracellular calcification marker (calcyanin) and two calcification-associated genes with potential mineralization-promoting roles (carbonic anhydrase [CA] and urease) across the Bacteria and Archaea domains. High-sequence-coverage homologs of calcyanin are restricted to oxygenic cyanobacteria and consistent with vertical inheritance within seven families, suggesting a possible origin in a common ancestor of the Cyanobacteriia class, although some cases likely reflect horizontal gene transfer (HGT). In contrast, CA genes are widespread across all domains of life, with phylogenetic and structural analyses supporting independent origins of the α-, β-, and γ-classes, followed by extensive inter-phylum and possible inter-domain HGT events. Urease genes are distributed broadly and most likely originated in Pseudomonadota or Cyanobacteriota, and their phylogenetic placement is consistent with extensive bacterial and archaeal diversification and a possible bacterial contribution to plant and fungal ureases. Together, these findings not only reveal distinct evolutionary trajectories of microbial calcification-associated genes but also provide a genomic framework for generating hypotheses that microbial calcification may have interacted with ocean chemistry and the global carbon cycle since the Archaean.

IMPORTANCE: Microbes help regulate the global carbon cycle partly by influencing when and where carbonate minerals form on Earth's surface. However, the genes connected to microbial calcification have not been evaluated broadly across the bacterial and archaeal tree of life or in relation to early Earth history. Here, we analyze a previously experimentally validated intracellular calcification marker and two widespread enzymes that can influence carbonate chemistry under suitable conditions. Our results show that these gene systems have distinct and complex evolutionary histories, including inheritance within lineages, gene loss, duplication, transfer between distantly related microbes, and possible transfers between bacteria and eukaryotes. Compared with previous taxon- or gene-specific studies, this work provides a broader evolutionary view of how mineralization-promoting functions emerged, diversified, and spread across microbial lineages. It provides a genomic framework for studying how microbial physiology may have interacted with ocean chemistry and carbon cycling through Earth history.},
}

@article {pmid42926523,
year = {2026},
author = {Oualline, G and Pandey, S and Zhang, XB and Boucher, C and Yu, YW},
title = {Approximate local alignment via chained MEM divergence estimation for detecting horizontal gene transfer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.01.756044},
pmid = {42926523},
issn = {2692-8205},
abstract = {Local alignment tools struggle at querying against thousands of bacterial genomes, because the reference indexes are memory-intensive and base-level dynamic programming is slow. We present alamem (https://github.com/yunwilliamyu/alamem), an approximate local aligner that streams unprocessed reference databases and estimates average nucleotide identity (ANI) from Maximal-Exact-Match (MEM) chaining statistics. Alamem can query a bacterial genome against >85,000 prokaryotic genomes in under 30 seconds (with multithreading) using 4 GB of memory, making it over 16x faster and 21x more memory-efficient than existing local aligners using their default running modes. On top of alamem, we built alasight (https://github.com/graceoualline/alasight) for detecting signatures of horizontal gene transfer (HGT) by finding pairs of alamem hits to divergent genomes. Alasight achieves over an order of magnitude better sensitivity on data from real bovid microbiomes than existing mobile genetic element-detection software and provides depth and sparsity information supporting each putative HGT region.},
}

@article {pmid42927278,
year = {2026},
author = {Eba, WW},
title = {Bacterial competence and genetic diversity: Implications for the design of diagnostics and vaccines.},
journal = {Biochemistry and biophysics reports},
volume = {48},
number = {},
pages = {102838},
pmid = {42927278},
issn = {2405-5808},
abstract = {Bacterial competence and genetic diversity are key determinants of microbial evolution, directly influencing pathogen adaptability, diagnostic reliability, and vaccine effectiveness. Natural transformation, together with horizontal gene transfer and homologous recombination, enables rapid genomic remodeling, facilitating the acquisition of antimicrobial resistance, modification of diagnostic targets, and generation of antigenic variants. These processes are particularly prominent in naturally competent and highly recombining pathogens, where population structures range from clonal to panmictic, shaping responses to selective pressures such as antibiotic use and immunization. This review synthesizes current understanding of the mechanisms governing bacterial competence and their role in generating genomic diversity, with emphasis on implications for diagnostics and vaccine design. Case studies-including Streptococcus pneumoniae, Neisseria meningitidis, and Helicobacter pylori-illustrate how recombination-driven diversification contributes to serotype replacement, diagnostic escape, and variable vaccine performance. Emerging approaches, including pan-genomic target selection, high-throughput sequencing, CRISPR-based diagnostics, and next-generation vaccine platforms, offer strategies to address these challenges but remain constrained by genomic variability and limited global surveillance. We argue that integrating evolutionary dynamics into diagnostic and vaccine development is essential for sustaining effectiveness. Continuous genomic monitoring and adaptive design frameworks will be critical to anticipate and mitigate competence-driven bacterial evolution in clinical and public health settings.},
}

@article {pmid42928328,
year = {2026},
author = {Galià-Camps, C and Gracia-Sancha, C and Cárdenas, P and Xavier, JR and Riesgo, A and Taboada, S},
title = {Demosponge (Porifera) mitogenomes reflect latitudinal structuration, reveal intraspecific architecture variation, and confirm mitochondrial intron splicing.},
journal = {Biology direct},
volume = {21},
number = {1},
pages = {},
pmid = {42928328},
issn = {1745-6150},
mesh = {Animals ; *Introns ; *Genome, Mitochondrial ; *RNA Splicing ; Phylogeny ; },
abstract = {BACKGROUND: Mitochondrial markers have historically been underused in demosponge genetic studies due to their low intra- and interspecific variability. Consequently, demosponge complete mitogenomes remain largely unexplored, even though they provide maternally inherited information that complements nuclear markers. Here, we assembled the mitochondrial genomes of 28 specimens of the ground-forming demosponge Phakellia ventilabrum across its North Atlantic distribution range to characterize them and evaluate their performance compared to already published results using restriction-site-associated DNA sequencing (RADseq) data.

RESULTS: Our assemblies revealed two region-specific mitogenomes with divergent architectures and differential copy numbers. Moreover, we identified two mitochondrial introns: one in the 16S gene and another in the cox1 gene. The cox1 intron could be assigned to a group II intron, whereas the 16S intron could not be confidently assigned either to group I or group II introns. Nevertheless, BLAST results suggested horizontal gene transfer events from yeasts in both cases. The integration of RNA-seq data showed that intronic expression was significantly lower than that of exons in both the 16S and cox1 genes, confirming intron boundaries and providing strong evidence for intron splicing functionality. The genetic differentiation pattern recovered with mitochondrial markers is consistent with previous nuclear data, suggesting a differentiation between southern and northern localities. We further revealed two sympatric mitogenomic lineages in the north. Significantly, nad2 mirrored the same lineages recovered using complete mitogenomes.

CONCLUSIONS: This study demonstrates the value of mitogenomes for the robust evaluation of lineage differentiation in demosponges and provides new approaches for research on mitochondrial intron acquisition.},
}

Animals
*Introns
*Genome, Mitochondrial
*RNA Splicing
Phylogeny

@article {pmid42929525,
year = {2026},
author = {Biswas, P and Nagaraja, V and Sengupta, S},
title = {Structure, function, and evolution of topoisomerase modulatory proteins in bacteria.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0041225},
doi = {10.1128/mmbr.00412-25},
pmid = {42929525},
issn = {1098-5557},
abstract = {SUMMARYDNA topoisomerases are essential for maintaining the integrity and functionality of the genome. By homeostatically controlling the genome topology in bacteria, these enzymes influence essential cellular processes such as gene expression, replication, recombination, and chromosome segregation. Although DNA topoisomerases were initially considered to act as stand-alone enzymes, they are now being recognized as integral components of dynamic protein complexes that perform diverse functions in vivo. The discovery of several proteinaceous modulators of DNA topoisomerases has expanded the understanding of their functional versatility. These are encoded either by the bacterial chromosome or extrachromosomal elements like plasmids and bacteriophages. Chromosomally encoded modulators are engaged in fine-tuning topoisomerase activity, enabling them to carry out specialized cellular functions beyond their canonical enzymatic roles. Crucially, they prevent genomic instability that may arise from dysregulated topoisomerase activity. By altering DNA topology, modulatory proteins can influence transcriptional bursting, leading to epigenetic heterogeneity within the bacterial populations, crucial for bacterial stress adaptation. In contrast, topoisomerase interacting proteins encoded by plasmids and phages have dedicated roles in facilitating plasmid maintenance and phage propagation by suppressing host defenses and promoting horizontal gene transfer. We present a comprehensive analysis of the topoisomerase modulatory proteins discovered so far, offering insights into the mechanisms by which DNA topology and homeostasis are maintained within the intracellular environment. We project the potential of topoisomerase modulator-based drug design as a promising strategy for combating multidrug-resistant bacterial pathogens.},
}

@article {pmid42931194,
year = {2026},
author = {El-Sayed Ahmed, MAE and Elghopashy, AEI and Ragab, YM and El-Lakany, RR and Abdelrahman, D and Omar, AA and Goda, RM},
title = {Molecular Epidemiology and Conjugative Transferability of blaOXA-48/blaNDM-1 Co-Occurrence in Extensively Drug-Resistant Klebsiella pneumoniae from Egyptian Tertiary Care Hospitals.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931194},
issn = {2076-0817},
mesh = {Egypt/epidemiology ; *Klebsiella pneumoniae/genetics/drug effects/isolation & purification/enzymology ; *beta-Lactamases/genetics ; Humans ; Tertiary Care Centers ; *Klebsiella Infections/epidemiology/microbiology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Multiple, Bacterial/genetics ; Molecular Epidemiology ; Plasmids/genetics ; *Bacterial Proteins/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Carbapenems/pharmacology ; },
abstract = {Carbapenem-resistant Klebsiella pneumoniae is a major threat to global health, with increasing incidence in developing countries, including Egypt. This study determined carbapenem-resistance prevalence among clinical K. pneumoniae isolates from two Egyptian tertiary hospitals, characterized the major carbapenemase genes, and assessed the transferability of the resistance plasmids. VITEK[®] 2 and MALDI-TOF MS identified 94 non-duplicate isolates. Susceptibility was determined by Kirby-Bauer diffusion and VITEK[®] 2. MICs of imipenem, meropenem and colistin were confirmed by broth microdilution. Isolates were classified as multidrug-resistant (MDR), extensively drug-resistant (XDR), or pandrug-resistant (PDR) according to established definitions. Phenotypic (modified Hodge test [MHT], modified carbapenem inactivation method [mCIM], modified Carba NP test [mCNP]) and genotypic (PCR/BlastN) evaluation of carbapenemase production and plasmid transferability by conjugation were carried out in 18 isolates, selected to represent every carbapenemase genotype identified in the collection. All isolates were MDR, and 94.68% were carbapenem-resistant and fulfilled the criteria for XDR, remaining susceptible only to colistin and tigecycline. Carbapenemase production was confirmed phenotypically in 98.9% and genotypically in 97.9% of isolates. blaOXA-48 (94.7%) and blaNDM-1 (69.1%) predominated, with 67.0% co-carriage; blaKPC occurred in 5.3%. Conjugation transferred carbapenemase-encoding plasmids to Escherichia coli J53 from 77.8% (14/18) of donors, conferring carbapenem non-susceptibility in all transconjugants. All isolates were colistin-susceptible by broth microdilution, the reference method. The high XDR prevalence, along with the conjugative transferability of blaOXA-48/blaNDM-1, is consistent with a mobile carbapenemase-encoding plasmid reservoir in Egyptian tertiary care, highlighting the significance of carbapenemase surveillance and stewardship. Plasmid characterization and clonal typing were not performed and are required to define that reservoir fully.},
}

Egypt/epidemiology
*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/enzymology
*beta-Lactamases/genetics
Humans
Tertiary Care Centers
*Klebsiella Infections/epidemiology/microbiology
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Multiple, Bacterial/genetics
Molecular Epidemiology
Plasmids/genetics
*Bacterial Proteins/genetics
*Conjugation, Genetic
Gene Transfer, Horizontal
Carbapenems/pharmacology

@article {pmid42935396,
year = {2026},
author = {Zhu, WM and Zhang, XZ and Wang, J and Fan, ZH and Gu, JL and Xing, DF},
title = {[Research Progress on Microalgae-bacteria Symbioses Influencing the Persistence and Spread of Antibiotic Resistance Genes].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {10},
pages = {6856-6868},
doi = {10.13227/j.hjkx.202507293},
pmid = {42935396},
issn = {0250-3301},
mesh = {*Microalgae/physiology ; *Symbiosis ; *Bacteria/genetics ; Waste Disposal, Fluid/methods ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Wastewater/microbiology ; },
abstract = {The dissemination of antibiotic resistance genes （ARGs） has become a major challenge in global public health， particularly in wastewater treatment plants， which serve as critical hubs. With the widespread use of antibiotics， the spread of resistant bacteria and ARGs in the environment has accelerated， making wastewater treatment facilities a significant source of ARG dissemination. Traditional wastewater treatment technologies， such as the activated sludge process and membrane filtration， can remove some organic pollutants and microorganisms from water， but their efficiency in eliminating ARGs remains low， often accompanied by high energy consumption and the use of chemical agents that risk secondary pollution. As a result， the development of efficient， eco-friendly， and sustainable wastewater treatment technologies has become an urgent priority. The microalgae-bacteria symbiotic system， an emerging approach， exhibits immense potential for ARG removal through the synergistic interplay of microalgae and bacteria. Microalgae fix carbon dioxide via photosynthesis and absorb nutrients from water， while bacteria utilize their robust degradative abilities to effectively break down ARGs and other harmful substances. This system not only excels in removing ARGs but also meets green and sustainable standards due to its low energy demands and minimal reliance on chemical reagents. The interactions between microalgae and bacteria， including metabolic cooperation and quorum sensing mechanisms， are central to its effectiveness in ARG removal. However， practical application of the microalgae-bacteria symbiotic system faces challenges， particularly in terms of system stability， scalability， and operational costs. Furthermore， quorum sensing plays a vital role in regulating ARG dissemination and removal， with microalgae potentially enhancing ARG elimination and inhibiting their horizontal transfer by modulating bacterial quorum sensing （QS）. This review examines the application of the microalgae-bacteria symbiotic system in ARG removal， its underlying mechanisms， environmental impacts， challenges， and future research directions， offering suggestions to improve system stability and achieve large-scale implementation， while highlighting its promising prospects for widespread use in wastewater treatment.},
}

*Microalgae/physiology
*Symbiosis
*Bacteria/genetics
Waste Disposal, Fluid/methods
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
Wastewater/microbiology

@article {pmid42920753,
year = {2026},
author = {Meski, S and Mojsoska, B and Krogfelt, KA and Cruz-Paredes, C},
title = {Bridging soil resistome and clinical inference: A four-tier evidentiary framework.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117815},
pmid = {42920753},
issn = {2589-0042},
abstract = {Soils support a varied range of microbial communities and are important repositories of antimicrobial resistance genes. Sequence-based techniques, such as quantitative polymerase chain reaction and shotgun metagenomics, have substantially aided soil-resistome cataloging. Nevertheless, discovery alone does not indicate activity, transferability, exposure, or clinical relevance. This review contends that better clinical inference requires tying presence-based signals to function, mobility, and exposure routes, rather than just increasing survey volume. We offer a four-tiered evidentiary paradigm that distinguishes between detection, functional or expression-based evidence, mobile genetic element context, and exposure-linked evidence in environmental, animal, and human compartments. Because activity, mobility, and cross-compartmental similarity support several claims, layered, claim-aligned approaches are required for careful One Health interpretation.},
}

@article {pmid42920789,
year = {2026},
author = {Loveymi, H and Roomiani, L and Tadayoni, M},
title = {Antibiotic resistance genes in aquaculture: Molecular detection, environmental dynamics, and biological control strategies.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117533},
pmid = {42920789},
issn = {2589-0042},
abstract = {Antibiotic resistance in aquaculture is a major threat to sustainable fish production and global public health. This review provides a comprehensive and critical synthesis of studies on antibiotic resistance in aquaculture published between 2005 and 2025, identified through a systematic and reproducible literature search. It clarifies the molecular basis of resistance, characterizes the environmental distribution of antibiotic resistance genes (ARGs), and evaluates current and emerging control strategies in aquaculture systems. Evidence is organized into thematic domains encompassing molecular mechanisms, environmental reservoirs and drivers, diagnostic and surveillance tools, and biological alternatives to antibiotics. In parallel, vaccines, probiotics, and bacteriophage therapy show promising, context-dependent potential when embedded in multifaceted biocontrol frameworks. This review highlights priorities including protocol standardization, rapid farm-deployable diagnostics, and optimized synergistic biocontrol strategies, supported by artificial intelligence and big data analytics, to facilitate a transition from reactive treatment to preventive, system-level resistance management in aquaculture.},
}

@article {pmid42924859,
year = {2026},
author = {Mayama, PM and Xingyang, D and Saila-Ngita, D and Liping, W},
title = {Mobile Genetic Elements Driving the Spread of Antimicrobial Resistance in Streptococci.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {1},
pages = {},
pmid = {42924859},
issn = {1865-1682},
support = {32473094//National Natural Science Foundation of China/ ; 2022YFD1800400//National Key Research and Development Program of China/ ; KYLH2025013//Fundamental Research Funds for the Central Universities/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {*Streptococcus/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Humans ; Animals ; Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; *Anti-Bacterial Agents/pharmacology ; *Streptococcal Infections/microbiology/veterinary ; },
abstract = {Streptococci are adaptable bacteria that persist as commensals or pathogens under selective pressures. This adaptability is influenced by mobile genetic elements (MGEs), which mediate horizontal gene transfer (HGT) and frequently carry antimicrobial resistance (AMR) and virulence-associated genes. This review provides an overview of MGEs involved in the acquisition and dissemination of AMR across Streptococcus species, including human, animal-associated, and zoonotic streptococci. Integrative and conjugative elements (ICEs), including members of the Tn916/Tn1545 and Tn5253 families, and TnGBS-related ICEs, are among the best-characterized vehicles for the dissemination of AMR genes (ARGs) because their modular organization supports integration, excision, regulation, and conjugative transfer. Integrative mobilizable elements (IMEs) promote the dissemination of resistance by exploiting conjugative machinery supplied by compatible coresident elements. Plasmids, although less prominent than chromosomally integrated MGEs in several streptococcal species, can carry resistance determinants together with replication and mobilization functions, contributing to HGT. Insertion sequences (ISs) and transposons (Tns) contribute to genome plasticity by promoting gene mobilization, recombination, and the generation of complex resistance regions. Resistance-associated elements such as Tn917, Tn3872, Tn6002, and Tn1207.1-related structures illustrate the diversity of genetic platforms involved in macrolide and tetracycline resistance. Prophages, including Φm46.1-like elements, contribute to genome diversification and can serve as determinants of resistance transfer. Genomic islands and cis-mobilizable elements (CIMEs) expand mobilome diversity through recombination and mobilization in association with compatible ICEs. Collectively, these interconnected MGEs drive the dissemination of AMR, genome plasticity, ecological adaptation, and evolutionary diversification in streptococci. Reducing the need for antimicrobial use in livestock through improved biosecurity, vaccination, hygiene, nutrition, husbandry, disease prevention, and timely diagnosis is therefore essential to reduce selection pressure and limit the persistence and spread of resistance. These measures, integrated with genomic surveillance, antimicrobial stewardship, and One Health approaches, can help limit the circulation of resistance-associated MGEs across human, animal, and environmental interfaces.},
}

*Streptococcus/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Humans
Animals
Gene Transfer, Horizontal
*Interspersed Repetitive Sequences
*Anti-Bacterial Agents/pharmacology
*Streptococcal Infections/microbiology/veterinary

@article {pmid42919800,
year = {2026},
author = {Bhuiyan, MNI},
title = {Microbiome Continuum: Connecting Environmental, Host-Associated and Engineered Microbiomes Through One Health and Artificial Intelligence.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {},
pmid = {42919800},
issn = {1758-2229},
mesh = {*Artificial Intelligence ; *Microbiota ; Humans ; Animals ; *One Health ; Climate Change ; Gene Transfer, Horizontal ; Ecosystem ; *Host Microbial Interactions ; Multiomics ; },
abstract = {Microbiomes are increasingly understood as interconnected ecological systems spanning soil, water, plants, animals, humans and engineered environments rather than as isolated host-associated communities. This microbiome continuum provides a mechanistic perspective for One Health by linking microbial cells with the movement of metabolites, genes, signalling molecules and ecological functions across environmental boundaries. Here, we critically examined the biological processes that maintain this continuity, including dispersal, horizontal gene transfer (HGT), metabolic exchange, environmental exposure and host-microbe communication. We consider how climate change and anthropogenic disturbance reshape these interactions and influence antimicrobial resistance (AMR), non-communicable disease, ecosystem function and pathogen emergence. We further evaluate how artificial intelligence (AI), including machine learning and deep learning, can integrate multi-omics and longitudinal data, while emphasizing that predictive performance does not establish causality and that AI remains dependent on data quality, biological knowledge and experimental validation. Engineered microbiomes offer opportunities for targeted intervention, but ecological stability, biosafety, HGT and translational uncertainty remain important constraints. We propose a One Health Microbiome Intelligence Framework (OH-MIF) as a conceptual architecture for cross-domain integration, with emphasis on standardized data, causal validation, equitable participation and human oversight.},
}

*Artificial Intelligence
*Microbiota
Humans
Animals
*One Health
Climate Change
Gene Transfer, Horizontal
Ecosystem
*Host Microbial Interactions
Multiomics

@article {pmid42920203,
year = {2026},
author = {Fjellheim, S and Pereira, L and Sandve, SR},
title = {Ten rules for identifying horizontal gene transfers in deep plant phylogenies.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71680},
pmid = {42920203},
issn = {1469-8137},
abstract = {Horizontal gene transfer (HGT) is one of the most intriguing aspects of genome evolution, challenging classical views of vertical inheritance. Growing genome availability across the tree of life offers opportunities to discover HGT, yet recent reanalyses suggest many reported cases may not withstand scrutiny. Detecting ancient transfers is especially difficult, as phylogenetic signal erodes over time and analytical choices strongly shape conclusions. Here we propose 10 practical rules for evaluating HGT in deep plant phylogenies, organised around three themes: genomic foundation, rigorous analytical framework, and biological interpretation. A reliable genomic foundation requires excluding contamination, verifying genomic integration, and avoiding biased taxon sampling. Rigorous phylogenetics is essential, as deep phylogenies are sensitive to alignment parameters, substitution model, rooting strategy, and branch support. We illustrate this with three glycosyl hydrolase families: for GH9 and GH32, analytical choices can eliminate apparent HGT signals entirely, while GH18 shows why complex, multi-domain families resist confident inference. Finally, HGT signatures demand cautious, biologically plausible interpretation. Recurrent gene duplication, loss, and domain shuffling commonly produce HGT-like patterns and should always be considered as alternatives. Our rules offer a pragmatic checklist helping authors and reviewers distinguish robust HGT from artefacts, fostering more reliable evidence on HGT in plants.},
}

@article {pmid42914239,
year = {2026},
author = {Jia, L and Zhong, Y and Liu, Z and Chu, C and Yi, J and Wang, T},
title = {Microbial interactions in the food industry: Mechanisms, applications, and future perspectives.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 3},
pages = {120796},
doi = {10.1016/j.foodres.2026.120796},
pmid = {42914239},
issn = {1873-7145},
mesh = {Fermentation ; *Food Microbiology/trends ; *Microbial Interactions ; *Fermented Foods/microbiology ; *Food Industry/trends ; Food Handling ; Artificial Intelligence ; Nutritive Value ; },
abstract = {Microbial interactions are the ecological drivers of food fermentation and safety. They determine product quality, functionality, and shelf life. This review systematically illustrates the core ecological modes (synergism, antagonism, and competition) and their underlying molecular mechanisms, such as metabolic cross-feeding, quorum sensing, and horizontal gene transfer. This review analyzes the application of these interactions in traditional fermentations. Specifically, it examines their roles in driving flavor complexity, enhancing nutritional value, and providing natural bio-preservation. The shift from empirical craftsmanship to precision fermentation is further elaborated. This encompasses ecological modeling and the rational design of synthetic microbial consortia. It also includes intelligent monitoring systems and artificial intelligence (AI)-enabled digital twins for real-time process optimization. Additionally, it includes AI-enhanced development of functional foods and microbial valorization of food processing by-products for the circular bioeconomy. Finally, this review addresses critical challenges. These include the constraints imposed by uncultivable microorganisms, the robustness of AI-driven models under industrial complexity, and regulatory hurdles for engineered systems. This review provides a scientific foundation for the rational design of fermented foods with enhanced quality, safety, and functional attributes.},
}

Fermentation
*Food Microbiology/trends
*Microbial Interactions
*Fermented Foods/microbiology
*Food Industry/trends
Food Handling
Artificial Intelligence
Nutritive Value

@article {pmid42914392,
year = {2026},
author = {Huang, Y and Zhang, Q and Chu, S and Xu, D and Han, J and Qu, D},
title = {Mixed-species slaughterhouses represent potential ecological hotspots associated with IS1-driven plasmid evolution and dissemination of tet(X4).},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 2},
pages = {120548},
doi = {10.1016/j.foodres.2026.120548},
pmid = {42914392},
issn = {1873-7145},
mesh = {*Plasmids/genetics ; Animals ; *Abattoirs ; Gene Transfer, Horizontal ; Chickens/microbiology ; *Tetracycline Resistance/genetics ; },
abstract = {The rapid dissemination of the plasmid-borne tigecycline resistance gene tet(X4) in food production systems poses a severe threat to global public health. While slaughterhouses are recognized as antimicrobial resistance (AMR) reservoirs, the specific ecological factors associated with tet(X4) evolution within these environments remain oversimplified. Challenging the assumption of uniform risk across processing facilities, this study systematically investigated how distinct operational settings (pig, chicken, and mixed-species slaughterhouses) influence plasmid-mediated horizontal gene transfer and host fitness adaptation. Among 410 isolates, a representative mixed-slaughterhouse-derived strain (DAR-EC600) demonstrated an exceptional ecological advantage, exhibiting significantly enhanced conjugation efficiency and remarkable plasmid stability (>95% retention over 14 days) compared to single-species facility isolates. Rather than suffering typical AMR fitness costs, multi-omics and in vivo analyses revealed that DAR-EC600 employs an immune modulation-driven colonization strategy. This is achieved through the coordinated up-regulation of motility (fliA/Z), adhesion (fimA/H), and nutrient transport (rbsA/B), effectively neutralizing fitness burdens and triggering pronounced intestinal inflammation and microbiota perturbation. Mechanistically, integrated plasmid and metagenomic profiling identified a highly plastic IncHI1 plasmid architecture (IS1-tet(X4)-blaTEM-1-intI1), where IS1-enriched recombination hotspots facilitate the synergistic co-selection of resistance and virulence determinants. Collectively, these findings suggest that mixed-species slaughterhouses may represent important ecological interfaces associated with enhanced plasmid adaptability, stability, and dissemination potential of tet(X4)-carrying plasmids. This study connects localized AMR surveillance to broader One Health discourses, underscoring the urgent need to target environmental transmission hotspots in global food safety frameworks.},
}

*Plasmids/genetics
Animals
*Abattoirs
Gene Transfer, Horizontal
Chickens/microbiology
*Tetracycline Resistance/genetics

@article {pmid42916978,
year = {2026},
author = {Li, Z and Qin, J and He, L and Nie, C and Liu, F and Hou, Y and Tong, M},
title = {Freeze-Thaw Cycles Greatly Affect the Conjugative Transfer of Antibiotic-Resistant Genes: Effects of the Secretion of Extracellular Polymeric Substances.},
journal = {Environmental science & technology},
volume = {60},
number = {39},
pages = {28026-28039},
doi = {10.1021/acs.est.6c06057},
pmid = {42916978},
issn = {1520-5851},
support = {42507496//National Natural Science Foundation of China (NSFC)/ ; 42530701//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Freezing ; Extracellular Polymeric Substance Matrix ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents ; Drug Resistance, Bacterial/genetics ; },
abstract = {Freeze-thaw (FT) cycle, a ubiquitous and important physical process in natural environments, may influence the horizontal gene transfer (HGT) process of antibiotic-resistant genes (ARGs), yet its impact and underlying mechanisms remain unclear. This study investigated the impact and mechanisms of FT cycles on ARG conjugative transfer among intra- and interspecies under different solution ionic strength conditions. The results showed that despite ionic strengths and species pairs, different FT treatment cycles induced diverse influences on ARG conjugation frequency with inhibition effect of 1 FT cycle (decreased by 3.5-76-fold) and facilitation effect of 2 and 3 FT cycles (promoted by 2-27-fold). The reduced conjugation frequency after 1 FT treatment cycle is mainly attributed to energy deficiency caused by the starvation process during FT treatment. The enhanced cell-cell adhesion induced by the increased hydrophobicity and secretion of bacterial extracellular polymeric substances (EPS) facilitated the formation of conjugative pilus, primarily promoting the ARG conjugative transfer process after 2 and 3 FT treatment cycles. The results of our study clearly show that FT cycles (intensified by the ongoing climate change) exhibit profound influence on the dissemination of ARGs, which helps understand and predict ARG risks in different natural environments.},
}

*Freezing
Extracellular Polymeric Substance Matrix
*Gene Transfer, Horizontal
Anti-Bacterial Agents
Drug Resistance, Bacterial/genetics

@article {pmid42918601,
year = {2026},
author = {Tian, H and Liu, J and Zhang, Y},
title = {Metagenomic Insights into Microplastic Micro-interfaces: Transforming Pollutants and Spreading Resistance.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129408},
doi = {10.1016/j.envpol.2026.129408},
pmid = {42918601},
issn = {1873-6424},
abstract = {Microplastic micro-interfaces (MPMI) in wastewater treatment plants (WWTPs) serve as critical hubs for microbial colonization, pollutant transformation, and antibiotic resistance gene (ARG) dissemination. In this study, a large-scale genome-resolved metagenomic approach was employed to reconstruct 463 high-quality metagenome-assembled genomes (MAGs) from biofilms established on polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) within a municipal WWTP. Taxonomic profiling revealed that MPMI selectively enriched strict anaerobes and uncultured taxa, driving a profound ecological shift from the surrounding water and indicating the formation of localized hypoxic micro-niches. Functionally, the MPMI microbiome constructed a highly integrated metabolic network. Key dominant lineages were found to synergistically couple aromatic hydrocarbon degradation (via the shikimate pathway and β-oxidation) with complex carbon, nitrogen, and sulfur cycling, while deploying energy-efficient nucleotide salvage strategies to ensure biofilm stabilization under nutrient stress. Crucially, horizontal gene transfer (HGT) emerged as a fundamental mechanism for functional diversification, facilitating the active cross-genomic exchange of key adaptive traits associated with pollutant metabolism and biofilm regulation. Furthermore, MPMI harbored a highly diverse resistome comprising 36 ARG categories and 289 subtypes, highlighted by the critical genomic co-localization of mobile elements and clinical resistance markers (e.g., mcr-5.1, mupA) in core colonizers. Ultimately, these genomic insights elucidate the MPMI as a profound ecological hotspot driving the concurrent adaptation of metabolic networks and the resistome, thereby exacerbating the risks of ARG dissemination in aquatic environments.},
}

@article {pmid42918805,
year = {2026},
author = {Liu, P and Lv, Y and Zhang, Y and Wang, Y and Zhu, K and Cao, Z and Dong, L and Xiao, X and Pan, Y and Li, J},
title = {Extensive horizontal gene transfer drives microbial adaptation and diversification in Kermadec Trench hadal microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918805},
issn = {2041-1723},
support = {42225402//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Metagenome ; *Adaptation, Physiological/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; },
abstract = {Hadal trenches, plunging beyond six kilometers depth, harbor a dynamic yet enigmatic microbial biosphere. From ~10 km depth Kermadec Trench sediments, we integrated metagenomics, in situ metatranscriptomics, and phylogenetics to reconstruct 300 prokaryotic species and 186,496 viral populations. In hadal sediment metagenomes analyzed here, we detect distant horizontal gene transfer (DHGT) across phyla/domains and estimate that it contributes on average ~13% of each genome and accounting for >46.7% of multi-copy gene expansions, with four phyla acquiring more than 30% of their genes via DHGT. These DHGT genes encode critical adaptations, including reactive oxygen species detoxification, aromatic compound degradation, and fatty acid/heme biosynthesis, which help microbes survive extreme pressure, low temperatures, and oligotrophy. While classical mechanisms such as conjugation (~0.27%), transduction (~2.1%), and transformation account for a fraction of events, additional potential gene flow conduits are proposed: magnetotaxis-mediated encounters by magnetotactic bacteria (~17.4% of DHGT events), possibly increasing opportunities for gene exchange. These findings suggest that DHGT can contribute substantially to metabolic diversification in the hadal genomes, representing an evolutionary mode distinct from gradualist Darwinian inheritance and consistent with the idea that episodic acquisition of functional modules can contribute to rapid metabolic diversification.},
}

*Gene Transfer, Horizontal
Phylogeny
*Microbiota/genetics
*Bacteria/genetics/classification
Metagenome
*Adaptation, Physiological/genetics
*Geologic Sediments/microbiology
Metagenomics

@article {pmid42919271,
year = {2026},
author = {Kumar, S and Chenchula, S and Bhalsenge, R and Gupta, RK and R, P and Yadav, M and Gupta, M and Atal, S and Reddy, CS and Yadav, S and Patel, D and Rai, N and Baheti, TC and Sharma, RK and Padavala, A and Ghanta, MK and T, SV},
title = {Geographic and genomic determinants of antimicrobial resistance in indian children: a systematic review and meta-analysis.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {42919271},
issn = {1471-2431},
mesh = {Humans ; India/epidemiology ; Child ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; beta-Lactamases/genetics ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major public health challenge, especially in the pediatric population in low- and middle-income countries, particularly India, where the burden of pediatric infections is high. However, nationally representative, pediatric-specific estimates of AMR with geographic stratification remain lacking. We conducted a systematic review and meta-analysis to define the magnitude and regional variation of AMR among Indian children.

METHODS: We conducted a systematic review and meta-analysis in accordance with PRISMA 2020 and the Joanna Briggs Institute guidelines. PubMed/MEDLINE, Scopus, and the Cochrane Library were searched from inception to December 2025 for studies reporting antimicrobial resistance in bacterial isolates from children (≤ 18 years) in India. Given substantial clinical and methodological heterogeneity across pathogens, antibiotic classes, and settings, we conducted stratified random-effects meta-analyses by geographic zone for key resistance phenotypes.

RESULTS: Forty-seven studies met the inclusion criteria, of which 23 contributed to the quantitative synthesis. Pronounced geographic heterogeneity in AMR was observed across India. The number of studies contributing to each pooled estimate ranged from 2 to 8, and heterogeneity (I²) ranged from 19% to 79%. Carbapenem resistance among neonatal intensive care unit isolates ranged from 12% (95% CI 8-18) in Central India to 80% (70-88) in North India. Extended-spectrum β-lactamase production was consistently high (60-80%) across most regions, but lower in Central India (38%). Methicillin-resistant Staphylococcus aureus prevalence ranged from 35% (26-44) to 61% (49-72). Fluoroquinolone resistance exceeded 85% in North, South, and East/Northeast regions, whereas colistin resistance remained ≤ 8% nationally. Genomic data demonstrated widespread dissemination of blaCTX-M-15 and regional clustering of carbapenemase genes (blaNDM, blaOXA), supporting both clonal spread and horizontal gene transfer.

CONCLUSION: Antimicrobial resistance in Indian children is highly prevalent and geographically heterogeneous, with up to five-fold regional differences in carbapenem resistance. In high-burden regions, these resistance levels are likely to compromise the effectiveness of standard empirical therapies, particularly in neonatal and critical care settings. These findings support the urgent need for region-specific empirical treatment guidelines, pediatric-focused antimicrobial stewardship, and integrated phenotypic-genomic surveillance systems.},
}

Humans
India/epidemiology
Child
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/therapeutic use/pharmacology
beta-Lactamases/genetics

@article {pmid42905278,
year = {2026},
author = {Hellmuth, M and Lindeberg, A and Moulton, V},
title = {Regularizing and Normalizing DAGs and Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {88},
number = {11},
pages = {},
pmid = {42905278},
issn = {1522-9602},
mesh = {*Phylogeny ; *Models, Genetic ; Mathematical Concepts ; Gene Transfer, Horizontal ; Evolution, Molecular ; Algorithms ; Cluster Analysis ; },
abstract = {Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A central question is which parts of such graphs are essential with respect to leaf-observable information, and which parts can be removed without changing this information. Resolving this question can lead to principled simplification methods for phylogenetic networks, such as the recent normalization approach of Francis et al. In this paper, we study this question from three related perspectives: clusters displayed by a DAG G, least common ancestors (LCAs) of subsets of its leaf set, and visibility, a path-based property of vertices. We first introduce an LCA-based simplification procedure called i-regularization. For a DAG G and i ≥ 1 , the DAG R E G i (G) retains precisely those vertices that occur as unique LCAs of leaf subsets of size at most i, removes the remaining non-leaf vertices by a graph-editing operation ⊖ , and then deletes shortcuts. We show that R E G i (G) admits a Hasse-diagram characterization in terms of the corresponding lca-clusters. We then compare LCA-based regularization with normalization. Using the same ⊖ -operator, we describe the cover construction underlying normalization, identify visible vertices that are nevertheless removed, and characterize when regularization and normalization coincide. Together, these results provide a unified framework for cluster-based, LCA-based, and visibility-based simplifications of DAGs and phylogenetic networks.},
}

*Phylogeny
*Models, Genetic
Mathematical Concepts
Gene Transfer, Horizontal
Evolution, Molecular
Algorithms
Cluster Analysis

@article {pmid42905297,
year = {2026},
author = {Abuden, AV and Çolak, ÇY},
title = {Genomic Exploration of CRISPR-Cas Systems in Raoultella species: Diversity and Architecture.},
journal = {Current microbiology},
volume = {83},
number = {12},
pages = {},
pmid = {42905297},
issn = {1432-0991},
mesh = {Phylogeny ; *CRISPR-Cas Systems ; *Enterobacteriaceae/genetics/classification ; *Genome, Bacterial ; *Genetic Variation ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genomics ; },
abstract = {Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems are adaptive immune mechanisms that protect bacteria against invading mobile genetic elements. They can influence horizontal gene transfer, phage resistance, and antimicrobial resistance (AMR) dynamics. Although these systems have been investigated in several Klebsiella species, information on historically defined Raoultella species remains limited. In this study, 103 complete genomes representing Raoultella species, currently placed within the broader Klebsiella lineage, were analyzed to characterize the distribution, architecture, and diversity of CRISPR-Cas systems. CRISPR-Cas loci were identified using CRISPRCasFinder and CRISPRone, followed by subtype classification, direct repeat and leader sequence analyses, spacer matching, Cas1-based phylogenetic analysis, and AMR determinant screening. Complete CRISPR-Cas systems were detected in 23 genomes, predominantly in R. ornithinolytica strains. All complete systems were chromosomally located, whereas plasmid-associated orphan CRISPR arrays were observed in selected R. ornithinolytica strains. Two major architectures were identified, with Type I-E being dominant and Type I-F restricted to fewer strains. Direct repeat analysis revealed six consensus sequences, while leader regions displayed conserved AT-rich motifs and strain-specific divergence. Spacer analyses suggested historical interactions with phages and plasmids, particularly mobile genetic elements associated with Klebsiella and other Enterobacteriaceae. Cas1 phylogeny showed subtype-dependent clustering, indicating that CRISPR-Cas evolution does not strictly follow core genome phylogeny. The coexistence of predicted CRISPR-Cas loci and AMR determinants indicates that the presence of these loci does not necessarily preclude the carriage of resistance determinants. Overall, this study expands current knowledge of CRISPR-Cas diversity among the analyzed Raoultella genomes and provides a genomic framework for future functional studies.},
}

Phylogeny
*CRISPR-Cas Systems
*Enterobacteriaceae/genetics/classification
*Genome, Bacterial
*Genetic Variation
Clustered Regularly Interspaced Short Palindromic Repeats
Genomics

@article {pmid42905765,
year = {2026},
author = {Snir, S and Wolf, YI and Brezner, S and Koonin, EV and Steel, M},
title = {On the Distribution of Synteny Block Lengths in Prokaryote Genomes under a Neutral Model of Genome Dynamics.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261491602},
doi = {10.1177/15578666261491602},
pmid = {42905765},
issn = {1557-8666},
abstract = {In bacterial and archaeal genomes, functionally linked genes often cluster in operons that enable coregulation of expression of these genes and production of their protein products in stoichiometric amounts. Many operons are shared by genomes of distantly related bacteria and archaea due in part to evolutionary conservation and in part to horizontal gene transfer (HGT). In contrast, similarity between species in their gene order along the chromosome can be merely a result of evolutionary closeness such that synteny has not yet been disrupted by genome dynamic events occurring during evolution. In general, however, accurate differentiation of operons from spurious gene clusters is a non-trivial task that depends on an underlying model of neutral genome evolution. Here, we employ a recently developed stochastic model of genome rearrangement ("jump model") that accounts for HGT across prokaryote species evolving along a phylogenetic tree to infer the size distribution of shared gene strings (synteny blocks) under neutral evolution. Analytic expressions are derived for the expected number of synteny blocks of a given size (or of maximal size) depending on the evolutionary distance between the genomes and the rates of different types of evolutionary events. This analysis is related to the well-studied family of stick-breaking problems, but the discrete structure and stochastic nature of the evolutionary process provide for the development of a simple, independent model. We demonstrate the predictive power of this model by computer simulations of synthetic data as well as by simulating genomes on real trees obtained from the Alignable Tight Genome Clusters database.},
}

@article {pmid42906245,
year = {2026},
author = {Chen, C and Li, K and Liu, S and Wang, J and Wang, D and You, J},
title = {Salinity-dependent effects of erythromycin on biofilm development and conjugative plasmid transfer on poly(vinyl chloride) microplastics.},
journal = {Marine environmental research},
volume = {223},
number = {},
pages = {108490},
doi = {10.1016/j.marenvres.2026.108490},
pmid = {42906245},
issn = {1879-0291},
abstract = {Microplastics (MPs) and antibiotics frequently co-occur in aquatic environments and jointly influence the dissemination of antibiotic resistance genes (ARGs). However, the modulatory role of salinity, a highly dynamic factor in estuarine and coastal regions, remains underexplored. This study investigated the effects of erythromycin (ERY) on biofilm development and RP4 plasmid conjugative transfer on poly(vinyl chloride) (PVC) MPs across varying salinity levels (5‰, 10‰, and 15‰). Results demonstrated that MP hydrophobicity increased with salinity, while the ERY adsorption capacity followed the order: 5‰ > 15‰ > 10‰. A higher salinity (15‰) promoted biofilm biomass and extracellular polymeric substance (EPS) secretion on MPs. Notably, conjugative transfer frequencies within MP-associated biofilms were consistently higher than those in planktonic cultures. Under varying salinities, the conjugation frequencies in biofilms displayed a U-shaped trend, with higher rates observed at 5‰ and 15‰ compared to 10‰. Crucially, the impact of ERY on plasmid transfer was highly salinity-dependent, i.e., the addition of ERY promoted conjugation at 5‰ and 10‰ but significantly inhibited it at 15‰. Physiological assessments revealed that exposure to varying salinities and ERY induced non-lethal oxidative stress, evidenced by elevated reactive oxygen species and upregulated antioxidant enzymes (CAT and SOD), while lipid peroxidation (MDA) remained relatively low. Concurrently, intracellular proline accumulation and cell membrane permeability increased significantly with rising salinity. These findings provide direct experimental evidence that salinity fluctuations and antibiotic residues jointly alter bacterial physiological states and antibiotic resistance dissemination on MPs, which highlights the necessity of considering dynamic environmental variables in ecological risk assessments.},
}

@article {pmid42906682,
year = {2026},
author = {Walters, KA and Tomah, KR and Pham, V and Baker, P and Golbeck, JH and Redding, KE},
title = {Characterization of NfnAB of Heliomicrobium modesticaldum, an Electron Bifurcating Enzyme Involved in Phototrophic Energy Conversion.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113662},
doi = {10.1016/j.jbc.2026.113662},
pmid = {42906682},
issn = {1083-351X},
abstract = {Analysis of the Heliomicrobium modesticaldum genome suggests that polypeptides encoded by the genes HM1_0289 and HM1_0290 correspond to the NfnA and NfnB subunits of an NAD-dependent ferredoxin:NADP[+] oxidoreductase electron-bifurcating enzyme, NfnAB, similar to that found in archea and anaerobic bacteria. NfnA contains a flavin cofactor and a [2Fe-2S] cluster, whose potential has not been previously measured. It exists in two spectroscopically distinct populations: a major species with Em ≈ -364 mV and a minor species with Em ≈ -423 mV. NfnB contains two [4Fe-4S] clusters, one with Em ≈ -430 mV and the other with Em ≤ -650 mV. Individually, NfnA and NfnB were selective for oxidation of NADH and NADPH respectively. Together, the NfnAB holoenzyme catalyzes the electron bifurcation reaction (2 Fd[ox] + NAD[+] + 2 NADPH ⇆ 2 Fd[red] + NADH + 2 NADP[+]), where Fd corresponds to a heliobacterial dicluster ferredoxin. In the absence of a traditional FNR, heliobacteria may use NfnAB in electron confurcation to accomplish two functions: light-driven cyclic electron transport and transfer of reducing equivalents from NADH to NADP[+]. Deletion of the nfnAB genes resulted in mutants that were viable in all growth modes tested, but in vivo spectroscopic analysis indicated that light-driven electron transport was limited in the absence of NfnAB. As heliobacteria are considered descendants of a clostridial-type bacterium that received the genes for phototrophy via lateral gene transfer, NfnAB may be an archaic protein that was re-purposed for use in phototrophic energy conversion, a function not previously reported for this enzyme.},
}

@article {pmid42907311,
year = {2026},
author = {Clasen, F and Jin, Y and Brett, J and Garcia-Guevara, F and Ehrlich, SD and Shoaie, S},
title = {Microbial resistance from genotype to metabolic phenotype.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.009},
pmid = {42907311},
issn = {1878-4380},
abstract = {Antimicrobial resistance (AMR) poses an escalating global threat, yet surveillance and mechanistic understanding remain anchored in individual resistance genes, an approach that is inadequate for capturing the ecological, genomic, and metabolic complexity through which resistance emerges and spreads. In this opinion article, we argue that genome-scale metabolic models (GEMs) offer a principled framework for advancing AMR research beyond this gene-centric paradigm. Strain-resolved GEMs embed resistance determinants within metabolic networks, with the potential to generate quantitative, context-dependent phenotypic predictions, including minimum inhibitory concentrations and environment-conditional resistance, that sequence-based tools do not provide. Expanded GEM frameworks incorporating mobile genetic elements, horizontal gene transfer, and community-level interactions support ecology-aware resistance profiling. At the therapeutic level, whole-network modelling can identify metabolic vulnerabilities, synthetic lethal interactions, and microbiome-targeted strategies. Integrating GEMs with multiomics and data-driven approaches represents a critical step toward a mechanism-aware AMR platform connecting surveillance, diagnosis, and drug discovery.},
}

@article {pmid42907924,
year = {2026},
author = {Wang, X and Gao, Q and Ge, L and Qin, Z},
title = {The evolutionary processes of bacterial aromatic polyketide ketosynthases.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42907924},
issn = {1474-760X},
support = {32170079//National Natural Science Foundation of China/ ; 2024A1515012593//Natural Science Foundation of Guangdong Province/ ; 2024B1111130001//Guangdong S&T Program/ ; 2021QN020100//Guangdong Talent Scheme/ ; },
mesh = {*Evolution, Molecular ; *Polyketide Synthases/genetics/chemistry/metabolism ; *Polyketides/metabolism ; *Bacteria/enzymology/genetics ; Phylogeny ; Algorithms ; Gene Transfer, Horizontal ; Multigene Family ; *Bacterial Proteins/genetics/chemistry/metabolism ; Protein Domains ; },
abstract = {BACKGROUND: The biosynthesis of bacterial aromatic polyketides (type II polyketides, T2PKs) employs a single set of catalysts (ketosynthases, KSs or KSα, with chain length factors, CLFs or KSβ) and iteratively assembles a carbon backbone with precise chain length control. Considering the increasing number of T2PKs discovered in laboratory settings, it is necessary to understand the evolutionary trajectories of KSs and CLFs.

RESULTS: We employ our recently developed algorithm, MAAPE, based on large protein language model to glean insights into the evolution process of KSs and CLFs. Our findings indicate the evolutionary history of KS and CLF domains from bacterial T2PKSs and identify a shared ancestral cluster (Cluster A), supporting a common origin. Despite structural homology, KSs and CLFs followed distinct evolutionary paths, shaped by coevolution and early horizontal gene transfer.

CONCLUSIONS: Understanding the evolutionary lineage of these enzymes will illuminate the natural optimization processes of their functions and present opportunities for the rational design of novel polyketides with enhanced efficacy.},
}

*Evolution, Molecular
*Polyketide Synthases/genetics/chemistry/metabolism
*Polyketides/metabolism
*Bacteria/enzymology/genetics
Phylogeny
Algorithms
Gene Transfer, Horizontal
Multigene Family
*Bacterial Proteins/genetics/chemistry/metabolism
Protein Domains

@article {pmid42909470,
year = {2026},
author = {Rubin, E and Shimpi, G and Rouzé, H and Bentlage, B},
title = {Comparative genomics reveals modular virulence repertoires and extensive horizontal gene transfer in Vibrio species associated with white syndrome of Porites cylindrica.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001862},
pmid = {42909470},
issn = {2057-5858},
mesh = {*Vibrio/genetics/pathogenicity/classification/isolation & purification ; *Gene Transfer, Horizontal ; Animals ; Virulence/genetics ; Genomics/methods ; Genome, Bacterial ; Phylogeny ; *Anthozoa/microbiology ; Whole Genome Sequencing ; Virulence Factors/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Coral white syndrome (WS) is a widespread condition characterized by tissue loss and skeletal exposure, with multiple bacterial pathogens - particularly Vibrio species - implicated in its aetiology. To investigate the genomic basis of potential virulence in Vibrio associated with WS of Porites cylindrica, we isolated 57 Vibrio strains from healthy and diseased coral tissues collected from reefs in Guam. Thirteen representative strains from five dominant species - Vibrio coralliilyticus, Vibrio owensii, Vibrio tubiashii, Vibrio harveyi and Vibrio tetraodonis - were selected for whole-genome sequencing using Oxford Nanopore Technology. Comparative genomic analyses revealed a conserved repertoire of extracellular enzymes, including haemolysins, cytolysins, metalloproteases and subtilisin-like peptidases, alongside lineage-specific toxin and regulatory modules. Variation in secretion systems (T1SS-T6SS), particularly in T3SS, T4SS and T6SS subtypes, reflected diversification in host interactions and competitive capacities across species. Mobile genetic elements, including plasmids and prophages, contributed additional virulence-associated genes and secretion clusters, underscoring the role of horizontal gene transfer in shaping the accessory genome content. Notably, V. coralliilyticus harboured homologues of the cholera toxin-associated genes ace and zot, although their relatively low aa similarity to characterized Vibrio cholerae toxins suggests that their functional roles remain uncertain. Together, these comparative genomic analyses suggest that virulence-associated gene repertoires are broadly distributed among coral-associated Vibrio and are organized as a conserved ecological core complemented by flexible, horizontally acquired accessory modules. These findings provide hypotheses regarding the genomic basis of opportunistic pathogenicity that will require future functional validation. This study provides the first comparative genomic framework for Vibrio associated with P. cylindrica, providing a foundation for future investigations into how genomic plasticity and modular virulence gene repertoires may contribute to opportunistic disease dynamics in coral reef ecosystems.},
}

*Vibrio/genetics/pathogenicity/classification/isolation & purification
*Gene Transfer, Horizontal
Animals
Virulence/genetics
Genomics/methods
Genome, Bacterial
Phylogeny
*Anthozoa/microbiology
Whole Genome Sequencing
Virulence Factors/genetics
Interspersed Repetitive Sequences

@article {pmid42909907,
year = {2026},
author = {Angles-Yanqui, E and Yauri-Condor, K and Velásquez-Pomar, J and Hernandez-Hernandez, R and Salazar, A and Yañez, P and Flores-Leon, D and Gavilan, RG},
title = {Molecular epidemiology and resistance mechanisms of carbapenem-resistant Gram-negative bacilli in a referral hospital in Lima, Peru.},
journal = {JAC-antimicrobial resistance},
volume = {8},
number = {5},
pages = {dlag236},
pmid = {42909907},
issn = {2632-1823},
abstract = {BACKGROUND: Carbapenem-resistant Gram-negative bacilli (CR-GNB) represent a significant public health threat, as they are associated with high mortality in healthcare settings. Carbapenemase production is the predominant resistance mechanism, and horizontal gene transfer drives the rapid dissemination of antimicrobial resistance (AMR).

OBJECTIVES: This study aimed to characterize the phenotypic and genotypic AMR profiles of CR-GNB isolated from patients at Arzobispo Loayza National Hospital (Lima, Peru) between October 2021 and January 2022.

METHODS: We conducted a cross-sectional study and collected clinical and epidemiological data from patients with bacterial infections. MALDI-TOF identified pathogens, and antimicrobial susceptibility was interpreted according to CLSI guidelines. A subset of isolates underwent whole-genome sequencing (Illumina) to determine genomic resistance markers.

RESULTS: A total of 159 patients were included (median age = 54 years; 66.7% male); 72.3% had confirmed clinical infections, and 66% were admitted to the ICU. The most frequent infection types were pneumonia, urinary tract infection and bacteraemia. Overall, 97.5% of isolates were classified as XDR. Carbapenem resistance approached 100% (imipenem 99.4%, meropenem 98.7%). Whole-genome data revealed clonal diversity among Klebsiella pneumoniae (ST13/ST15) carrying bla NDM-1; Acinetobacter baumannii uniformly harboured bla OXA-23; and Pseudomonas aeruginosa included high-risk clones ST357 (bla IMP-93) and ST111 (bla IMP-18, bla VIM-2).

CONCLUSIONS: These findings demonstrate a critical burden of XDR-GNB and the presence of multiple carbapenemases (NDM, IMP, KPC and VIM) associated with clinically relevant high-risk lineages. Strengthening molecular surveillance, optimizing antimicrobial stewardship and reinforcing infection-control measures are urgently needed to contain CR-GNB in critical-care settings in Peru.},
}

@article {pmid42910054,
year = {2026},
author = {Mahdizade Ari, M and Al-Ahmad, A and Cieplik, F and Scholz, KJ},
title = {Invasive guests: the role of non-oral bacteria in oral dysbiosis and systemic health.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2745592},
pmid = {42910054},
issn = {2000-2297},
abstract = {BACKGROUND: The human oral cavity harbors a diverse microbiota essential for maintaining oral and systemic health. While most resident microorganisms are commensals adapted to specific oral niches, increasing evidence highlights the presence of non-oral bacteria, including Helicobacter pylori, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterobacteriaceae, Staphylococcus aureus, Acinetobacter baumannii, Enterococcus faecalis and Clostridioides difficile. Traditionally associated with other body sites, these bacteria may enter the oral cavity and, under favorable ecological conditions, persist through mechanisms such as biofilm formation, stress tolerance, entry into a viable but non-cultivable (VBNC) state, coaggregation with the oral microbiota, and evasion of host immune responses. Their colonization has been reported particularly in dysbiotic oral environments, including periodontitis and immunocompromised conditions, where overgrowth may also facilitate their recovery by conventional culture methods.

OBJECTIVE: This review aims to summarize the current evidence on the presence, persistence mechanisms, clinical significance, and detection challenges of non-oral bacteria in the oral cavity, and to highlight the need for integrated diagnostic approaches.

DESIGN: A comprehensive literature review was conducted focusing on studies reporting the isolation, detection, and clinical relevance of non-oral opportunistic bacteria in the oral cavity, with emphasis on culture-based and molecular diagnostic methods.

RESULTS: Clinically, non-oral bacteria presence has been associated with dental caries, periodontal disease, endodontic infections, systemic dissemination, and their potential role as reservoirs of antibiotic resistance genes. Although several non-oral opportunistic bacteria can be readily isolated by culture when present at sufficient abundance, particularly in immunocompromised patients, detection may remain challenging in healthy individuals or low-biomass samples because of their transient or low-abundance occurrence, increasing the risk of misinterpretation.

CONCLUSIONS: Recognizing the oral cavity as a dynamic niche for non-oral bacteria underscores the need for integrated culture- and molecular-based diagnostic approaches, improved infection control strategies, and further research into their pathogenic potential.},
}

@article {pmid42910333,
year = {2026},
author = {Sharma, T and Maurya, IK and Chandley, P},
title = {Emerging Molecular Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens: A Comprehensive Review.},
journal = {Journal of the Royal Society of New Zealand},
volume = {56},
number = {5},
pages = {e70087},
pmid = {42910333},
issn = {1175-8899},
abstract = {The rise of antimicrobial resistance has marked ESKAPE pathogens as a serious global health threat, primarily due to the limitations and frequent failures of broad-spectrum antibiotic-based treatment. Moreover, the misuse and overuse of antibiotics have further complicated the management of bacterial infections by enhancing the risk of secondary infections. Despite traditional antibiotic development, there is a need for novel strategies to tackle the rising menace of ESKAPE pathogens. During the past few decades, various cellular and molecular-level investigations based on multidrug-resistant bacterial species have emerged. These investigations have played a major role in unraveling the intrinsic pathways that are involved in conferring AMR to ESKAPE pathogens. The molecular mechanisms of AMR in ESKAPE involve expression of efflux pumps, persistent biofilms, enzymatic drug inactivation, alterations in antibiotic targets, genetic mutations, and horizontal gene transfer. This review highlights the major molecular mechanisms of antimicrobial resistance in ESKAPE pathogens. By understanding these mechanistic pathways, more specific/targeted diagnostics and therapeutic approaches may be developed. This review outlines key findings from recent research studies on AMR trends in ESKAPE pathogens. This comprehensive review also provides current research gaps and future directions for combating AMR.},
}

@article {pmid42914073,
year = {2026},
author = {Huang, B and Chen, B and Li, Z and Yang, E and Lu, J and Hu, L and Hou, X and Chao, Y and Luan, T and Yuan, K},
title = {Fates and Characteristics of Antibiotic Resistance Genes Carried by Viruses during a Full-Scale Anaerobic Sludge Digestion.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125980},
doi = {10.1016/j.envres.2026.125980},
pmid = {42914073},
issn = {1096-0953},
abstract = {The transmission of antibiotic resistance genes (ARGs) mediated by viruses in sludge represents an emerging concern for antibiotic resistance dissemination. This study investigated the virus-carried ARGs (vARGs) profiles and potential risks in sludges collected from an entire anaerobic sludge digestion plant. A total of 79 unique vARGs spanning 10 antibiotic resistance classes were identified, with trimethoprim resistance genes being the most diverse. Although most vARGs (94.9%) exhibited low sequence similarity (< 70%) to known ARGs, the representative functional validation showed that virus-carried dfr genes could confer trimethoprim resistance to Escherichia coli. Thermal hydrolysis reduced the levels and diversity of vARGs, whereas subsequent anaerobic digestion led to substantial enrichment. More than 90% of vARGs in sludge viromes were removed after all treatment processes, but a significant number of ARG-carrying viruses (10[5] - 10[6] VLPs/g) still remained in the final sludges. In the metagenomes, the levels of vARGs increased approximately 7-fold, suggesting that vARGs were more difficult to be moved than plasmid-associated ARGs and chromosome-associated ARGs. The host prediction suggested associations between some vARG-carrying viruses and potential pathogenic bacteria, which worthing further experimental validation. In summary, the persistence of vARGs in sludge remains a concern, even after the implementation of sludge treatment processes.},
}

@article {pmid42889346,
year = {2026},
author = {Keshri, A and Choudhary, S and Kumar, A and Singh, I and Singh, H and Sharma, D and Kumar, A and Verma, S and Ratn, A},
title = {Coagulase-Negative Staphylococci (CoNS): An Emerging Threat, Antimicrobial Resistance, and Health Concern.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {6678972},
pmid = {42889346},
issn = {1687-918X},
abstract = {Coagulase-negative staphylococci (CoNS) have evolved from a harmless commensal group to an alarming threat to patient, environmental, and population health due to their challenging treatment and their impact on health outcomes. The widespread presence of CoNS in these environments poses a public health concern due to various virulence factors, biofilm formation, and toxin production, which contribute to pathogenicity and antimicrobial resistance (AMR). Major clinical manifestations include device-related infections, bloodstream infections, and neonatal sepsis. Nonclinical reservoirs, such as soil, water, animals, and food-processing environments, are considered critical sources of resistance gene flow. The mechanisms of resistance include the mecA gene and a variety of SCCmec elements, as well as horizontal gene transfer via plasmids and transposons, and tolerance via biofilm formation. This review summarizes current findings on the epidemiology, AMR mechanisms, biofilm-linked pathogenicity, diagnostic advances, and One Health implementations of CoNS across nonclinical and clinical contexts, while recognizing priorities for therapeutic and surveillance development. Here, the reviewed literature suggests considerable variation in drug resistant CoNS and distribution landscapes across nonclinical and clinical contexts, with MGEs, biofilm establishment, and environmental repertoires reflecting imperative determinants in the dissemination and persistence of AMR. An analysis of the existing literature indicates that genetic links between clinical and environmental isolates remain insufficiently established and that surveillance data are lacking; accordingly, future research should focus on these gaps. Addressing the threat of CoNS requires enhanced surveillance, improved diagnostic precision, and the development of novel antimicrobial and antibiofilm strategies. Future research should focus on epidemiological surveillance, innovation in therapy, and systems-based approaches, which consider the interrelationship of human, animal, and environmental health.},
}

@article {pmid42890805,
year = {2026},
author = {Coche-Miranda, J and Arros, P and Canales, N and Berríos-Pastén, C and Azziz, G and Lagos, R and Orlando, J and Chávez, FP and Marcoleta, AE},
title = {Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta-lactamases.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70118},
pmid = {42890805},
issn = {2996-9514},
abstract = {Antimicrobial resistance is a major global health threat shaped not only by clinical settings but also by environmental reservoirs, in line with the One Health framework. Antarctic and Subantarctic soils represent a largely unexplored component of the environmental resistome, particularly beta-lactamases, whose diversity, structural features, and biogeographic patterns remain poorly resolved. Here, we applied an integrative metagenomic approach combining sequence-, structure-, and function-based similarity to systematically identify putative beta-lactamase orthologs across an extensive collection of Antarctic and Subantarctic soil metagenomes. We detected multiple beta-lactamase classes and families, with a predominance of class A serine beta-lactamases and subclass B3 metallo-beta-lactamases. Several previously uncharacterized families and divergent variants were identified, many of which retain conserved catalytic architectures. Beta-lactamase diversity and relative abundance were strongly patterned across three major biogeographic clusters: Subantarctic islands, the Antarctic Peninsula and surrounding islands, and continental cold deserts, mirroring shifts in microbial community composition. The Antarctic Peninsula and maritime Antarctica exhibited the highest overall beta-lactamase abundance. Analysis of more than 3500 metagenome-assembled genomes indicated that most beta-lactamases were encoded by members of p_Pseudomonadota and p_Bacteroidota, with additional representatives distributed across other bacterial phyla. A subset was linked to mobile genetic elements, suggesting a latent but limited potential for horizontal gene transfer. Together, these findings reveal a geographically organized and compositionally diverse repertoire of beta-lactamases in (sub)Antarctic soils, underscoring the evolutionary persistence of conserved catalytic frameworks in cold environments and highlighting the contribution of remote ecosystems to global resistome diversity.},
}

@article {pmid42892002,
year = {2026},
author = {Joshi, M and Kaur, S and Mouafo, HT},
title = {Biomaterials for environmental control of AMR dissemination.},
journal = {Journal of infection and public health},
volume = {19},
number = {12},
pages = {103392},
doi = {10.1016/j.jiph.2026.103392},
pmid = {42892002},
issn = {1876-035X},
abstract = {Antimicrobial resistance (AMR) threatens human, animal, agricultural, and environmental health, driven by horizontal and vertical gene transfer. Conventional wastewater treatment removes 63-94% of antibiotic resistance genes (ARGs) but fails to eliminate ARGs and antibiotic-resistant bacteria, while generating toxic sludge. This review evaluates advanced biomaterials, including silver and gold nanoparticles, reactive oxygen species, magnetic nanocomposites, targeted disruption of metabolic pathways, carbon-based sorbents, biopolymers, metal-organic frameworks, functionalized enzymes/peptides, and engineered biofilms, for reducing ARG and resistant-bacteria loads, inhibiting horizontal gene transfer, and reducing the selective pressure exerted by residual antibiotics. These approaches offer enhanced performance across wastewater/agriculture/air/food supply chain systems. Challenges in scalability, ecological safety, and regulation remain, requiring integration with AI monitoring, CRISPR tools, and One Health strategies. This review aims to summarize and discuss the literature on the development and use of innovative biomaterial-based intervention strategies that address the environmental aspects of AMR in order to provide a comprehensive overview of what has been learned and developed to date.},
}

@article {pmid42893782,
year = {2026},
author = {Kussia, GG and Kassa, BA and Amdiyee, AA and Abate, TA and Tessema, TS},
title = {Dynamics of Antimicrobial Resistant Bacteria in Water Environments: Risks via Surface Waters and Combating Strategies.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70451},
doi = {10.1111/1462-2920.70451},
pmid = {42893782},
issn = {1462-2920},
mesh = {*Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Water Microbiology ; *Fresh Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Humans ; Animals ; },
abstract = {Water sustains all living systems, maintaining human, animal, and environmental health. However, as open systems, surface waters are highly exposed to microbial and chemical pollutants, including antimicrobials. These contaminants exert selective pressure on densely packed bacterial genomes and drive mutations leading to adaptation. This review explores the dynamics and key drivers underlying the emergence and persistence of antibiotic-resistant bacteria (ARB) in aquatic environments. It delineates both classical and novel horizontal gene transfer (HGT) mechanisms, ranging from conjugation, transduction, and transformation to outer membrane vesicles, gene transfer agents, and intercellular nanotubes. These mechanisms promote the evolution, distribution, and stable persistence of antibiotic resistance genes (ARGs) in aquatic systems, including freshwater sources. Furthermore, the review outlines surface water contaminants and their biomagnification risks in the environment and through the consumption of food from freshwater food webs, drinking water, and animal products. Finally, the review discusses potential mitigation strategies, highlighting advanced treatment technologies, constructed wetlands, and biocontrol approaches using aquatic macrophytes (e.g., water hyacinth), microalgae, and phage-based remediation, while addressing concerns regarding safety, applicability, and scalability. Stewardship programs aligned with One Health frameworks remain vital to mitigating these global risks.},
}

*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
*Water Microbiology
*Fresh Water/microbiology
Anti-Bacterial Agents/pharmacology
Humans
Animals

@article {pmid42894133,
year = {2026},
author = {Zhang, B and Tang, J and Wang, H and Wang, B and Zhang, Z and Liu, G and Li, Y and Wei, J and Zhang, J},
title = {Assembly and comparative analysis of the complete mitochondrial genome of a orchid cultivar 'Jingzi' reveals multichromosomal architecture and plastid-derived DNA transfers.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42894133},
issn = {1471-2229},
support = {XY-TD-22-05//Research Fund from Chief Expert Team Project of Beijing Vocational College of Agricultural/ ; KJCX20230203, KJCX20230120//Beijing Academy of Agriculture and Forestry Sciences Science Foundation/ ; },
mesh = {*Orchidaceae/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plastids/genetics ; Gene Transfer, Horizontal ; },
abstract = {BACKGROUND: Orchidaceae is one of the most diverse flowering plant families in angiosperms and holds significant cultural, economic, and ecological value in China. Despite economic and horticultural significance, the mitochondrial genomes of Cymbidium kanran remain poorly characterized.

RESULTS: We assembled and annotated the complete mitochondrial genome of a new orchid variety, 'Jingzi', using PacBio HiFi sequencing technology. The mitochondrial genome is 704, 624 bp in length with a GC content of 43.91%, comprising 24 circular contigs. It contains 38 protein-coding genes (PCGs), including 24 unique core mitochondrial genes, 27 tRNA genes, and 3 rRNA genes. Notably, atp6 exhibits an unprecedented duplication event. Intracellular gene transfer analysis revealed 91 fragments homologous between mitochondria and chloroplasts, totaling 92, 762 bp (13.16% of the mitochondrial genome). Based on 24 conserved PCGs from 20 angiosperm species, our phylogenetic analysis indicated a potential affinity between 'Jingzi' and Paphiopedilum from Shenzhen. Given the poor sampling of closely related genera within Cymbidium, this observation is preliminary and awaits validation from future studies with expanded taxon coverage.

CONCLUSIONS: This study elucidates the main features of the 'Jingzi' mitochondrial genome, highlights extensive mitochondrial-chloroplast homology, and reports the presence of two copies of atp6 in the mitochondrial genome. These findings provide valuable insights for genetic and evolutionary studies of orchids.},
}

*Orchidaceae/genetics
*Genome, Mitochondrial/genetics
Phylogeny
*Plastids/genetics
Gene Transfer, Horizontal

@article {pmid42898522,
year = {2026},
author = {Liu, Z and Dong, D and Jia, N and Li, Y and Gao, Y and Zhu, Y},
title = {Characterization of a conjugative IncA plasmid co-harbouring bla NDM-5 and bla VIM-1 in a KPC-producing Klebsiella pneumoniae clinical isolate K27.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1959757},
pmid = {42898522},
issn = {1664-302X},
abstract = {OBJECTIVES: Multiple-carbapenemase-producing Klebsiella pneumoniae has emerged as a critical threat to global health due to limited treatment options and high mortality. This study aimed to characterize the genomic features of a triple-carbapenemase-producing K. pneumoniae clinical isolate.

METHODS: A carbapenem-resistant K. pneumoniae (CRKP) strain K27 was collected from a patient in a tertiary hospital in January 2025. Antimicrobial susceptibility testing, carbapenemase detection, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), conjugation experiments, and plasmid fitness cost assays were performed. Whole-genome sequencing (WGS) of strain K27 was carried out on Illumina and PacBio platforms, bioinformatic analyses were performed using tools such as PlasmidFinder, ResFinder and ISfinder to characterize plasmid architecture, including replicon typing, resistance gene profiling, and mobile genetic element identification.

RESULTS: Strain K27 was an extensively drug-resistant ST11 K. pneumoniae producing three carbapenemases (NDM, KPC and VIM). Both S1-PFGE and WGS revealed that strain K27 carried four plasmids. The bla KPC-2 gene was located on an IncFIIpHN7A8:IncR hybrid plasmid (assigned as pK27-KPC2) and carried by a truncated transposon Tn6296, while the bla NDM-5 and bla VIM-1 genes were co-harboured on a single IncA plasmid (assigned as pK27-NDM5/VIM1), where they were carried by a truncated transposon Tn125 and integron In916, respectively. The two corresponding genetic elements were separated by ISCR1, and this arrangement was highly similar to that of plasmid p24A20009_B_NDM. Conjugation experiments demonstrated that the plasmid pK27-NDM5/VIM1 was transferable at a frequency of (4.5 ± 1.2) × 10[-2], and the resulting transconjugant was designated as K27-C. Independent sample t-tests further revealed significant differences between the transconjugant K27-C and the Escherichia coli J53Azi[R] groups, both in the area under the curve (t = 3.63, p = 0.002) and in the maximum optical density (t = 2.57, p = 0.02).

CONCLUSION: The finding of two different class B metallo-carbapenemase genes co-harboured on a single conjugative IncA plasmid in a KPC-producing ST11 K. pneumoniae clinical isolate is alarming. This co-production of three distinct carbapenemases in a single strain could pose considerable challenges for the selection of clinical anti-infective therapies. Furthermore, the isolate may pose a high risk of subsequent clonal dissemination and/or horizontal gene transfer, necessitating ongoing epidemiological surveillance.},
}

@article {pmid42901408,
year = {2026},
author = {Gill, A and Romero-Barrios, P and Jenkins, C and Morabito, S and Coulombe, G and Lavoie, MC and Feng, P},
title = {The Evolution of Shiga Toxin-Producing Escherichia coli Characterization and Risk Categorization Strategies.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100946},
doi = {10.1016/j.jfp.2026.100946},
pmid = {42901408},
issn = {1944-9097},
abstract = {Shiga toxin-producing Escherichia coli (STEC) are a group of E. coli that cause food and waterborne enteric illness. STEC are genotypically and phenotypically diverse as they do not have a single evolutionary origin, instead multiple STEC lineages have appeared independently following horizontal gene transfer events. The diversity of STEC is also reflected in an apparent variability in the potential of individual STEC strains to cause severe illness (bloody diarrhea or hemolytic uremic syndrome) or be involved in large foodborne outbreaks. In the context of food safety decision making, the variable characteristics of STEC strains and their potential health outcomes have resulted in an ongoing debate on how STEC should be categorized into risk groups. The aim of this review is to clarify that debate by examining how STEC characterization and risk categorization strategies have evolved over time in response to changes in analytical techniques, understanding of STEC epidemiology, and pathogenicity mechanisms. The origin of established perspectives and practices is explored, from the recognition of STEC O157:H7 as an emerging pathogen in the 1980s, through serotype-based identification and characterization of STEC, to contemporary approaches based on molecular markers for virulence. The evidence for the role of specific virulence factors in STEC pathogenicity is reviewed and their utility in STEC risk categorisation assessed. Finally, a binary categorization scheme is proposed, based on evidence for the correlation of hemolytic uremic syndrome, with the presence of Shiga toxin subtypes Stx2a, Stx2c, Stx2d, and colonisation factors including the Locus of Enterocyte Effacement (intimin/eae) and Enteroaggregative attachment (aggR/aaiC).},
}

@article {pmid42903469,
year = {2026},
author = {Ponce-Cusi, R and Barletta-Carrillo, C and Pilco-Ferreto, N},
title = {Microplastics and nanoplastics as potential ecological oncogenic co-drivers: rewiring host-microbe interactions in cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1923626},
pmid = {42903469},
issn = {2235-2988},
mesh = {Humans ; *Neoplasms/microbiology/etiology/chemically induced/pathology ; *Microplastics/adverse effects/toxicity ; *Host Microbial Interactions/drug effects ; Tumor Microenvironment/drug effects ; Animals ; *Carcinogenesis ; Microbiota/drug effects ; Environmental Exposure/adverse effects ; Host-Pathogen Interactions ; },
abstract = {Microplastics and nanoplastics (MPs/NPs) are increasingly recognized as biologically active interfaces that may reshape host-microbe interactions in carcinogenesis. This review proposes a hypothesis-generating mechanistic framework in which MPs/NPs may influence cancer-related processes through the integration of environmental exposure, epithelial barrier disruption, immune dysregulation, and tumor microenvironment remodeling. Although applicable to multiple epithelial interfaces, the framework primarily focuses on the intestinal mucosa, where the most substantial evidence exists. Through plastisphere formation, MPs/NPs adsorb pollutants, virulence factors, and microbial communities, potentially facilitating pathogen persistence, horizontal gene transfer, and antibiotic resistance enrichment. Upon host exposure, MPs/NPs have been associated with compromised epithelial integrity, enhanced microbial translocation, and activation of inflammatory pathways involving pattern recognition receptors, NF-κB, and the NLRP3 inflammasome. At the microbiome level, MPs/NPs may promote dysbiosis, alter microbial metabolism, and favor pro-inflammatory and genotoxic metabolites that could reinforce oncogenic signaling. These processes may converge to sustain chronic inflammation, immune evasion, extracellular matrix remodeling, angiogenesis, and tumor-permissive niches. While experimental and biomarker-based evidence support this axis, direct human data remain limited. Collectively, this review provides a conceptual basis for understanding environmentally associated carcinogenesis through MPs/NPs as ecological mediators bridging the environmental exposures, microbiome, and cancer biology.},
}

Humans
*Neoplasms/microbiology/etiology/chemically induced/pathology
*Microplastics/adverse effects/toxicity
*Host Microbial Interactions/drug effects
Tumor Microenvironment/drug effects
Animals
*Carcinogenesis
Microbiota/drug effects
Environmental Exposure/adverse effects
Host-Pathogen Interactions

@article {pmid42903900,
year = {2023},
author = {Song, Y and Mu, Y and Wong, NK and Yue, Z and Li, J and Yuan, M and Zhu, X and Hu, J and Zhang, G and Wei, D and Wang, C and Wu, W and Bai, F and Feng, J},
title = {Emergence of hypervirulent Pseudomonas aerug inosa pathotypically armed with co-expressed T3SS effectors ExoS and ExoU.},
journal = {hLife},
volume = {1},
number = {1},
pages = {44-56},
pmid = {42903900},
issn = {2949-9283},
abstract = {Pseudomonas aeruginosa is a significant pathogen mainly causing healthcare-associated infections (HAIs). Newly emerging high-risk clones of P. aeruginosa with elevated virulence profiles furtherly cause severe community-acquired infections (CAIs). Usually, it is not common for P. aeruginosa to co-carry exoU and exoS genes, encoding two type III secretion system (T3SS) effectors. The pathogenicity mechanism of exoS [+]/exoU [+] strains of P. aeruginosa remains unclear. Here, we provide detailed evidence for a subset of hypervirulent P. aeruginosa strains, which abundantly co-express and secrete the T3SS effectors ExoS and ExoU. The exoS [+]/exoU [+] P. aeruginosa strains were available to cause both HAIs and CAIs. The CAI-associated strains could elicit severe inflammation and hemorrhage, leading to higher death rates in a murine acute pneumonia model, and had great virulence potential in establishing chronic infections, demonstrating hypervirulence when compared to PAO1 (exoS [+]/exoU [-]) and PA14 (exoS [-]/exoU [+]). Both ExoS and ExoU were co-expressed and co-secreted in abundance in exoS [+]/exoU [+] strains. Their abundant protein secretion could boost exoS [+]/exoU [+] strains' potentials for cytotoxicity in vitro and pathogenicity in vivo. Genomic evidence indicates that exoU acquisition is likely mediated by horizontal gene transfer (HGT) of the pathogenicity island PAPI-2, while deletion of exoU was sufficient to mitigate virulence in the exoS [+]/exoU [+] strains. Furthermore, bioinformatics analysis showed that such exoS [+]/exoU [+] P. aeruginosa strains turned out to be widely distributed across the globe. Overall, the research provide detailed evidence for the high virulence and epidemicity of exoS [+]/exoU [+] strains of P. aeruginosa, highlighting an urgent need for surveillance against these high-risk hypervirulent strains.},
}

@article {pmid42904219,
year = {2026},
author = {Ke, Z and Wu, Q and Gao, M and Wang, Q and Wang, L and Yuan, C},
title = {Metabolic gene analysis of newly isolated Pseudochrobactrum sp. BJQ-1 and BJQ-2 reveals global dissemination of the chlorothalonil hydrolytic dehalogenase chd gene.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1965943},
pmid = {42904219},
issn = {1664-302X},
abstract = {Chlorothalonil (TPN; 2,4,5,6-tetrachloroisophthalonitrile) is a globally used, persistent chlorinated fungicide. Its bacterial detoxification is driven mainly by the hydrolytic dehalogenase Chd. Although the chd gene and its association with mobile genetic elements have been reported, the extent to which identical chd modules have spread across distinct hosts on a global scale remains unclear. Here we isolated two chlorothalonil-degrading strains, BJQ-1 and BJQ-2, from geographically distinct sites. Both were identified as Pseudochrobactrum spp. by 16S rRNA phylogeny. Shotgun cloning and sequence comparison revealed that both strains harbor a chd ORF essentially identical (≥99.7% nucleotide identity) to those of Pseudomonas sp. CTN series, Paracoccus sp. XF-3 and Ochrobactrum lupini TP-D1. The same chd gene is embedded in three distinct mobile-element configurations, an IS21-like composite transposon in CTN series, an IS6-family transposase TnpA plus Pin recombinase in BJQ-1, and a λ Rac-like invertase in BJQ-2, a pattern incompatible with vertical inheritance. Upstream spacer analysis showed that a conserved IS21-like fusion promoter, composed of an IRR-borne -35 box fused to the native -10 element of chd gene, and the 179-bp istB-chd intergenic spacer (100% identical between the BJQ isolates and the CTN series) are preserved. Mining of the Prokaryotic Genome dataset retrieved chd-like sequences from diverse prokaryotic genomes spanning soil, aquatic and plant-associated habitats, confirming a broad phylogeography of the cassette. The recovery of an identical, transposon-associated chd module from two distantly sampled Pseudochrobactrum strains, together with its global genomic distribution, indicates that the chd detoxification cassette has disseminated worldwide, providing a general mechanism for the rapid recruitment of TPN biodegradation capacity in microbial communities.},
}

@article {pmid42904661,
year = {2026},
author = {Sakib, N and Abaya, LMM and Ruddell, B and Aga, DS and Howe, A and Jarboe, L},
title = {Antidepressant desvenlafaxine identified in wastewater promotes transformation and antibiotic resistance risk in Acinetobacter baylyi ADP1 via metabolic adaptations.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0168326},
doi = {10.1128/aem.01683-26},
pmid = {42904661},
issn = {1098-5336},
abstract = {Wastewater treatment plants (WWTPs) are known reservoirs of antibiotic resistance genes (ARGs). Non-antibiotic compounds, such as antidepressants, may further promote ARG acquisition through horizontal gene transfer (HGT). Desvenlafaxine, a serotonin-norepinephrine reuptake inhibitor (SNRI) listed on the EU Surface Water Watch List, is among the most frequently detected antidepressants in WWTP effluents, yet its role in HGT has not been examined. Here, we detected desvenlafaxine at the highest concentrations among four antidepressants monitored across three municipal WWTPs in western New York. Using Acinetobacter baylyi ADP1 as a model recipient in natural transformation assays (n = 6), we found that desvenlafaxine significantly increased transformation frequency at 10 mg/L (1.74 ± 0.33-fold) and 50 mg/L (1.49 ± 0.19-fold; Padj < 0.05). Effects occurred without induction of reactive oxygen species or loss of membrane integrity, consistent with its very low toxicity (IC20 ~1,300 mg/L). Instead, desvenlafaxine induced dose-dependent increases in membrane fluidity and shifts to less negative zeta potentials, suggesting that electrostatic interactions between its cationic amine group and the negatively charged membrane reduce surface repulsion and facilitate plasmid proximity during uptake. Non-targeted proteomics revealed a biphasic response: at 10 mg/L, competence-associated proteins (PilB, ComM) were upregulated, and STRING analysis identified networks linked to membrane transport, transcriptional regulation, and envelope remodeling, while no connected network was recovered at 50 mg/L. Electron microscopy confirmed higher pilus frequency at both doses. Together, these findings reveal a non-oxidative, envelope-mediated route by which a widely detected antidepressant increases bacterial competence.IMPORTANCEThe spread of antibiotic resistance poses a serious and escalating threat to human health worldwide. While antibiotic use is widely recognized as a key driver, non-antibiotic pharmaceuticals released into the environment through wastewater have received far less attention. Antidepressants are among the most frequently detected drugs in treated wastewater effluents, yet their potential to promote antibiotic resistance transfer in bacteria remains poorly understood. This study demonstrates that desvenlafaxine, one of the most abundant antidepressants found in municipal wastewater, can increase the uptake of antibiotic resistance genes in an environmental bacterium at concentrations above those currently measured in effluent, and identifies the bacterial cell-surface changes that enable this without cytotoxicity.},
}

@article {pmid42883039,
year = {2026},
author = {Liu, D and Huang, L and Yan, M and Huang, Y and Wang, C and Ku, Q and Deng, Y and Yuan, X},
title = {Beyond Co-Occurrence: A Framework for Interpreting Antibiotic-ARG Decoupling in Aquatic Systems and Its Implications for Aquatic Animal Health in a Changing World.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
pmid = {42883039},
issn = {2076-2615},
abstract = {Antibiotics and antibiotic resistance genes (ARGs) are widespread in aquatic ecosystems affected by climate variability, urbanization, and intensifying aquaculture. Yet parent-antibiotic concentrations and resistance-related genetic endpoints do not always vary in parallel across seasons, sites, or environmental compartments. This discrepancy matters for aquatic animals as ecological receptors, potential vectors, and targets for antimicrobial resistance monitoring and management. To examine whether transport, retention, and biological processes may contribute to these mismatches, we conducted a structured narrative review. We screened studies retrieved from Web of Science Core Collection, Scopus, and PubMed for paired measurements in aquatic systems. Of 98 field studies, 25 provided sufficient paired data for matched chemical-genetic assessment. Among these, 16 provided Moderate evidence and 9 provided Suggestive evidence for coupled, mismatched, or compartment-dependent responses. No study met the stricter criteria for field-supported legacy persistence. Seasonal reversals, spatial divergence, and differences among water, particles, and sediments suggest that water-column antibiotic concentrations alone are incomplete proxies for ARG abundance. Such measurements alone cannot assess ARG mobility or host context. Potential contributors include sediment and biofilm retention, extracellular DNA, hydrodynamic redistribution, horizontal gene transfer, transformation products, and co-selective stressors, although their relative roles remain unresolved. These findings support monitoring that combines chemical and genetic endpoints with information on sources, hydrology, compartments, and hosts to inform aquatic-animal risk assessment and management.},
}

@article {pmid42883902,
year = {2026},
author = {Provorov, NA and Kurchak, N and Onishchuk, OP and Evsyukov, IV and Chizhevskaya, EP and Aksenova, TS and Kimeklis, AK and Gladkov, GV and Goncharova, AA and Pinaev, AG and Andronov, EE},
title = {Post-Release Changes of the Goat's Rue Rhizobia (Neorhizobium galegae bv. orientalis) Genomes in the Field: Prospects for Breeding the Symbiotically Effective Strains.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
pmid = {42883902},
issn = {1422-0067},
support = {Agreement of May 29, 2025 No. 075-15-2025-472//the Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Symbiosis/genetics ; *Genome, Bacterial ; *Rhizobium/genetics ; Root Nodules, Plant/microbiology ; Fabaceae/microbiology ; },
abstract = {Root nodule bacteria (rhizobia) fixing N2 in cooperation with legumes are broadly used for improving production of these plants inoculated with strains selected for high symbiotic activity. These bacteria are characterized by enormous evolutionary plasticity based on genomic rearrangements and horizontal gene transfer. However, this native plasticity is still poorly used for symbiotic improvement of the inoculant strains. In the presented paper, we analyzed genomic structure and symbiotic efficacy in ten clones isolated from nodules formed by the highly effective strain Gr30-13 of goat's rue rhizobia (Neorhizobium galegae bv. orientalis) on the host plant (Galega orientalis) grown for 1 or 2 years in the soil devoid of aboriginal populations of this rhizobia species. The genome analysis based on nanopore sequencing technology revealed different genomic rearrangements (IS transpositions, tandem duplications) in three clones, which exceed the remaining six clones in symbiotic efficiency. One clone with two tandem duplications in its genome significantly outperformed the initial strain in symbiotic efficiency by more than 35%. We tentatively suggest that the enhanced symbiotic efficiency may be linked to the detected genomic changes; if confirmed, such effects could be described as the "self-improvement" of rhizobia, driven by genomic plasticity and subsequent selection under field conditions. The presented model experiment suggests a new approach for breeding programs using nature-like technology based on the spontaneous genetic variability of symbiotically active rhizobia.},
}

*Symbiosis/genetics
*Genome, Bacterial
*Rhizobium/genetics
Root Nodules, Plant/microbiology
Fabaceae/microbiology

@article {pmid42881294,
year = {2026},
author = {Gitzen, T},
title = {The social life of viruses: a queer sort of science.},
journal = {History and philosophy of the life sciences},
volume = {48},
number = {4},
pages = {},
pmid = {42881294},
issn = {1742-6316},
mesh = {*Biological Evolution ; *Virus Physiological Phenomena ; *Viruses ; *Virology ; },
abstract = {A burgeoning microbiology field, sociovirology is the study of how viruses interact with one another and the effects such interactions have on social evolution. Challenging dominant narratives that viruses are individualistic pathogens, sociovirologists explore the social interaction of viruses through the language of cooperation, altruism, and cheating, social concepts with biological definitions. Viruses cannot self-replicate-they must rely on living cells to reproduce-and thus are commonly believed to be biologically nonliving. By focusing on virus-virus interaction and evolution, sociovirologists are displacing reproduction as a chief engine of aliveness and queering biology and the concept of life. I contend that in sociovirological publications, the aliveness of viruses is indexed through sociovirologists' use of language reserved for the interactions and social behaviors of life-forms alongside viruses' ability to evolve. This paper illustrates that by attending to social behavior and evolution, sociovirologists are proffering novel approaches to both viruses and the concept of life that displaces individual organism reproduction and vertical inheritance as normative of life with species reproduction and species evolution as normative for viruses even if nonnormative for biological understandings of life. Viruses are alive because, as species, they evolve despite an individual viral particle's fate.},
}

*Biological Evolution
*Virus Physiological Phenomena
*Viruses
*Virology

@article {pmid42879189,
year = {2026},
author = {Andrews, M and Russo, L and Hodge, S and Zhang, J},
title = {Biogeography and specificity of legume rhizobial symbiovars.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.007307},
pmid = {42879189},
issn = {1466-5034},
mesh = {*Fabaceae/microbiology/classification ; *Symbiosis ; *Phylogeny ; Root Nodules, Plant/microbiology ; Nitrogen Fixation ; *Rhizobium/classification/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Phylogeography ; },
abstract = {The majority of legume species (plant family Fabaceae) can fix atmospheric nitrogen (N2) via symbiotic bacteria (general term 'rhizobia') in root nodules. Symbiovars are defined as strains of rhizobia that can establish an N2-fixing symbiosis with distinct legume species and have specific symbiosis gene phylogenies. Here, symbiovar occurrence across rhizobial species was related to rhizobia and legume host taxonomy and geographic location of the symbiosis, and then their specificity was assessed in relation to legume species they did or did not nodulate. Sixty-eight rhizobial symbiovars occurred across 183 of the 275 described rhizobial species in all main rhizobial genera in different countries on all continents except Antarctica. Generally, individual symbiovars occurred within one rhizobial genus, but there were exceptions. Symbiovars associated with widely grown crop legume species were of different rhizobial species on different continents. Most other symbiovars occurred within rhizobial species isolated from one legume species, genus or clade/tribe in a single country. Data on legume nodulation are limited for half of the symbiovars, such that judgements on their wider specificity are not possible. However, several of these symbiovars were shown to be specific to particular legume species within a genus. All other symbiovars showed legume specificity, but this was variable. Overall, further nodulation and symbiosis gene phylogenetic studies are required to more clearly define symbiovars.},
}

*Fabaceae/microbiology/classification
*Symbiosis
*Phylogeny
Root Nodules, Plant/microbiology
Nitrogen Fixation
*Rhizobium/classification/genetics/physiology
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Sequence Analysis, DNA
Phylogeography

@article {pmid42879859,
year = {2026},
author = {Zhu, Q and Wang, Y and Wang, X and Jin, Z and Gong, P and Yuan, M and Yao, H},
title = {From passive carriers to selective filters: how microplastic aging shapes antibiotic resistance gene abundance.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131163},
doi = {10.1016/j.jenvman.2026.131163},
pmid = {42879859},
issn = {1095-8630},
abstract = {Microplastics (MPs) are widely recognized as vectors for antibiotic resistance genes (ARGs). However, pristine MPs are virtually nonexistent in nature. While environmental aging fundamentally alters MPs physicochemical properties, current studies report highly contradictory findings on how aging impacts ARG proliferation-ranging from synergistic enrichment to oxidative suppression-thereby precluding accurate ecological risk assessments. To resolve this conflict, we conducted a global meta-analysis of 701 independent observations. Aging significantly increased both absolute and relative ARG abundance (mean lnRR = 0.67 and 0.61, respectively), shifting MPs from passive carriers toward selective habitats. Critically, ARG abundance displayed non-linear temporal trajectories inferred from cross-study comparisons: absolute ARG abundance peaked at approximately 15 days of aging MPs, whereas relative ARG abundance showed a U-shaped pattern with a minimum at approximately 37.5 days. We propose a "boom-and-bust" conceptual model, in which an initial non-selective biomass surge is followed by late-stage, multi-stressor filtering; this model integrates our meta-analytic patterns with previously reported mechanisms and represents a hypothesis for direct experimental testing. Resistance mechanisms further diverged: efflux-pump genes peaked at mid-term aging on biodegradable polymers, while target-modification genes and mobile genetic elements remained enriched on high-surface-area recalcitrant plastics. Together, these findings suggest that aged MPs act as selective filters shaping the plastisphere resistome, and that aging state, temporal dynamics, and matrix-specific hotspots merit integration into antimicrobial resistance surveillance frameworks.},
}

@article {pmid42878466,
year = {2026},
author = {Khasbaatar, G and Han, Q and Wang, X-K and Song, L and Liu, C and Sun, X and Liu, Z-S and Liu, Y and Jiang, C-Y and Qiu, J-G and Liu, S-J and Zheng, Y and Li, D-F},
title = {Diversity of dirammox microorganisms.},
journal = {mBio},
volume = {},
number = {},
pages = {e0164526},
doi = {10.1128/mbio.01645-26},
pmid = {42878466},
issn = {2150-7511},
abstract = {UNLABELLED: Our knowledge of the nitrogen cycle has been advanced by the discovery of anammox bacteria, ammonia-oxidizing archaea, and comammox bacteria, along with their high diversity. Direct ammonia oxidation (dirammox), a recently discovered heterotrophic nitrification pathway, converts ammonium and organic nitrogen directly to N2 through the DnfABC multienzyme system, further expanding our understanding of the nitrogen cycle. However, the taxonomic distribution, prevalence, and nitrogen metabolic potential of microorganisms encoding dirammox genes remain poorly understood. Here, large-scale genome mining identified complete dnfABC gene clusters in 690 genomes representing 3 phyla and 26 genera. The dnfABC cluster showed a striking bimodal prevalence: it was nearly ubiquitous in Alcaligenes, Delftia, and Microvirgula but occurred sporadically in most other genera. These microorganisms were recovered from diverse environments, particularly organic nitrogen-rich habitats. Comparative analyses of DnfABC phylogeny, gene cluster organization, GC content, and flanking mobile genetic elements indicate that the dnfABC cluster is conserved within several core genera, whereas its sporadic distribution in other lineages suggests that horizontal gene transfer may have contributed to its dissemination. The dnfABC cluster co-occurs with genes associated with assimilatory nitrate/nitrite reduction to ammonium, dissimilatory nitrate/nitrite reduction to ammonium, denitrification, and/or nitrogen fixation, but not with marker genes for nitrification or anammox, indicating diverse nitrogen metabolic potential among potential dirammox microorganisms. Functional assays further showed that diverse dnfABC clusters consistently conferred ammonium- and glutamine-oxidizing activities in Escherichia coli, despite exhibiting low activities in their native hosts. These results suggest that dirammox is a broadly distributed, metabolically flexible, and tightly regulated pathway and may represent an overlooked route of nitrogen transformation in organic-rich habitats.

IMPORTANCE: Nitrogen is essential for all life, and our understanding of the nitrogen cycle has advanced substantially with the discovery of anammox bacteria, ammonia-oxidizing archaea, and comammox bacteria, which exhibit remarkable taxonomic and metabolic diversity. This study suggests that the recently discovered dirammox pathway may be more widespread in nature than previously recognized. Potential dirammox microorganisms exhibit broad phylogenetic and ecological distributions, high genomic diversity, and notable metabolic versatility. Functional assays indicate that dirammox activity is tightly regulated in native hosts, suggesting that its ecological role depends on specific environmental conditions. Unlike canonical nitrification and anammox, dirammox operates under conditions where other nitrogen transformations are limited, highlighting an important route of nitrogen loss in organic-rich habitats. These findings highlight the previously overlooked potential role of dirammox in nitrogen cycling, expand our understanding of microbial contributions to the global nitrogen cycle, and provide a foundation for future ecological and environmental research.},
}

@article {pmid42878877,
year = {2026},
author = {Xiong, L and Cui, Y and Shi, Z and Yang, Y and Shen, X and Cai, Y and Ji, X},
title = {Comparative genomic analysis of Agrobacterium salinitolerans provides insights into genetic diversity and pathogenic potential.},
journal = {Archives of microbiology},
volume = {209},
number = {1},
pages = {},
pmid = {42878877},
issn = {1432-072X},
support = {202402AE090018//Science and Technology Program of Yunnan Province/ ; CARS-23-G56//China Agriculture Research System of MOF and MARA/ ; 2024RCYP-10//Yunnan Academy of Agricultural Sciences Talent Introduction and Training Project/ ; 202501CF070036//Yunnan Fundamental Research Project/ ; 202404BI090009//Innovation Guidance and Technology Oriented Enterprise Cultivation Plan/ ; },
mesh = {*Genetic Variation ; *Agrobacterium/genetics/pathogenicity/classification/isolation & purification ; *Genome, Bacterial ; Genomics ; Virulence Factors/genetics ; Plant Tumors/microbiology ; Gene Transfer, Horizontal ; Phylogeny ; Interspersed Repetitive Sequences ; Plant Diseases/microbiology ; },
abstract = {Agrobacterium spp. are widespread plant pathogens, particularly associated with crown gall disease, and their genomic features and ecological adaptations underlie complex plant-microbe interactions. Agrobacterium salinitolerans, a relatively understudied member of this genus, exhibits distinct genomic traits that may contribute to its pathogenicity and environmental persistence, yet its genetic architecture and adaptive mechanisms remain poorly characterized. In this study, we conducted a comparative genomic analysis of A. salinitolerans strain YN6, isolated from crown gall tissue of Rosa spp., alongside 14 publicly available A. salinitolerans genomes. Pan-genome analysis, supported by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), revealed an open pan-genome structure indicative of high genetic diversity. This diversity is primarily driven by mobile genetic elements (MGEs) and horizontal gene transfer (HGT), while most core and accessory genes are maintained under purifying selection. We identified numerous virulence factors and antibiotic resistance genes linked to macromolecular secretion systems, underscoring the strain's genomic features associated with plant-pathogenic interactions. Additionally, a rich repertoire of carbohydrate-active enzyme (CAZyme) genes was detected, suggesting broad metabolic versatility and enhanced survival across diverse ecological niches. This study provides a comprehensive genomic characterization of A. salinitolerans, revealing its high genetic plasticity, evolutionary dynamics, and multifaceted ecological adaptations. The findings highlight the species genetic repertoire linked to host colonization and environmental survival strategies, laying a critical foundation for future functional genomic investigations.},
}

*Genetic Variation
*Agrobacterium/genetics/pathogenicity/classification/isolation & purification
*Genome, Bacterial
Genomics
Virulence Factors/genetics
Plant Tumors/microbiology
Gene Transfer, Horizontal
Phylogeny
Interspersed Repetitive Sequences
Plant Diseases/microbiology

@article {pmid42875441,
year = {2026},
author = {Pianezza, R and Saadain, S and Beaumont, M and Signor, S and Kofler, R},
title = {The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42875441},
issn = {2041-1723},
support = {R35GM155272//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P35093//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P34965//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
mesh = {Animals ; *Endogenous Retroviruses/genetics/classification ; *Drosophila melanogaster/genetics/virology ; Phylogeny ; Gene Transfer, Horizontal ; DNA Transposable Elements/genetics ; Genome, Insect ; },
abstract = {Transposable elements (TEs) are mobile DNA sequences that can proliferate within host genomes, occasionally capable of crossing species boundaries via horizontal transfer (HT). Here, we report the discovery and characterization of Kuruka, a recently invading TE in natural D. melanogaster populations. Kuruka encodes an envelope protein and belongs to the gypsy/gypsy superfamily, also called insect endogenous retroviruses. Analysis of over 1000 D. melanogaster genomes revealed that Kuruka first appeared in sub-Saharan Africa in 2010. Kuruka had spread to Asia, Europe and America in 2017-2019, and is still actively invading Europe and Oceania as of 2021. Phylogenomic analyses suggest that Kuruka entered in D. melanogaster via a recent HT from an Afrotropical Drosophila species, most likely D. erecta. This provides an example of recent TE transfer between an Afrotropical donor species and D. melanogaster. In D. erecta, Kuruka has a single genomic insertion, which is located within flamenco, a master regulator of TE activity. The presence of an active host defense (piRNAs) suggests that Kuruka is silenced in D. erecta. By capturing an invasion still in progress, our study sheds light on the processes that govern the emergence, establishment, and spread of TEs across species boundaries.},
}

Animals
*Endogenous Retroviruses/genetics/classification
*Drosophila melanogaster/genetics/virology
Phylogeny
Gene Transfer, Horizontal
DNA Transposable Elements/genetics
Genome, Insect

@article {pmid42877987,
year = {2026},
author = {Zhang, Y and Ren, G and Wu, J and Xu, J and Ji, Y and Li, G and Wang, Z and Wang, J and Jiao, X and Sun, L},
title = {Genomic evidence of clonal and IncX3 plasmid-mediated dissemination of blaNDM-7 in the Klebsiella pneumoniae complex.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {11},
pages = {},
doi = {10.1093/jac/dkag346},
pmid = {42877987},
issn = {1460-2091},
support = {BRA2020002//fifth phase of the '333 Project' scientific research project in Jiangsu Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institution (PAPD)/ ; SJCX23_1958//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
mesh = {*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/enzymology ; *beta-Lactamases/genetics ; *Plasmids/genetics ; Humans ; Phylogeny ; *Klebsiella Infections/microbiology/epidemiology ; China/epidemiology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Genome, Bacterial ; },
abstract = {BACKGROUND: Carbapenem-resistant Enterobacterales (CRE), particularly those carrying New Delhi metallo-β-lactamase (NDM) variants, pose a major global health threat. Among these, NDM-7 has attracted increasing attention due to its enhanced carbapenemase activity and clinical relevance. This study investigated the prevalence, genomic characteristics and dissemination of blaNDM-7-positive Klebsiella pneumoniae complex isolates from clinical and environmental sources in Yangzhou, China.

METHODS: A total of 401 clinical isolates, 282 hospital surface swabs and 366 wastewater samples collected between 2018 and 2024 were screened for blaNDM. Antimicrobial susceptibility testing and whole-genome sequencing were performed to characterize resistance profiles, genomic features and phylogenetic relationships. Conjugation and serial-passage assays were used to assess plasmid transferability and stability, respectively.

RESULTS: Seven blaNDM-7-positive isolates were identified, including one clinical isolate, one hospital environmental isolate and five wastewater isolates. All exhibited multidrug resistance. The blaNDM-7 gene was located on highly conserved ∼46 kb IncX3 plasmids that exhibited high conjugation frequencies (10-5-10-4) and stability (96.0%-98.7% mean retention after approximately 600 generations). Phylogenetic analysis revealed close genomic relatedness among the six ST196 K. quasipneumoniae isolates recovered from different sources, with only 0-7 core-genome SNP differences. All six isolates were recovered within approximately 6 months, consistent with recent common ancestry and possible clonal dissemination across settings.

CONCLUSIONS: The close genomic relatedness of ST196 isolates from different sources supports possible clonal dissemination, while the high conservation, transferability and stability of IncX3 plasmids highlight their important role in the dissemination of blaNDM-7. These findings underscore the importance of continued genomic surveillance of blaNDM-7 and its associated mobile genetic elements across clinical and environmental settings.},
}

*Klebsiella pneumoniae/genetics/drug effects/isolation & purification/enzymology
*beta-Lactamases/genetics
*Plasmids/genetics
Humans
Phylogeny
*Klebsiella Infections/microbiology/epidemiology
China/epidemiology
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Gene Transfer, Horizontal
Wastewater/microbiology
Genome, Bacterial

@article {pmid42878156,
year = {2026},
author = {Pan, J and Singh, A and Gamladdalage, SW and Hicks, J and Williamson, A},
title = {DNA ligase LigE increases bacterial transformation with damaged extracellular DNA.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70483},
pmid = {42878156},
issn = {1873-3468},
support = {UOW2501//Marsden Fund/ ; Rutherford Discovery 20-UOW-004//Royal Society Te Apārangi/ ; Doctoral Scholarship- Avi Singh//University of Waikato/ ; Doctoral Scholarship- Jolyn Pan//University of Waikato/ ; 21/754//Health Research Council of New Zealand/ ; 23/534//Health Research Council of New Zealand/ ; #354//Waikato Medical Research Foundation/ ; },
abstract = {LigE is a periplasm-targeted ATP-dependent DNA ligase found in many Gram-negative bacteria, including Neisseria gonorrhoeae. Although LigE has been shown to have a role in biofilm formation, many LigE-possessing bacteria are also naturally competent, suggesting a possible role in transformation with extracellular DNA. Here, we demonstrate that LigE participates in competence by increasing transformation with nuclease-damaged extracellular DNA that contains single-stranded or cohesive breaks, and that this activity is dependent on its secretion signal peptide, indicating an extra-cytoplasmic location of activity. We show that increased transformation with this restricted DNA is ATP-dependent; however, the physiological source of ATP in the natural host remains unknown. Our findings highlight a potential role of Ngo-LigE in Neisseria gonorrhoeae competence and horizontal gene transfer.},
}

@article {pmid42867787,
year = {2027},
author = {Wang, J and He, L and Shen, J and Asimi, S and Lv, L},
title = {Conjugation Assay for Antimicrobial Resistance Plasmids in Salmonella enterica.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3078},
number = {},
pages = {135-144},
pmid = {42867787},
issn = {1940-6029},
mesh = {*Salmonella enterica/genetics/drug effects ; *Plasmids/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The conjugation assay is an essential technique for investigating horizontal gene transfer and assessing the mobility of antimicrobial resistance plasmids in Enterobacteriaceae. Here we describe a commonly used method for performing conjugation experiments to quantify resistance plasmid transfer in Salmonella enterica under laboratory conditions. It outlines the required materials, experimental conditions, and verification of transconjugants. The method is applicable to most plasmid incompatibility groups within Enterobacteriaceae and can be adapted to other bacterial species.},
}

*Salmonella enterica/genetics/drug effects
*Plasmids/genetics
*Conjugation, Genetic
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42868168,
year = {2026},
author = {Nangolo, LN and Kakungu, A and Musundi, S and Kandanda, GK and Odoyo, S and Oclu, A and Danso, J and Egyir, B and Onywera, H and Githinji, G and Shilangale, R and Mwapagha, LM},
title = {Phenotypic and genomic characterization of antimicrobial resistance in Escherichia coli and Klebsiella spp. from livestock in Namibia.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0359106},
pmid = {42868168},
issn = {1932-6203},
mesh = {Animals ; Namibia ; *Escherichia coli/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; *Livestock/microbiology ; *Klebsiella/genetics/drug effects/isolation & purification ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Phenotype ; Cattle ; Sheep/microbiology ; Escherichia coli Infections/microbiology/veterinary ; Whole Genome Sequencing ; *Drug Resistance, Multiple, Bacterial/genetics ; Chickens/microbiology ; Genome, Bacterial ; Feces/microbiology ; Genomics ; },
abstract = {OBJECTIVES: Antimicrobial resistance (AMR) is a growing concern within the One Health framework. This study characterized AMR in Escherichia coli and Klebsiella spp. isolated from livestock fecal samples across commercial and communal farms in Namibia.

METHODS: About 140 fecal samples were collected from cattle, sheep, and chickens on farms in Namibia. Isolates were identified using the VITEK® 2 system and MALDI-ToF mass spectrometry. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method against nine antibiotics. Genomic DNA was extracted and subjected to whole-genome sequencing (WGS) using Illumina NextSeq 2000 platform.

RESULTS: AMR genes were identified using ResFinder and Abricate, plasmid-associated replicons using plasmid analysis tools, and virulence-associated genes using VirulenceFinder. Phenotypic analyses showed resistance to β-lactams, tetracyclines, aminoglycosides, and fluoroquinolones among the tested isolates. WGS identified diverse resistance determinants and sequence types, including E. coli ST101 and ST1431, K. oxytoca ST2, and K. pneumoniae ST22. Multiple plasmid replicons were detected; however, their presence alone does not establish that individual resistance genes were plasmid-borne or that horizontal gene transfer occurred.

CONCLUSIONS: This study provides the first genomic evidence of livestock-associated AMR in Namibia, identifying resistance determinants and multidrug-resistant E. coli and Klebsiella spp. in the sampled livestock population. The findings provide baseline genomic data for AMR surveillance and support strengthened antimicrobial stewardship and One Health monitoring. The concurrent detection of chromosomal resistance-associated mutations and diverse plasmid replicons illustrates the complexity of resistance mechanisms, although the present short-read data do not establish the direct physical linkage of individual ARGs to plasmids. These findings highlight the need for coordinated surveillance across animal, human, and environmental health sectors in Namibia.},
}

Animals
Namibia
*Escherichia coli/genetics/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
*Livestock/microbiology
*Klebsiella/genetics/drug effects/isolation & purification
Microbial Sensitivity Tests
Plasmids/genetics
*Drug Resistance, Bacterial/genetics
Phenotype
Cattle
Sheep/microbiology
Escherichia coli Infections/microbiology/veterinary
Whole Genome Sequencing
*Drug Resistance, Multiple, Bacterial/genetics
Chickens/microbiology
Genome, Bacterial
Feces/microbiology
Genomics

@article {pmid42869431,
year = {2026},
author = {Kyriacou, RG and Herbette, M and Baird, RB and Monteith, KM and Yamashita, YM and Ross, L and Hodson, CN},
title = {Gene-rich fungus gnat germline-restricted chromosomes are largely transcriptionally quiescent.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag283},
pmid = {42869431},
issn = {1943-2631},
abstract = {Germline-restricted chromosomes (GRCs) constitute a unique class of chromosomes confined to germ cells. Arising in multiple evolutionarily distant lineages, GRCs have been identified in three insect families (non-biting midges, gall midges, and fungus gnats), each within the order Diptera. Genomic characterisation in fungus gnats has revealed GRCs to be large, gene-rich chromosomes, which, together with their persistence over millennia, implies they play important biological roles within this clade. However, transcription from these chromosomes has yet to be demonstrated, leaving key questions about their function and activity unresolved. Here, we present the first direct analysis of GRC transcription in Diptera, combining immunofluorescence staining with bulk RNA-seq data in the fungus gnat Bradysia coprophila (Sciaridae). We find that transcription from GRCs is highly limited during key developmental stages. In larval and adult gonads, elongating polymerase II appears to be active at all chromosomes except the GRCs in most cells. Furthermore, using stringent filtering criteria, we identify only 10 confidently expressed GRC-linked genes, mostly of unknown function. In addition, we report the surprising presence of a ∼290 kb region of bacterial-derived sequence on GRC2, likely acquired through horizontal transfer from germline-associated endosymbionts. Overall, these findings identify GRCs in fungus gnats as unique chromosomes, largely transcriptionally quiescent during key stages of B. coprophila development, yet capable of maintaining both endogenous and potentially horizontally acquired genes over evolutionary timescales. This raises fundamental questions about the mechanisms that maintain gene content in these chromosomes and their contribution, if any, to germline biology.},
}

@article {pmid42869870,
year = {2026},
author = {Zhou, Y and Haile, AT and Kibret, M and Li, H and Haileselassie, MM and Bekele, TW and Kassa, JM and Demissie, K and Wyrsch, ER and Djordjevic, SP and Jobling, K and Quintela-Baluja, M and Su, JQ and Mateo-Sagasta, J and Graham, DW},
title = {Inadequate waste management drives the spread of antimicrobial resistance across the watershed of a large African city.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110554},
doi = {10.1016/j.envint.2026.110554},
pmid = {42869870},
issn = {1873-6750},
abstract = {Rapid urbanization in the Global South consistently outpaces sanitation infrastructure, transforming urban rivers into AMR reservoirs. Yet watershed-scale quantification of resistomes in such settings remains scarce, limiting exposure risk assessment and intervention planning. Here we present the most detailed spatial baseline for waterborne AMR in sub-Saharan Africa, using the Akaki River (Addis Ababa, Ethiopia) as a model system for rapidly urbanizing megacity watersheds with inadequate sanitation. We sampled 38 sites across an extreme pollution gradient during the dry season, when low flow produces maximum pollutant concentrations and the highest resident exposure risk. Water quality, microbiome marker data, 309 antibiotic resistance genes (ARGs), and 57 mobile genetic elements (MGEs) were quantified by high-throughput quantitative PCR. ARG and MGE abundances in central urban reaches exceeded 10[10] gene copies L[-1], indistinguishable from untreated sewage. Critically, clinically important ARGs co-occurred widely with broad-host-range MGEs, including the IncP-1α plasmid backbone, IS26, ISEcp1, IS6100, and class 1 integron integrase genes, indicating that ARGs are primed for potential horizontal gene transfer in waters where hundreds of thousands of Addis residents bathe, wash, and irrigate food crops. Dissolved oxygen depletion and elevated NH4-N correlated significantly with resistome expansion (p < 0.01), serving as robust chemical proxies for diffuse, system-wide raw sewage inputs that carry the actual mechanistic AMR drivers (e.g., heavy metals, antibiotic residues, and resistant hosts). The 38-site spatial design and dry-season worst-case conditions together provide a replicable model for AMR exposure assessment in comparable Global South cities.},
}

@article {pmid42870292,
year = {2026},
author = {Maull, V and Aguadé-Gorgorió, G and de Lorenzo, V and Solé, R},
title = {Synthetic horizontal gene transfer for ecosystem restoration.},
journal = {Biology direct},
volume = {21},
number = {1},
pages = {},
pmid = {42870292},
issn = {1745-6150},
mesh = {*Gene Transfer, Horizontal ; *Ecosystem ; *Soil Microbiology ; Plasmids/genetics ; *Genes, Synthetic ; *Synthetic Biology ; },
abstract = {Restoring endangered ecosystems has become a pressing issue as the effects of global warming continue to harm existing communities. During the last decade, several studies have suggested the use of synthetic biology as a tool to protect these biodiverse communities by increasing their functionality. A critical example concerns soil microbiome communities in drylands, where increasing water retention by some of the constituent species could effectively protect the ecosystem from abrupt degradation. However, how to effectively deploy a functional synthetic construct that can scale its impact to the community level remains an open question. Recent experimental research has designed recombinant gene plasmids with the capacity to horizontally transfer across soil microbial communities. Here, we explore the impacts of synthetic horizontal gene transfer in models of ecological consortia. We define a consumer-resource model in which species can share an engineered plasmid that reduces resource loss, effectively coupling multispecies dynamics and gene spreading. By doing so, we identify a wide range of parameters and the optimal gene transfer conditions for which the intervention promotes biodiversity and biomass gains, while regulating gene propagation and the spread of engineered organisms. Our work provides a first step toward understanding the mechanisms and opportunities of engineered plasmid transfer in multispecies ecological communities.},
}

*Gene Transfer, Horizontal
*Ecosystem
*Soil Microbiology
Plasmids/genetics
*Genes, Synthetic
*Synthetic Biology

@article {pmid42872063,
year = {2026},
author = {Wei, S and Lin, J and Xue, R and Xu, W},
title = {Vibrio alginolyticus: an emerging marine pathogen at the intersection of aquaculture, public health, and antimicrobial resistance.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1965608},
pmid = {42872063},
issn = {2297-1769},
abstract = {Vibrio alginolyticus is a halophilic, Gram-negative marine bacterium that has emerged as a significant opportunistic pathogen affecting both marine animals and humans. As one of the most abundant vibrios in coastal and estuarine environments worldwide, V. alginolyticus causes substantial economic losses in aquaculture through vibriosis in fish, shrimp, and shellfish, while also being responsible for wound infections, otitis externa, and occasionally gastroenteritis in humans following seawater exposure or seafood consumption. The pathogenesis of V. alginolyticus is multifactorial, involving an arsenal of virulence determinants including secretion systems (type III, type VI, and type II), haemolysins, adhesins, biofilm formation, quorum sensing-regulated factors, and the recently recognized contributions of non-coding RNAs and outer membrane vesicles. Recent genomic analyses have revealed considerable genetic diversity among isolates and identified a ubiquitous presence of β-lactam resistance genes, raising concerns about natural resistance and the potential for horizontal gene transfer. The interplay between rising seawater temperatures, intensive aquaculture practices, and increasing antimicrobial resistance has positioned V. alginolyticus as an emerging pathogen of growing concern. This Review synthesizes current knowledge on the epidemiology, genomics, virulence mechanisms, host interactions, and control strategies of V. alginolyticus, with an emphasis on the molecular determinants of pathogenesis, including the regulatory networks governing adhesion, biofilm formation, and metabolic adaptation, and the challenges posed by antimicrobial resistance. We also discuss promising alternative control approaches, including phage therapy, vaccination, and probiotic strategies, and identify key knowledge gaps that warrant future investigation.},
}

@article {pmid42873111,
year = {2026},
author = {Abrahao, JS},
title = {Primer: Giant viruses of protists.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0125726},
doi = {10.1128/jvi.01257-26},
pmid = {42873111},
issn = {1098-5514},
abstract = {Giant viruses infecting protists have expanded our understanding of viral diversity. These members of the phylum Nucleocytoviricota possess genomes that can exceed 2.5 Mb and encode hundreds to thousands of proteins, including functions once thought unique to cellular organisms. They infect amoebae, algae, and other unicellular eukaryotes, forming large factories and interacting with virophages and mobile genetic elements. Their virions display diverse architectures, from icosahedral particles to amphora-shaped pandoraviruses and tail-bearing tupanviruses. Comparative genomics highlights evolutionary processes such as horizontal gene transfer, gene duplication, de novo gene birth, and genome rearrangements, which contribute to their genomic diversity. Despite their widespread presence in aquatic and terrestrial ecosystems, many aspects of their biology remain unknown, including the roles of lineage-specific ORFan genes (open reading frames with no detectable homologs in current databases) and the molecular strategies used to manipulate hosts. This minireview provides an accessible overview of protist-infecting giant viruses, summarizing their classification, virion architecture, replication strategies, and evolutionary scenarios, and points to key questions that remain open.},
}

@article {pmid42862870,
year = {2026},
author = {Liu, Z and Good, BH},
title = {Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria.},
journal = {PLoS biology},
volume = {24},
number = {10},
pages = {e3004052},
doi = {10.1371/journal.pbio.3004052},
pmid = {42862870},
issn = {1545-7885},
abstract = {The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein-coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations.},
}

@article {pmid42866320,
year = {2026},
author = {Bao, Z and Mao, Z and Tu, Y},
title = {Genomic characteristics of a carbapenem-resistant NDM-1-producing Aeromonas caviae isolate from extraintestinal infection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953006},
pmid = {42866320},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aims to clarify the drug resistance characteristics and genomic background of bile-derived NDM-1-producing Aeromonas caviae (A. caviae) isolate from extraintestinal infection, providing a theoretical basis for the prevention and control of clinical infections.

METHODS: A bile-derived LHL25108073-A. caviae isolate (NCBI accession number: JBSUSV000000000) was chosen as the study focus. Through flight mass spectrometry, VITEK-2 drug susceptibility phenotype validation, and whole-genome sequencing, multi-point sequence typing (MLST), VFDB database, CARD database, PlasmidFinder 2.1 software, whole-genome alignment, plasmid synteny analysis, and plasmid conjugation assay were applied for an integrative analysis.

RESULTS: This isolate was identified to be ST2281, a sequence type rarely reported across clinical, environmental, and agricultural sources, with a genome size of 4,885,524 bp and a GC content of 61.27%, carrying one chromosome (4,687,937 bp) and one drug-resistant plasmid (197,587 bp). A total of 58 high-confidence virulence genes were detected, covering common flagella, polar flagella, lateral flagella, type IV pili, Msh pili, type VI/II secretion system (T6SS/T2SS), heme-uptake systems, Endotoxins, and hemolysin, forming multiple pathogenic mechanisms. Among 14 drug resistance genes, the carbapenem-resistant NDM-1 gene was highly consistent with the genotype, only sensitive to a few drugs such as amikacin and aztreonam, based on the results of drug susceptibility tests. The drug-resistant plasmid could not autonomously conjugate and transfer due to the loss of the oriT site and was untypable by conventional plasmid typing. This plasmid shared 99-100% homology in the resistance core regions with two NDM-1-carrying A. caviae plasmids, pK433-NDM (OK287926) from sputum in Taizhou, Zhejiang, and pFAHZZU2447_NDM (CP100393) from bile in Zhengzhou, with identical bla NDM-1 sequences. Genetic background analysis based on the genomes of 157 A. caviae isolates from China and neighboring regions identified that ST313 was the dominant sequence type (ST), which accounted for the largest proportion among in Chinese isolates.

CONCLUSION: This study characterizes the molecular profiles of an extraintestinal, bile-derived NDM-1-producing A. caviae isolate belonging to ST2281, validates its abundant reservoir of virulence genes and comprehensive multi-drug resistance mechanisms, and further reveals the potential risk of NDM-1 dissemination via alternative horizontal gene transfer pathways, such as transformation and transduction. Genomic evolutionary analysis reveals that although the ST2281 isolate identified in this study shares certain phylogenetic relatedness with the prevalent ST313 lineage in China at the housekeeping gene level, whole-genome SNP-based phylogenetic analysis confirms a substantial genetic distance between them. ST2281 represents an independent and rare genetic lineage with limited global prevalence, which warrants heightened vigilance against its concealed transmission and potential clinical infection risks. Collectively, these results offer crucial genomic evidence for molecular tracing, targeted clinical antimicrobial therapy, and epidemiological containment of carbapenem resistant A. caviae.},
}

@article {pmid42866372,
year = {2026},
author = {Wei, Q and Li, Y and Ruan, A},
title = {A metagenomic snapshot of metabolic potentials in wintertime eutrophic sediments of Lake Taihu inferred from metagenome-assembled genomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929411},
pmid = {42866372},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding the metabolic potential of microbial communities in eutrophic lake sediments at the genome-resolved level is essential for predicting nutrient cycling and stress responses in contaminated freshwater ecosystems.

METHODS: In this study, we reconstructed 206 dereplicated metagenome-assembled genomes (MAGs) from sediment cores collected across four regions of Lake Taihu.

RESULTS: These dereplicated MAGs spanned 34 classified phyla and 72 classified genera, with 97.6% unclassified at the species level, indicating substantial genomic novelty. The cyanobacterial MAGs harbored diverse secondary metabolite biosynthetic gene clusters, suggesting a genomic basis for potential adaptive traits. Across all dereplicated MAGs, the highest biosynthetic potential for secondary metabolites was observed in Chloroflexota and Pseudomonadota. Putative antibiotic resistance genes were predominantly represented by glycopeptide resistance determinants (vanT/vanW) and resistance-nodulation-division (RND) efflux pumps, which together accounted for 86.1% of the detected resistome. Additionally, 490 predicted horizontal gene transfer (HGT) events were identified, with transferred genes being most prevalent in energy metabolism (12.4%), translation (10.8%), and transcriptional regulation (7.2%).

DISCUSSION: This genome-resolved survey provides a foundation for understanding the metabolic and genomic potential of sediment microbiomes in eutrophic freshwater systems.},
}

@article {pmid42867246,
year = {2026},
author = {Amin, NH and Troian, EA and Maldonado, HM and Woychik, NA},
title = {Acquisition of a toxin-antitoxin system within a mobile genetic element likely enhances Mycobacterium abscessus fitness by enforcing cargo retention.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093426},
doi = {10.1128/msystems.00934-26},
pmid = {42867246},
issn = {2379-5077},
abstract = {UNLABELLED: Infections caused by the emerging pathogen Mycobacterium abscessus (Mab) require prolonged multidrug treatment regimens that frequently fail because its accessory genome has incorporated a daunting array of poorly defined resistance mechanisms. However, the processes governing acquisition and retention of new genetic material within the Mab accessory genome remain poorly understood. Here, we first identified two Mab clinical strains that harbor the same uncharacterized toxin-antitoxin (TA) system at different genomic positions. Using computational analyses of the surrounding DNA context, we discovered that each TA system resides within identical mobile genetic element (MGE) cassettes whose positions exchange between the two strains via site-specific recombinases. We then applied a specialized 5' RNA-seq approach to identify initiator tRNA[fMet] as the exclusive RNA target of the VapC2 TA toxin residing within the MGE. VapC2-mediated tRNA[fMet] inactivation by cleavage at its anticodon stem loop leads to growth arrest and global translation inhibition. This activity ensures stable inheritance of the MGE and its resident cargo genes through a mechanism similar to postsegregational killing. Our findings uncover the mechanism for durable expansion of the Mab accessory genome and suggest a selective advantage whereby toxin-mediated entry into a reversible growth-arrested state may reduce antibiotic susceptibility. Together, these results illustrate how retention of horizontally acquired MGEs containing a potent TA system can drive adaptive genome evolution to enhance fitness in this highly drug-resistant pathogen.

IMPORTANCE: Mycobacterium abscessus (Mab) causes chronic lung disease and skin and soft tissue infections, posing a major threat to individuals with cystic fibrosis, underlying lung disease, lung transplants, or weakened immune systems. Unlike Mycobacterium tuberculosis, Mab has a large and highly plastic accessory genome generally thought to be predominantly shaped by horizontal gene transfer and recombination. However, the mechanisms that stabilize newly acquired genetic material in this pathogen remain poorly understood. Here, we identify a toxin-antitoxin (TA) system embedded within a mobile genetic element (MGE) predicted to enforce stable retention of the MGE through a mechanism similar to postsegregational killing. The toxin inactivates initiator tRNA[fMet], inducing reversible growth arrest that likely reduces antibiotic efficacy. By functioning as an addiction module, this TA system also ensures stable inheritance of co-transferred accessory genes within the MGE, providing a mechanism for long-term retention of horizontally acquired genetic material that enhances pathogen fitness.},
}

@article {pmid42857538,
year = {2026},
author = {El Belghiti, I and Wardi, M and Amin, AB and Lemkhente, Z and Sadki, K and Boubrik, F and Belmouden, A},
title = {Bacteriophages in the environmental control of antimicrobial resistance: opportunities, risks, and surveillance challenges.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938962},
pmid = {42857538},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a major global public health challenge, driven by the persistence and dissemination of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). These resistance determinants can accumulate and spread across diverse environmental compartments, including wastewater, hospital effluents, agricultural systems, and landfills, facilitating their dissemination through mechanisms such as horizontal gene transfer. Bacteriophages have emerged as promising tools for the targeted control of antibiotic-resistant bacterial populations, as their lytic activity can overcome conventional antibiotic resistance mechanisms and effectively target multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. In addition, phage-encoded enzymes, including endolysins and polysaccharide depolymerases, can disrupt bacterial cell structures and biofilms, further enhancing their potential as alternative antimicrobial strategies. However, the role of bacteriophages in AMR dynamics is inherently dual, as lytic phages can reduce antibiotic-resistant bacterial populations, whereas temperate phages may contribute to the dissemination of ARGs through transduction-mediated gene transfer. This duality represents an important biosafety concern that requires rigorous assessment before their large-scale application in environmental settings. This review critically examines the role of bacteriophages in addressing environmental antimicrobial resistance within a One Health framework. It first explores environmental ARG reservoirs and current surveillance approaches, followed by bacteriophage biology and mechanisms of action, their applications in clinical medicine, veterinary science, and environmental biocontrol, and finally the biological constraints and strategies to address these challenges. This work integrates environmental surveillance with phage-based intervention strategies to support the rational and responsible deployment of bacteriophages as complementary tools in the global response to AMR.},
}

@article {pmid42858667,
year = {2026},
author = {Li, X and Huang, H and Chen, H and Huang, B and Fan, R and Du, J and Cui, P},
title = {Combination-specific effects of antibiotic and disinfectant co-contamination on the enrichment of antibiotic resistance genes in sediments.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143867},
doi = {10.1016/j.jhazmat.2026.143867},
pmid = {42858667},
issn = {1873-3336},
abstract = {The environmental co-occurrence of disinfectants and antibiotics has emerged as a typical multi-pollutant issue, with river sediments serving as critical sinks and accumulation media. However, whether their combined exposure accelerate antibiotic resistance genes (ARGs) dissemination in sediments remains unclear. Here, we systematically evaluated the effects of single and combined exposures to sodium hypochlorite and representative antibiotics on the sediment resistome and microbial communities. The results demonstrated that combined exposure generally increased the relative abundances of ARGs (1.83- to 3.57-fold) and mobile genetic elements (MGEs, 2.39- to 22.28-fold). Notably, sodium hypochlorite-gentamicin combination exhibited the most pronounced synergistic effect, consistent with toxicological model prediction. Combined exposure also reshaped bacterial community structure and enriched potential ARG-host taxa, while co-occurrence network analysis identified Limosilactobacillus as a candidate genus associated with multiple ARGs. Mechanistically, partial least squares path modeling indicated that MGE-mediated horizontal gene transfer was the dominant pathway driving ARGs enrichment. Plasmid conjugation assays further showed that NaClO + gentamicin increased conjugation frequency by 3.81-fold, supporting enhanced horizontal gene transfer. Overall, this study elucidates the intrinsic mechanisms by which complex pollution drives ARGs propagation in sediments, highlighting the overlooked ecological risks associated with disinfectant-antibiotic co-contamination in aquatic environments.},
}

@article {pmid42858671,
year = {2026},
author = {Zhou, Q and Zhao, M and Daouda, M and Tian, H and Yu, X and Ye, C and Wang, L},
title = {Stage-wise far-UVC/chlorine process curbs antimicrobial resistance in hospital wastewater: Short-burst inactivation and sustained suppression of recovery and resistance transfer.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143868},
doi = {10.1016/j.jhazmat.2026.143868},
pmid = {42858671},
issn = {1873-3336},
abstract = {Conventional UV254/chlorine can leave incomplete genetic damage and create a low-dose window that promotes horizontal gene transfer (HGT), limiting reliable antimicrobial-resistance (AMR) control. Here, UV222/chlorine (1 mg/L free chlorine) was evaluated in 0.22-μm-filtered hospital wastewater inoculated with E. coli DH5α-RP4 and compared with UV222, UV254, and UV254/chlorine. During UV222/chlorine treatment in hospital wastewater, free available chlorine (FAC) declined rapidly and approached the detection limit at approximately 35 mJ/cm[2], whereas UV254/chlorine retained measurable FAC at 100 mJ/cm[2]. Chloride promoted conversion of Cl· to selective Cl2·[-], whereas tert-butanol quenching indicated a smaller contribution from ·OH. Accordingly, the process comprised an initial chlorine-enhanced phase (0-35 mJ/cm[2]), which delivered ∼2.5-log greater ARB inactivation than UV222 alone, followed by a UV222-dominated phase after FAC depletion. Membrane permeabilization largely saturated during Stage 1, supporting an acute rather than dose-proportional envelope attack. At 100 mJ/cm[2], UV222/chlorine prevented regrowth, reduced intracellular antibiotic resistance genes (ARGs) by 76.6-88.3%, and drove RP4 conjugation toward zero. In contrast, UV254/chlorine transiently increased conjugation to ∼150% of the control at low doses. Transcriptomics showed concurrent suppression of envelope maintenance, DNA repair, protein homeostasis, and metabolism. Thus, UV222/chlorine combines a short RCS shock with sustained multi-target damage to control ARB, ARG persistence, and plasmid-mediated HGT in complex wastewater.},
}

@article {pmid42858969,
year = {2026},
author = {Liu, X and Feng, C and Fan, Q and Li, F and Liu, J and Yi, S and Lu, H and Wu, Y and Liu, Y and Tian, J},
title = {Temporal dynamics of the antibiotic resistome in pepper fruits: The trade-off between phytochemical defenses and heavy metal-induced co-selection.},
journal = {Food research international (Ottawa, Ont.)},
volume = {244},
number = {},
pages = {120411},
doi = {10.1016/j.foodres.2026.120411},
pmid = {42858969},
issn = {1873-7145},
mesh = {*Metals, Heavy/analysis ; *Capsicum/microbiology/chemistry/genetics ; *Fruit/chemistry/microbiology ; Capsaicin/analysis ; *Phytochemicals/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Pepper fruits are globally consumed vegetables and spices that may serve as potential vectors for the dissemination of antibiotic resistance genes (ARGs) into the human food chain. This study investigated the associations of endogenous capsaicin and exogenous heavy metals with the resistome dynamics of peppers across successive harvest stages. Metagenomic analyses revealed temporal variations in the pepper resistome within the agroecosystem. High capsaicin levels during early harvest stages were negatively associated with ARG abundance, whereas the gradual decline of phytochemical defenses during later stages coincided with increased heavy metal accumulation and ARG enrichment. Analysis of large-scale field samples further supported the inverse relationship between capsaicin content and ARG abundance. RT-qPCR assays conducted under controlled laboratory conditions indicated that, unlike capsaicin, heavy metals (such as Cu and Cd) directly promoted the expression of metal resistance and efflux-related genes in a dose-dependent and synergistic manner. Exposure to 50 mg/L of Cu[2+] increased the abundance of CopR by 11.63-fold, while 0.6 mg/L Cd[2+] exposure increased the abundances of baeR and mdtB by 8.51- and 7.89-fold, respectively. Furthermore, heavy metal stress substantially enhanced horizontal gene transfer, with Cd exposure increasing conjugation frequencies by 2.57-fold. These findings demonstrate that the pepper microenvironment represents a dynamic ecological niche in which plant-derived chemical defenses and abiotic contaminants jointly influence ARG dissemination. This study provides new insights into the multifactorial mechanisms driving ARG migration in soil-pepper systems and offers a scientific basis for reducing antibiotic resistance risks in agricultural production.},
}

*Metals, Heavy/analysis
*Capsicum/microbiology/chemistry/genetics
*Fruit/chemistry/microbiology
Capsaicin/analysis
*Phytochemicals/analysis
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42859255,
year = {2026},
author = {Cornacchia, A and Comini, S and Pomilio, F and Quirino, A and Paglietti, B and Greco, R and Costa, C and Boattini, M and Bianco, G and , },
title = {Multi-carbapenemase-producing Klebsiella pneumoniae: Genomic characterization and In Vitro evaluation of cefiderocol and novel β-lactam/β-lactamase inhibitor combinations.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42859255},
issn = {1573-4978},
mesh = {Cefiderocol ; *Klebsiella pneumoniae/genetics/drug effects ; Cephalosporins/pharmacology ; Humans ; Cefepime/pharmacology ; Microbial Sensitivity Tests/methods ; *beta-Lactamases/genetics/metabolism ; *beta-Lactamase Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Aztreonam/pharmacology ; Azabicyclo Compounds/pharmacology ; Italy/epidemiology ; Drug Resistance, Multiple, Bacterial/genetics ; Klebsiella Infections/microbiology/drug therapy ; beta-Lactams/pharmacology ; Drug Combinations ; Cyclooctanes/pharmacology ; Whole Genome Sequencing ; Plasmids/genetics ; Third Generation Cephalosporins ; Multilocus Sequence Typing ; Piperidines ; Triazoles ; },
abstract = {BACKGROUND: Multi-carbapenemase-producing Klebsiella pneumoniae (MCP-Kp) represents an emerging threat due to its extensive drug resistance and the scarcity of effective therapeutic options. This study characterizes the epidemiology, genomic features, and in vitro activity of novel antimicrobial agents against MCP-Kp isolates recovered from bloodstream infections in Italy.

METHODS AND RESULTS: From 2022 to 2023, a total of 414 non-duplicate carbapenemase-producing K. pneumoniae isolates were collected from 14 Italian hospitals. Antimicrobial susceptibility testing of the MCP-Kp isolates included cefiderocol, aztreonam/avibactam, cefepime/zidebactam, cefepime/enmetazobactam and relevant comparators. Whole-genome sequencing was performed to determine multilocus sequence types (STs), capsule loci, plasmid replicons, resistance determinants, and virulence-associated genes. MCP isolates accounted for 2.4% of all carbapenemase producers and displayed six distinct carbapenemase combinations. Genomic analysis revealed a polyclonal population (ST512, ST147, ST383, ST35, ST320, ST6668) characterized by heterogeneous capsule loci, diverse plasmid replicons, extensive β-lactamase repertoires, porin alterations, and widespread non-β-lactam resistance determinants. Two isolates carried mgrB disruptions associated with colistin resistance. MCP isolates exhibited high-level resistance to most β-lactams and to first- and second-generation β-lactam/β-lactamase inhibitor combinations. Aztreonam/avibactam, cefepime/zidebactam, and cefiderocol retained potent in vitro activity, with susceptibility rates of 100%, 100%, and 80%, respectively. Synergy was consistently observed between aztreonam and ceftazidime/avibactam, meropenem/vaborbactam, or cefepime/enmetazobactam across all aztreonam-resistant, metallo-β-lactamase-producing MCP-Kp isolates.

CONCLUSIONS: MCP-Kp in Italy exhibited substantial genomic diversity and multidrug resistance, driven by horizontal gene transfer and plasmid-mediated dissemination. The preserved activity of aztreonam/avibactam and cefepime/zidebactam, alongside the observed synergistic combinations, underscores promising therapeutic strategies for managing infections caused by these highly resistant pathogens.},
}

Cefiderocol
*Klebsiella pneumoniae/genetics/drug effects
Cephalosporins/pharmacology
Humans
Cefepime/pharmacology
Microbial Sensitivity Tests/methods
*beta-Lactamases/genetics/metabolism
*beta-Lactamase Inhibitors/pharmacology
Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics/metabolism
Aztreonam/pharmacology
Azabicyclo Compounds/pharmacology
Italy/epidemiology
Drug Resistance, Multiple, Bacterial/genetics
Klebsiella Infections/microbiology/drug therapy
beta-Lactams/pharmacology
Drug Combinations
Cyclooctanes/pharmacology
Whole Genome Sequencing
Plasmids/genetics
Third Generation Cephalosporins
Multilocus Sequence Typing
Piperidines
Triazoles

@article {pmid42861648,
year = {2026},
author = {Miller, O and Jacobi, D and Carmel, L and Pines, O},
title = {Evolution and metabolite signaling of fumarases (class I and II): origin, function, and subcellular targeting.},
journal = {Molecular biology and evolution},
volume = {43},
number = {10},
pages = {},
pmid = {42861648},
issn = {1537-1719},
support = {1765/26//Israel Science Foundation/ ; 1561//German-Israeli Foundation for Scientific Research and Development/ ; },
mesh = {Phylogeny ; *Evolution, Molecular ; *Fumarate Hydratase/genetics/metabolism/chemistry ; Gene Transfer, Horizontal ; Signal Transduction ; Bacteria/enzymology/genetics ; Animals ; Archaea/genetics/enzymology ; Eukaryota/genetics/enzymology ; },
abstract = {This study explores the evolutionary origins of class I and II fumarases across the tree of life, focusing on the prevalence and phylogenetic patterns of their enzymes. Using a dataset of ∼21,000 complete proteomes and MMseqs2 easy-search against known fumarase sequences, we identified representative sequences for each class and constructed phylogenetic trees. Class I fumarases are found primarily in bacteria and in several eukaryotic groups, including Protozoa, SAR, and algae, with absence in fungi and archaea and low presence in plants and animals. Their patchy distribution and absence in archaea suggest horizontal gene transfer from bacteria to eukaryotes. Class II fumarases are ubiquitously distributed across bacteria, archaea, and eukaryotes. Phylogenetic and genetic analyzes suggest a closer relationship between eukaryotic class II fumarases and bacterial homologs (particularly Alphaproteobacteria) compared to archaea. These results support the hypothesis that class II fumarase originated early on in bacteria and was then inherited by vertical gene transfer by eukaryotes. Analysis of protein sequences and structures for both classes demonstrates high evolutionary conservation, consistent with their essential catalytic function. Fumarases, TCA cycle enzymes, have been implicated in DNA damage response in numerous organisms, in all domains of life. These enzymes have also been shown to be dual targeted to mitochondria and the cytosol/nucleus in eukaryotes. We have examined how these two functions are linked to the evolution of fumarases and concluded that the extramitochondrial functions and subcellular localization of fumarases were determined much later in evolution. We conclude that metabolic signaling and its specific metabolites may provide the driving force for the fumarases' dual function, dual targeting, and interaction with different entities in the cell.},
}

Phylogeny
*Evolution, Molecular
*Fumarate Hydratase/genetics/metabolism/chemistry
Gene Transfer, Horizontal
Signal Transduction
Bacteria/enzymology/genetics
Animals
Archaea/genetics/enzymology
Eukaryota/genetics/enzymology

@article {pmid42854809,
year = {2026},
author = {Bonato, T and Benna, C and Adelodun, B and Pal, T and Di Maria, F},
title = {Understanding the complexity of microplastics, antibiotic resistance, and their interaction with human health and ecosystems: a review towards global environmental sustainability.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125879},
doi = {10.1016/j.envres.2026.125879},
pmid = {42854809},
issn = {1096-0953},
abstract = {Microplastics (MPs), defined as particles with a diameter <5 mm, are increasingly recognized as important global environmental stressors due to their ubiquity and harmful effects on organisms. Although most studies have investigated the direct biological effects of MPs, their role in the spread of pathogens and antibiotic resistance remains less explored. Thanks to their hydrophobic surfaces, MPs act as substrates for microbial colonization, giving rise to the plastisphere-a microenvironment that hosts opportunistic and clinically relevant bacteria, including Escherichia coli, Vibrio spp., and Aeromonas spp., some of which are multidrug-resistant. The plastisphere has emerged as a hotspot for antibiotic resistance genes (ARGs), promoting horizontal gene transfer (HGT) and contributing to the environmental spread of resistance. Human exposure to MPs is widespread, as have been detected in water, food, and air. Once ingested or inhaled, they can accumulate in tissues, cross biological barriers, and cause gastrointestinal irritation, dysbiosis of the microbiota, endocrine disruptions, oxidative stress, and immunotoxicity. MPs carrying biofilms containing resistant bacteria and ARGs represent a direct route of exposure for the introduction of resistance factors into the human body, increasing the risk of untreatable infections. Despite growing evidence, significant knowledge gaps remain regarding the role of MPs in the spread of antimicrobial resistance (AMR) and associated health risks. To date, no legislation specifically considers MPs as vectors of pathogens and ARGs. This review aims to clarify the concept of the plastisphere, its implications for AMR, and the urgent need for interdisciplinary approaches to address this emerging global threat.},
}

@article {pmid42856694,
year = {2026},
author = {Soveral, LF and Holanda, LRL and Assunção, IBF and Gomes, LG and de Souza, IB and Rodrigues, GS and Vanny, PA and Bruna-Romero, O and Palmeiro, JK and Scheffer, MC and Sincero, TCM and Zárate-Bladés, CR},
title = {Identification of antibiotic resistance genes in fecal microbiota selected donors during the establishment of a biobank in the south of Brazil.},
journal = {Frontiers in antibiotics},
volume = {5},
number = {},
pages = {1905540},
pmid = {42856694},
issn = {2813-2467},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is increasingly explored for other dysbiosis-related disorders. However, its implementation as a regulated therapeutic strategy requires robust donor screening, biosafety frameworks, and standardized processing workflows. Here, we describe the establishment of the first fecal microbiota biobank in southern Brazil and evaluate the incorporation of metagenomic sequencing as a complementary layer of donor characterization and safety assessment. A structured donor selection pipeline based on international guidelines was implemented, integrating clinical screening, biochemical and serological testing, and microbiological analyses. Of 100 screened candidates, only four donors met all eligibility criteria and were included in the biobank, highlighting the stringency of the selection process. Shotgun metagenomic sequencing revealed a diverse resistome across all donors, including a shared core set of resistance genes alongside marked interindividual variability. Dominant resistance determinants included tetracycline-associated genes, ermF, CfxA-type β-lactamases, and aminoglycoside-modifying enzymes, which were associated with specific gut taxa. Genomic context analysis further identified four ARG-containing contigs with features compatible with potential mobility, although active horizontal gene transfer was beyond the scope of this study. Notably, tet(Q) and ermF were predominantly associated with Bacteroides fragilis, supporting its role as a reservoir of resistance determinants in the gut microbiota. These findings support the use of metagenomic profiling as a complementary approach to donor characterization and risk assessment rather than as a standalone criterion for donor exclusion. Overall, this study provides a framework for microbiota biobank implementation and highlights the potential of metagenomic analysis to complement conventional biosafety screening in FMT.},
}

@article {pmid42848959,
year = {2026},
author = {Nie, K and Zhao, J and Yin, C and Gu, S and Ji, H and Dai, X and Wang, X and Wang, L and Huang, J},
title = {Intergeneric mobilization of a genomic island mediated by a helper integrative conjugative element from Streptococcus suis to Enterococcus faecalis.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {11},
pages = {},
doi = {10.1093/jac/dkag338},
pmid = {42848959},
issn = {1460-2091},
support = {2024AAC05098//Natural Science Foundation/ ; 32573429//National Natural Science Foundation of China/ ; 32172917//National Natural Science Foundation of China/ ; KYCXJC2025001//Fundamental Research Funds for the Central Universities/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 325QN366//Hainan Provincial Natural Science Foundation/ ; },
mesh = {*Enterococcus faecalis/genetics/growth & development ; *Streptococcus suis/genetics/growth & development ; *Genomic Islands ; *Conjugation, Genetic ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; Genetic Complementation Test ; },
abstract = {BACKGROUND AND OBJECTIVES: Mobile genetic elements drive antimicrobial-resistance dissemination in Gram-positive pathogens. In Streptococcus suis we previously identified a genomic island, GISsuJHJ17_rpsI, integrated at the conserved rpsI locus and carrying erm(B) and aadE. Here we investigated the genetic features and helper functions associated with mobilization of this island, including its transfer from S. suis to E. faecalis.

METHODS: Genetic annotation established that GISsuJHJ17_rpsI lacks a self-encoded conjugation apparatus but harbours an origin of transfer (oriT) sharing ∼85% nucleotide identity with the co-resident integrative and conjugative element (ICE). We performed filter-mating assays to test ICE-mediated mobilization in trans, constructed precise deletions of oriTGISsuJHJ17 and of the ICE relaxase, carried out complementation, and assessed fitness by growth and head-to-head competition of transconjugants.

RESULTS: Filter-mating assays showed that mobilization of GISsuJHJ17_rpsI in the S. suis recipient model required the helper-ICE relaxase and the candidate GI oriT region. Deletion of either determinant yielded no verified transconjugants under the assay conditions, whereas relaxase complementation and chromosomal oriT repair restored detectable transfer. These findings support a model in which the helper ICE provides the DNA-processing function required for GI mobilization, using the co-resident ICE transfer apparatus, as inferred from the ICE gene content. Fitness assays revealed no measurable growth defect or competitive disadvantage associated with acquisition of GISsuJHJ17_rpsI, indicating a minimal short-term fitness cost.

CONCLUSIONS: These findings show that GISsuJHJ17_rpsI can transfer from S. suis to E. faecalis and integrate at an rpsI-associated site. In the S. suis recipient model, mobilization required the helper-ICE relaxase and the GISsuJHJ17_rpsI oriT region, supporting a helper-ICE-dependent mechanism for genomic-island mobilization.},
}

*Enterococcus faecalis/genetics/growth & development
*Streptococcus suis/genetics/growth & development
*Genomic Islands
*Conjugation, Genetic
*Gene Transfer, Horizontal
*Interspersed Repetitive Sequences
Genetic Complementation Test

@article {pmid42849440,
year = {2026},
author = {Vixseboxse, PB and Moody, ERR and Donoghue, PCJ and McMahon, S and Liu, AG},
title = {Temporal heterogeneity in the animal fossil record driven by proliferation of microbial collagenases.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.09.045},
pmid = {42849440},
issn = {1879-0445},
abstract = {The animal fossil record is a non-uniform archive of evolutionary history in which exceptional preservation diminishes toward the present,[1][,][2][,][3] with biomineralized skeletal elements constituting the majority of the fossil record. Preservation of soft tissues requires rare combinations of chemical, biological, and physical conditions that preclude or delay decay until biological substrates can be geologically stabilized via mineralization or maturation.[4] However, during the late Ediacaran Period (∼579-539 mya) fossilization of soft-bodied macroorganisms was common across a wide range of depositional settings.[5][,][6] Taphonomic models seeking to explain Ediacaran exceptionalism typically appeal to unusual mineralogical and geochemical conditions or microbiological influence (e.g., Gehling,[7] Tarhan et al.,[8] Bykova et al.,[9] and Bobrovskiy et al.[10]), and the Paleozoic decline in exceptional preservation has invariably been explained in terms of expansion of the oxic zone through metazoan bioturbation (though see Cribb et al.[11]) and enhanced scavenging.[12] We explore the hypothesis that temporal heterogeneity in metazoan exceptional preservation is a consequence of the origin and/or proliferation of microbial collagenases.[13] Collagenase gene trees reconciled with a time-calibrated phylogeny show that collagenases arose and were produced by obligate anaerobes billions of years before proliferating by lateral gene transfer, approximately coincident with the diversification of early animals. These results support a link between the evolution of collagenases, animals, and the non-uniformity of the fossil record. Proliferation of collagenase-producing microbial lineages occurred in concert with early animal evolution. Evidence also indicates a shift in the locus of collagen degradation within the sediment redox profile, coincident with the decline of exceptional soft-tissue preservation in the marine realm.},
}

@article {pmid42849638,
year = {2026},
author = {Shareef, Z and Hussain, HI and Aqib, AI and Malik, MSU and Rehman, SU},
title = {Combating Antimicrobial Resistance: Emerging Non-Traditional Therapeutics, Clinical Translation Challenges, and Future Perspectives.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108871},
doi = {10.1016/j.micpath.2026.108871},
pmid = {42849638},
issn = {1096-1208},
abstract = {Antimicrobial resistance (AMR) has emerged as one of the most severe global health threats. The rapid expansion of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens compromises the effectiveness of conventional antibiotics. Globally, ESKAPE organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) have led to therapeutic failure, prolonged hospitalization, and increased mortality rates. This review identifies the molecular mechanisms, including enzymatic antibiotic inactivation, efflux pump overexpression, biofilm formation, and horizontal gene transfer, that underline the resistance of disseminated pathogens to antibiotics in clinical, agricultural, and environmental settings. Antibiotic overuse and pharmaceutical and agricultural discharges create persistent reservoirs for the dissemination of AMR genes. Furthermore, we evaluated the non-traditional antibacterial efficacy of antimicrobial peptides, bacteriophage therapy, monoclonal antibodies, probiotics, fecal microbiota transplantation, anti-virulence agents, CRISPR-Cas precision antimicrobials, and nanotechnology-based drug delivery platforms. Current preclinical and clinical evidence indicates the eradication of resistant pathogens, disruption of biofilms, and preservation of host microbiota, thereby reducing the selective pressure associated with broad-spectrum antibiotics. Despite these advances, major translational barriers, such as pharmacokinetic instability, manufacturing limitations, and insufficient clinical validation, restrict the implementation of the framework. In the future, the AMR management framework will require precision medicine, artificial intelligence, and One Health-based integration via multidisciplinary collaboration.},
}

@article {pmid42852186,
year = {2026},
author = {Wu, L and Simões, MF and Xu, X and Yin, W},
title = {Microbial adaptation and biological effects in the spaceflight environment.},
journal = {Mycology},
volume = {17},
number = {3},
pages = {697-717},
pmid = {42852186},
issn = {2150-1203},
abstract = {With the advancement of space exploration, space microbiology has become an important research area. Microorganisms show remarkable adaptive plasticity under extreme space environments. Space‑derived strains not only pose potential biosafety risks but also serve as valuable biotechnological resources. This review focuses on microbial phenotypic alterations, including colony morphology, biofilm formation, secondary metabolism, pathogenicity, and antibiotic resistance. These changes are mainly driven by genomic instability, horizontal gene transfer, and cellular pathway reprogramming. Here we uniquely integrate phenotypic, mechanistic, and application-level perspectives to provide a unified framework for understanding microbial adaptation in spaceflight environments.},
}

@article {pmid42853077,
year = {2026},
author = {Holtgrefe, N},
title = {PhyloZoo: a unified framework for phylogenetic network analysis in Python.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag748},
pmid = {42853077},
issn = {1367-4811},
abstract = {Reticulate evolutionary processes (events in which lineages merge, such as hybridization, recombination, and horizontal gene transfer) are widespread across nature but cannot be represented by phylogenetic trees alone. Phylogenetic networks have therefore become an important modelling tool, yet existing software is typically tied to specific inference paradigms and provides limited support for working with multiple network representations in a unified and programmable environment. PhyloZoo is an open-source Python framework that lowers the barrier to developing practical, easy-to-use software for phylogenetic network analysis. It provides data structures and algorithms covering the main representations used in the field, together with dedicated visualization tools and robust I/O for all major phylogenetic file formats. A particular emphasis lies on semi-directed phylogenetic networks, which explicitly represent root uncertainty and have so far received limited support in existing software. By offering a shared, scalable foundation for developing interoperable tools and a combinatorial layer that supports computational proofs and theoretical exploration, PhyloZoo enables reproducible workflows for applied, methodological, and theoretical studies of reticulate evolution. Availability and implementation: PhyloZoo is implemented in Python and installable from PyPI, with source code, documentation, and examples available at https://github.com/nholtgrefe/phylozoo.},
}

@article {pmid42853601,
year = {2026},
author = {Mendoza-Guido, B and Rojas-Jimenez, K},
title = {Plasmidomics: studying plasmids as ecological entities beyond their hosts.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
pmid = {42853601},
issn = {2057-5858},
mesh = {*Plasmids/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Symbiosis ; Evolution, Molecular ; Ecosystem ; },
abstract = {Plasmids are mobile genetic elements with autonomous replication, whose ecology extends beyond individual bacterial hosts. As molecular symbionts, they have the potential to traverse bacterial taxa and environments, disseminating adaptive genes and shaping microbial community structure through dynamics that are likely decoupled from host taxonomy. Plasmidomics - the omics discipline dedicated to the study of plasmids - has revealed that plasmid diversity and distribution respond to environmental gradients independently of their hosts, underscoring their roles as ecological entities. However, the field faces critical methodological constraints: short-read assemblies fragment plasmid sequences, culture-dependent approaches underrepresent environmental diversity and most metagenomic methods fail to capture plasmid-host associations. In addition, a universally accepted classification framework is still lacking. Advancing plasmidomics will require the integration of long-read sequencing, Hi-C proximity ligation, meta-epigenomics and ecology-informed classification frameworks grounded in genomic and functional criteria. Together, these approaches are essential to uncover the true diversity, evolutionary significance and ecological dynamics of plasmids across complex microbial ecosystems.},
}

*Plasmids/genetics/classification
*Metagenomics/methods
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Symbiosis
Evolution, Molecular
Ecosystem

@article {pmid42844282,
year = {2026},
author = {Zhou, S and Philo, SE and Saldana, MA and Vela, JD and Smith, AL and Stadler, LB},
title = {Plasmid-Host Networks Reveal Persistent Mobile Elements Across Wastewater Treatment.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844282},
issn = {2041-1723},
support = {R21AI190938//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21AI190938//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; NAS Grant G10001728//National Academies of Sciences, Engineering, and Medicine | National Academy of Sciences (NAS)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | U.S. Army Corps of Engineers (US Army Corps of Engineers)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | US Army Corps of Engineers | Engineer Research and Development Center (U.S. Army Engineer Research and Development Center)/ ; W9132T-23-2-0002//United States Department of Defense | United States Army | US Army Corps of Engineers | Engineer Research and Development Center (U.S. Army Engineer Research and Development Center)/ ; No. EEC-2133504//National Science Foundation (NSF)/ ; },
mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; Gene Transfer, Horizontal ; *Water Purification ; Metagenomics ; Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; *Interspersed Repetitive Sequences/genetics ; Drug Resistance, Bacterial/genetics ; Host Specificity/genetics ; Bacteria/genetics ; },
abstract = {Plasmids drive horizontal gene transfer and antimicrobial resistance spread in water resource recovery facilities, yet their in situ dynamics in complex microbial communities remain poorly characterized. We apply Hi-C metagenomics to resolve plasmid-host associations across influent, activated sludge, and effluent at three facilities. We identify 944 plasmid clusters with facility- and stage-specific distributions. Plasmid host range narrows from influent to effluent, indicating that treatment selectively constrains plasmid-host associations. Persistent plasmid clusters with detectable mobility markers show a trend toward broader, less modular host networks than those with no detected markers. Hi-C-supported antibiotic resistance gene associations highlight Burkholderiaceae and Rhodocyclaceae as prominent hosts of beta-lactam, tetracycline and sulfonamide resistance genes across facilities. These findings indicate that wastewater treatment narrows plasmid host range while maintaining dominant plasmid-carrying taxa and adaptive mobile elements, providing a framework for understanding plasmid persistence across treatment systems.},
}

*Plasmids/genetics
*Wastewater/microbiology
Gene Transfer, Horizontal
*Water Purification
Metagenomics
Sewage/microbiology
Anti-Bacterial Agents/pharmacology
*Interspersed Repetitive Sequences/genetics
Drug Resistance, Bacterial/genetics
Host Specificity/genetics
Bacteria/genetics

@article {pmid42846242,
year = {2026},
author = {Varadan, AC and Grasis, JA},
title = {Filamentous bacteriophages: impact on prokaryotic virulence, eukaryotic immunity, and implications for phage therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1904873},
pmid = {42846242},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Inovirus/immunology/pathogenicity/physiology ; Virulence ; *Phage Therapy/methods ; *Bacteria/virology/immunology ; *Eukaryotic Cells/immunology/virology ; *Bacterial Infections/therapy/immunology ; Host-Pathogen Interactions/immunology ; *Prokaryotic Cells/immunology/virology ; },
abstract = {Filamentous bacteriophages, of the family Inoviridae, are characterized by their reproduction and secretion by their bacterial hosts without killing them. These viruses have evolved mutualistic relationships with their bacterial hosts by impacting bacterial phenotypes in a variety of ways, including biofilm formation, horizontal gene transfer, colonization, and motility. Previous studies have reported that filamentous bacteriophages contain virulence factors that promote the pathogenesis of bacterial infections in animal models and are associated with exacerbating infections in humans. Additionally, these phages have been experimentally used as cloning vectors for DNA sequencing, phage display, and nanotechnological applications. Finally, viromic studies have revealed a substantial presence of filamentous bacteriophages in the human gut. However, their interactions with mammalian cells have not been extensively explored. Here, we review the immunogenicity of filamentous bacteriophages in eukaryotic cells. First, we address how filamentous bacteriophages impact the fitness of their prokaryotic hosts. Then, we review their immunogenicity by focusing on the direct interactions between filamentous bacteriophages and eukaryotic cells that may indicate how these viruses influence various functions. Finally, we provide some thoughts on their impact for use in therapeutics. Through their ubiquitous interactions with prokaryotic and eukaryotic cells, there is still much to be learned about how filamentous bacteriophages affect the biology, pathogenesis, and physiology of the human gut. Unraveling these interactions will provide further evidence as to the importance of the virome to human health.},
}

Humans
Animals
*Inovirus/immunology/pathogenicity/physiology
Virulence
*Phage Therapy/methods
*Bacteria/virology/immunology
*Eukaryotic Cells/immunology/virology
*Bacterial Infections/therapy/immunology
Host-Pathogen Interactions/immunology
*Prokaryotic Cells/immunology/virology

@article {pmid42847339,
year = {2026},
author = {Ragab, W and Kawato, S and Rathnapala, JMSN and Nozaki, R and Hirono, I},
title = {Comparative genomics of Photobacterium damselae from Penaeus (Marsupenaeus) japonicus: insights into pathogenicity and adaptation.},
journal = {Diseases of aquatic organisms},
volume = {168},
number = {},
pages = {1-17},
doi = {10.3354/dao03936},
pmid = {42847339},
issn = {0177-5103},
mesh = {*Photobacterium/genetics/pathogenicity ; Animals ; *Penaeidae/microbiology ; *Genome, Bacterial ; Genomics ; Phylogeny ; Virulence ; Adaptation, Physiological ; },
abstract = {Photobacterium damselae subsp. damselae (PDD), a halophilic, Gram-negative bacterium of the family Vibrionaceae, infects a wide range of aquatic organisms. PDD isolates originating from fish have been characterized in detail, but much less is known about those infecting invertebrates. Currently, only 3 complete PDD genomes isolated from Kuruma shrimp Penaeus (Marsupenaeus) japonicus from Japan are publicly available, severely limiting comparative studies of host adaptation. To address this, we present complete, plasmid-resolved genome assemblies of 4 novel PDD strains (TUMSAT-PD1, -PD2, -PD3, and -PD4) isolated from diseased Kuruma shrimp across multiple prefectures in Japan. Phylogenomic analysis reveals that shrimp PDD strains are genetically heterogeneous and closely related to those infecting other aquatic organisms, suggesting that pathogenicity against shrimp arose independently in multiple PDD strains. While core virulence determinants are chromosomally encoded, we identified key plasmid-borne virulence factors that are likely to enhance the pathogenicity of PDD strains. Comparative analysis with 3 publicly available PDD genomes demonstrated both conserved core virulence determinants and strain-specific accessory genes, reflecting local adaptation and evolutionary diversification. Our findings provide the first geographically expanded genomic framework for Kuruma shrimp-associated PDD, integrating 4 novel Japanese isolates with the existing public genomes. This integrated data set demonstrates that PDD exhibits a generalist evolutionary strategy, capable of rapid adaptation to diverse hosts through conserved virulence machinery and mobile genetic elements. This work significantly expands the genomic basis for understanding PDD epidemiology and pathogenesis within aquaculture systems.},
}

*Photobacterium/genetics/pathogenicity
Animals
*Penaeidae/microbiology
*Genome, Bacterial
Genomics
Phylogeny
Virulence
Adaptation, Physiological

@article {pmid42847705,
year = {2026},
author = {Pavinski Bitar, PD and Chowdhury, R and Bosire, EM and Keresztes, I and Stanhope, MJ and Altier, C},
title = {Members of the Enterobacteriaceae family produce a diffusible signal factor that modulates enteric pathogen virulence.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0040326},
doi = {10.1128/msphere.00403-26},
pmid = {42847705},
issn = {2379-5042},
abstract = {UNLABELLED: Diffusible signal factors (DSFs) are a gammaproteobacterial family of quorum-sensing signals that mediate the transition between sessile and planktonic lifestyles. In addition to coordinating behavior within producing species, DSFs can be sensed by surrounding organisms, enabling interspecies "eavesdropping." Several enteric pathogens that do not produce DSFs use these environmental signals to modulate their virulence, allowing them to conserve energy when expression of pathogenesis genes is not advantageous. Although DSFs have been detected in the gut, the microbial origins of these signals remain poorly defined. Here, we show that the ability to produce DSFs is more widespread among Gammaproteobacteria than previously appreciated. Using phylogenetic analysis, we identified more than 500 homologs of the DSF synthase RpfF that group into three distinct taxa. Our analysis further revealed evidence of horizontal gene transfer between Burkholderiales, a known reservoir of DSF production, and Enterobacterales, an order enriched in gut-associated bacteria. We found that Enterobacterales members Cronobacter sakazakii and Enterobacter cloacae produce the DSF cis-2-tetradecenoic acid in an rpfF-dependent manner. Furthermore, we demonstrated cis-2-tetradecenoic acid to be a potent repressor of virulence in the enteric pathogens Salmonella enterica, Shigella flexneri, and Vibrio cholerae. Finally, we have shown that in addition to its role in interspecies signaling, endogenous DSF production reduces biofilm formation and suppresses swarming in E. cloacae, while also promoting swimming motility, consistent with a shift to a free-living lifestyle. Together, these findings expand the known diversity of DSF signaling and identify gut-associated bacteria as a source of interspecies cues that shape pathogen behavior.

IMPORTANCE: Many bacterial pathogens rely on tightly regulated gene expression to cause disease, making virulence pathways attractive targets for new therapies. Diffusible signal factors (DSFs) are communication molecules that can suppress the virulence of several enteric pathogens, but their sources in the gut have not been well defined. Here, we identify gut-associated bacteria that produce the DSF molecule cis-2-tetradecenoic acid, capable of strongly repressing virulence in multiple enteric pathogens. Additionally, our work substantially expands the distribution of bacteria with the genetic capacity for DSF production, broadening the pool of candidate signal sources and paving the way for future discoveries in microbial communication.},
}

@article {pmid42840382,
year = {2026},
author = {Sundar, S and Bonhoeffer, S and Huisman, JS},
title = {Transfer potential of F-like plasmids in Escherichia coli differs by animal environment.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag256},
pmid = {42840382},
issn = {2730-6151},
abstract = {Plasmids play a key role in the spread of virulence and antimicrobial resistance genes to new genetic backgrounds. Genetic variation in the transfer operon, which contains the genes responsible for conjugation, can lead to substantial differences in transfer potential even between closely-related plasmids. However, it is not clear how much genetic diversity there is in transfer operons of natural bacterial populations. Here, we analyse the prevalence and transfer potential of F-like plasmids, a clinically important family of plasmids in Enterobacteriaceae, by searching for the presence of essential conjugation genes in 1200 Escherichia coli genomes isolated from three livestock-associated environments. We find that the fraction of functionally complete F-like transfer operons was significantly higher in poultry than in bovine- and swine-associated bacteria. This difference was not captured in methods that use the presence of replication genes to estimate plasmid prevalence. Confounders such as the phylogenetic relatedness of E. coli or the presence of antibiotic resistance could not explain these significant differences in transfer potential. Instead, it seems the poultry environment selects for plasmids with high transfer potential, as it also contained more conjugative plasmid types per isolate. While we find environment-specific differences in overall plasmid frequency, patterns of transfer gene presence/absence were similar across the three environments. Regulatory and exclusion genes are the exception to this pattern, suggesting environment-specific modulation of transfer rates. This highlights the use of genomic data to uncover environment-specific differences in plasmid prevalence and transfer potential, revealing the selection pressures shaping horizontal gene transfer in these environments.},
}

@article {pmid42840638,
year = {2026},
author = {Yan, G and Xuan, Y},
title = {Acanthamoeba as a microbial Trojan horse: intracellular endosymbionts, adaptive immune evasion and antimicrobial resistance dissemination from a one health perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874010},
pmid = {42840638},
issn = {1664-3224},
mesh = {*Acanthamoeba/microbiology/immunology ; Humans ; *Immune Evasion ; One Health ; Gene Transfer, Horizontal ; Animals ; *Symbiosis/immunology ; Drug Resistance, Microbial ; Drug Resistance, Bacterial ; Bacteria/immunology/drug effects ; },
abstract = {Antimicrobial resistance (AMR) is a global public health crisis driven not only by clinical antibiotic misuse but also by environmental reservoirs that remain insufficiently characterized. Free-living amoebae of the genus Acanthamoeba are ubiquitous eukaryotic protists that graze on diverse bacterial communities via phagocytosis, yet certain clinically important pathogens-including Legionella pneumophila, Mycobacterium spp. and Pseudomonas aeruginosa-have evolved sophisticated mechanisms to survive and replicate within the amoebal phagosome. This intracellular niche serves simultaneously as an evolutionary training ground for bacterial virulence and immune evasion, a physical shelter against environmental biocides, and a hotspot for horizontal gene transfer (HGT) of resistance determinants. Strikingly, the molecular strategies used to subvert amoebal killing are mechanistically conserved with those deployed against human macrophages, effectively shielding amoeba-trained bacteria from both innate and adaptive immune clearance. Recent studies demonstrate that Acanthamoeba-associated bacteria exhibit significantly elevated multidrug resistance indices compared with free-living counterparts, that plasmid-borne carbapenem-resistance genes can transfer between co-ingested species within the phagosome, and that the highly resistant cyst stage shields intracellular bacteria from chlorine disinfection at concentrations exceeding water-treatment standards. This review provides a comprehensive synthesis of the molecular and immunological mechanisms underlying intracellular bacterial survival within Acanthamoeba, evaluates the evidence for AMR amplification through protist-bacteria interactions, and frames these processes within the One Health paradigm connecting environmental reservoirs to clinical and veterinary outcomes.},
}

*Acanthamoeba/microbiology/immunology
Humans
*Immune Evasion
One Health
Gene Transfer, Horizontal
Animals
*Symbiosis/immunology
Drug Resistance, Microbial
Drug Resistance, Bacterial
Bacteria/immunology/drug effects

@article {pmid42841554,
year = {2026},
author = {Singh, I and Singh, H and Keshri, A and Sharma, P and Sharma, D and Kumar, A and Dhakad, MS and Beg, MMA},
title = {Pneumococcal-Driven Genetic Competence: A Key Driver of Pathobiont Adaptation and Disease Potential.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.70041},
pmid = {42841554},
issn = {2041-1014},
abstract = {High genetic variability in streptococci is driven by natural competence, specifically in Streptococcus pneumoniae and its close commensal species (Streptococcus pseudopneumoniae, Streptococcus oralis, and Streptococcus mitis), which drives rapid Streptococcal evolution. The genome of S. pneumoniae and its close commensal species exhibits high interspecies recombination, an open-pan genome, and a similar evolutionary origin. Mechanisms of natural competence are a highly regulated process driven by numerous molecular players at different stages. Natural competence in Streptococci drives the shift from commensal to pathogenic state. Streptococcus pneumoniae acquires various virulence and antibiotic-resistant genes (ARGs) via natural competence and also facilitates immune evasion, the emergence of multidrug-resistant strains, and capsule switching between strains. Most reports indicated that the natural competence in S. pneumoniae is a one-way street process; however, a few studies have proved that it is a two-way street process. The purpose of the current review is to elucidate (i) the genome of S. pneumoniae and its close relatives, (ii) the mechanism of HGT, (iii) HGT in S. pneumoniae and related commensal species, (iv) acquisition of drug-resistance genes and virulence factors, and (v) the implication of HGT in competence-driven gene transfer in IPD and interaction between host and pathogens.},
}

@article {pmid42841629,
year = {2026},
author = {Laurel, NR and Hibbs, GT and Satterlee, TR and Mitchell, TR and Severns, PM and Glenn, AE and Gold, SE and Kemerait, RC},
title = {SzMBL1, a metallo-β-lactamase gene in Sarocladium zeae, confers tolerance to the maize phytoanticipin 2-benzoxazolinone.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0125726},
doi = {10.1128/aem.01257-26},
pmid = {42841629},
issn = {1098-5336},
abstract = {Maize produces pre-formed secondary metabolites with antimicrobial and invertebrate anti-herbivory properties. Fusarium verticillioides, a mycotoxigenic maize pathogen, detoxifies the maize phytoanticipin 2-benzoxazolinone (BOA) through gene action of FvMBL1, which encodes a putative metallo-β-lactamase within the FDB1 gene cluster. This cluster is also present in other maize-colonizing fungi, including the pathogen Colletotrichum graminicola and, as reported here, the protective endophyte Sarocladium zeae, which exhibits antagonistic activity against mycotoxigenic fungi. The role of the FvMBL1 ortholog in S. zeae, designated SzMBL1, was assessed by gene deletion and add-back complementation. Deletion of SzMBL1 rendered S. zeae incapable of degrading BOA and therefore unable to grow on BOA-amended medium, whereas complemented add-back strains restored BOA tolerance and, in some cases, enhanced growth at higher concentrations of BOA. Quantitative PCR analyses revealed higher copy numbers and expression levels in all add-back transformants relative to the wild type, consistent with their enhanced growth. HPLC-MS/MS analysis further showed that SzMBL1 hydrolyzes BOA, ultimately resulting in biotransformation into the non-toxic metabolite N-(2-hydroxyphenyl)malonamic acid (HPMA). Together, this study confirms the conserved function of the SzMBL1 gene involved in BOA detoxification. This study suggests that the FDB1 gene cluster, harboring SzMBL1 in S. zeae, was likely transferred through horizontal gene transfer between maize-colonizing fungi and plays a role in the degradation of host-derived secondary metabolites that function as filters limiting which fungi are most frequently associated with maize.IMPORTANCEMaize produces secondary metabolites such as 2-benzoxazolinone (BOA) to help protect against microbes and insects. The pathogenic Fusarium verticillioides carries FvMBL1, a gene within the FDB1 gene cluster that helps break down BOA. This cluster is also present in other maize-associated fungi such as Colletotrichum graminicola and, as reported here, the protective fungus Sarocladium zeae. In our experiments, when a gene similar to FvMBL1, denoted SzMBL1, is deleted in S. zeae, the fungus could no longer break down BOA or grow on BOA-amended medium. Complementation restored BOA tolerance and growth phenotypes. Notably, some S. zeae add-back strains showed increased growth at higher BOA concentrations. Our analysis showed that these hypertolerant complemented strains had multiple, transcriptionally active copies of SzMBL1. The study highlights the role of SzMBL1 in BOA detoxification, thereby aiding fungal tolerance to antimicrobial compounds, and supports the hypothesis that the FDB1 gene cluster can be horizontally transferred among maize-colonizing fungi.},
}

@article {pmid42841727,
year = {2026},
author = {Wheeler, M and Bakkeren, E},
title = {Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
pmid = {42841727},
issn = {2057-5858},
mesh = {*Microbiota/drug effects/genetics ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gene Transfer, Horizontal ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics ; *Microbial Interactions ; Treatment Failure ; *Drug Resistance, Microbial ; },
abstract = {The failure of antibiotic treatment is a growing concern, driven in large part by the rising incidence of antimicrobial resistance (AMR). Increasing evidence points to the importance of microbial competition in preventing the colonization of disease-causing pathogens and the spread of AMR. Crucially, the pathogens we target with antibiotics do not exist in isolation but instead compete and interact with the microbial communities that colonize the human body, microbiomes. Here, we therefore argue that the key to approaching the challenge of antibiotic treatment failure is understanding the strategies and mechanisms that microbes use to succeed in microbiomes. We discuss how microbial competition influences the colonization of pathogens and the spread of resistance via horizontal gene transfer. We then discuss how microbial competition may be used to synergize with antibiotic treatment or even replace it. Overall, we argue that studying microbial interactions offers a powerful approach to understanding and even mitigating antibiotic treatment failure.},
}

*Microbiota/drug effects/genetics
*Anti-Bacterial Agents/therapeutic use/pharmacology
Gene Transfer, Horizontal
Humans
*Drug Resistance, Bacterial/genetics
*Bacteria/drug effects/genetics
*Microbial Interactions
Treatment Failure
*Drug Resistance, Microbial

@article {pmid42842003,
year = {2026},
author = {Yugay, Y and Rusapetova, T and Gorpenchenko, T and Vasyutkina, E and Degtyareva, V and Grigorchuk, V and Kudinova, O and Bulgakov, V and Shkryl, Y},
title = {Natural sweet potato transgene Ib-rolB/C enhances abiotic and biotic stress tolerance through redox and defense regulation.},
journal = {Planta},
volume = {264},
number = {5},
pages = {},
pmid = {42842003},
issn = {1432-2048},
support = {25-74-00041//Russian Science Foundation/ ; },
mesh = {*Ipomoea batatas/genetics/physiology ; Arabidopsis/genetics/physiology/microbiology ; Plants, Genetically Modified ; *Stress, Physiological/genetics ; Gene Expression Regulation, Plant ; Oxidation-Reduction ; DNA, Bacterial/genetics ; Pseudomonas syringae/physiology ; Reactive Oxygen Species/metabolism ; Transgenes ; Botrytis/physiology ; Antioxidants/metabolism ; Plant Diseases/microbiology/immunology ; Disease Resistance/genetics ; *Bacterial Proteins/genetics/metabolism ; beta-Glucosidase ; },
abstract = {Natural sweet potato transgene Ib-rolB/C enhances abiotic and biotic stress tolerance through coordinated regulation of ROS signaling, antioxidant defense, immune activation, and secondary metabolism. Horizontal gene transfer from Agrobacterium has contributed to plant genome evolution, yet the physiological roles of naturally integrated T-DNA genes remain poorly understood. Cultivated sweet potato (Ipomoea batatas) contains two cellular T-DNA regions, including the IbT-DNA2 locus harboring the naturally acquired gene Ib-rolB/C. Here, we investigated the stress-responsive expression and functional significance of Ib-rolB/C using transgenic Arabidopsis thaliana. The gene was strongly induced by cold, heat, and salinity. Moreover, Ib-rolB/C-expressing plants exhibited enhanced tolerance to abiotic stresses during germination, as well as increased resistance to Pseudomonas syringae and Botrytis cinerea. These phenotypes were associated with moderate ROS accumulation, enhanced antioxidant capacity, elevated GSH/GSSG ratios, reduced lipid peroxidation, and elevated basal expression of stress- and defense-related genes. In addition, Ib-rolB/C expression induced substantial metabolic reprogramming characterized by increased accumulation of flavonol glycosides and camalexin together with reduced glucosinolate levels. Our findings demonstrate that Ib-rolB/C functions as a multifunctional regulator integrating redox signaling, stress adaptation, immune responses, and secondary metabolism, highlighting the evolutionary significance of naturally acquired T-DNA genes in plants.},
}

*Ipomoea batatas/genetics/physiology
Arabidopsis/genetics/physiology/microbiology
Plants, Genetically Modified
*Stress, Physiological/genetics
Gene Expression Regulation, Plant
Oxidation-Reduction
DNA, Bacterial/genetics
Pseudomonas syringae/physiology
Reactive Oxygen Species/metabolism
Transgenes
Botrytis/physiology
Antioxidants/metabolism
Plant Diseases/microbiology/immunology
Disease Resistance/genetics
*Bacterial Proteins/genetics/metabolism
beta-Glucosidase

@article {pmid42842059,
year = {2026},
author = {Adesoji, AT and Mattioni Marchetti, V and Cortimiglia, C and Piscopiello, F and Petrizzi, I and Piazza, A and Alabi, ED and Cocconcelli, PS and Migliavacca, R},
title = {Emergence of multidrug resistant Enterobacter spp. in Nigeria: a genomic study.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42842059},
issn = {1573-0972},
support = {P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; P E00000007, INF-ACT//NextGenerationEU-MUR PNRR/ ; },
mesh = {Humans ; Nigeria/epidemiology ; *Enterobacter/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Multiple, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Animals ; Microbial Sensitivity Tests ; Plasmids/genetics ; Whole Genome Sequencing ; Genome, Bacterial ; beta-Lactamases/genetics ; Virulence Factors/genetics ; *Enterobacteriaceae Infections/microbiology/veterinary/epidemiology ; Genomics ; Bacterial Proteins/genetics ; Third Generation Cephalosporins ; Food Microbiology ; },
abstract = {BACKGROUND: Extended-spectrum β-lactamases (ESBL) and AmpC β-lactamase-producing Enterobacter species are pathogens of public health concern. In this study, we investigated the resistome, virulome, and plasmidome of circulating Enterobacter hormaechei isolated from humans, animals, and ready-to-eat (RTE) food in Dutsin-Ma, northwest Nigeria.

MATERIALS AND METHODS: Enterobacter species were isolated from human, and RTE food samples using MacConkey and CHROM agar. Species identification and antibiotics susceptibility testing (AST) were performed using Microscan autoSCAN-4 and MALDI-TOF MS, respectively. Whole-genome sequencing (WGS) and bioinformatics analysis were performed to validate the species identities. WGS also determined sequence types (STs), resistome, plasmidome, and virulome using PubMLST, ResFinder, PlasmidFinder, and Virulence Factors Database (VFDB) via ABRicate, respectively.

RESULTS: E. hormaechei subs. xiangfangensis was the dominant species isolated from humans (6/8, 75%) and animals (1/8, 12.5%), while E. hormaechei subs. oharae was exclusively found in RTE food (1/8, 12.5%). The most frequent sequence type (ST) was ST813, found solely in humans, along with ST511, ST454, and the emerging high-risk ST171. ST68 was identified in food, and novel ST (ST3186) were identified in animal and human samples, respectively. All isolates exhibited 100% resistance to ampicillin and amoxicillin-clavulanic acid, with 62.5% resistant to each of aztreonam, ceftazidime, ciprofloxacin, gentamicin, tobramycin and cefotaxime, and 25% to colistin. E. hormaechei (62.5%) isolates carried the blaCTX-M-15 gene, encoding ESBL-production, along with AmpC genes such as blaCMH-3, and also harbored resistance genes for aminoglycosides, fluoroquinolones, sulfonamides, tetracyclines, and trimethoprim. The IncHI2 (50%) was identified as the dominant plasmid type followed by Col (pHAD28) (25%), IncFIB (25%), and IncFII (11.1%). The most (62.5%) prevalence virulence gene among the isolates is ompA encoding adhesion while each of entA, entB and fepD encoding iron acquisition were least (12.5%) occurred.

CONCLUSION: This study provides the first genomic insight into Enterobacter species in northwest Nigeria, highlighting their role in the spread of antimicrobial resistance. E. hormaechei subsp. xiangfangensis was identified as the main reservoir of ESBL and AmpC β-lactamases in this study. The discovery of novel STs with diverse virulence factors and plasmid replicon indicates potential horizontal gene transfer across different ecological niches. Our findings underscore the need for robust surveillance and control measures to combat the spread of MDR Enterobacter species across human, animal, and food niches.},
}

Humans
Nigeria/epidemiology
*Enterobacter/genetics/drug effects/isolation & purification/classification
*Drug Resistance, Multiple, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Animals
Microbial Sensitivity Tests
Plasmids/genetics
Whole Genome Sequencing
Genome, Bacterial
beta-Lactamases/genetics
Virulence Factors/genetics
*Enterobacteriaceae Infections/microbiology/veterinary/epidemiology
Genomics
Bacterial Proteins/genetics
Third Generation Cephalosporins
Food Microbiology

@article {pmid42667951,
year = {2026},
author = {Kofler, R and Saadain, S and Pinhasi, R},
title = {Genomic time-series data may reveal the true magnitude of horizontal exchange between species.},
journal = {Current opinion in insect science},
volume = {78},
number = {},
pages = {101608},
doi = {10.1016/j.cois.2026.101608},
pmid = {42667951},
issn = {2214-5753},
mesh = {Animals ; *Gene Transfer, Horizontal ; *DNA Transposable Elements ; Genomics ; *Insecta/genetics ; },
abstract = {Species largely evolve in isolation, with little exchange of genetic material between them. Occasionally, however, mechanisms like horizontal transfer disrupt this isolation and transfer genetic information between species. Transposable elements (TEs), short DNA sequences that can multiply within genomes, are frequently involved in such exchanges. The frequency of horizontal transposon transfer (HTT) between species remains a fundamental open question in biology, as classical sequence comparison approaches may substantially underestimate the true extent of HTT. In this review, we highlight that genomic time-series (GTS), that is, genomes of specimens sampled across different years in the past, enable an alternative approach that may provide a more unbiased estimate of the true magnitude of HTT between species. Analysis of GTS in fruit flies suggests that HTT may be rampant, with 12 events found over the past 200 years. Species may thus exchange genetic material far more frequently than previously thought. We discuss the pros and cons of different approaches for detecting HTT, show how GTS can be generated for diverse species, and highlight various strategies for identifying HTT events. GTS may generally constitute a valuable resource for addressing a broad range of evolutionary questions.},
}

Animals
*Gene Transfer, Horizontal
*DNA Transposable Elements
Genomics
*Insecta/genetics

@article {pmid42834358,
year = {2026},
author = {Marchi, A and Wenne, M and Varga, V and Bengtsson-Palme, J},
title = {On the hunt for candidate genes involved in host-adaptation in Pseudomonas aeruginosa using comparative genomics.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42834358},
issn = {1471-2164},
support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse/ ; 2020-03629//Vetenskapsrådet/ ; FFL21-0174//Stiftelsen för Strategisk Forskning/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/physiology/isolation & purification ; *Genomics/methods ; Humans ; Virulence Factors/genetics ; *Host Adaptation/genetics ; Genome, Bacterial ; Bacterial Proteins/genetics ; Multigene Family ; Gene Transfer, Horizontal ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions/genetics ; },
abstract = {BACKGROUND: Pseudomonas aeruginosa is an opportunistic pathogen responsible for causing severe hospital-acquired infections, largely due to its adaptability, diverse range of virulence factors and drug resistance mechanisms. Despite extensive research, a substantial portion of the genome of P. aeruginosa remains functionally uncharacterized. The aim of this study was to identify candidate host-adaptation genes, including potential virulence factors, among these numerous uncharacterized genes.

RESULTS: We performed a comparative genomic analysis of P. aeruginosa strains isolated from human clinical sources versus those from natural environments to identify clusters of homologous proteins significantly enriched with sequences from bacteria isolated from humans. Our analysis revealed that approximately 3% of all protein clusters showed significant enrichment in sequences from human isolates. Functional characterization of 45 selected clusters with particularly large enrichment of human isolates showed that these clusters contained genes with roles primarily related to host interaction and horizontal gene transfer. Notably, twelve of the 45 selected clusters consisted of genes with unknown function, suggesting the existence of potentially novel virulence factors or genes involved in the infection process within human-derived isolates.

CONCLUSIONS: Our findings highlight specific uncharacterized protein clusters as promising targets for future investigation. The identification of both known virulence-associated functions and uncharacterized proteins among human-enriched clusters demonstrates the ability of our comparative genomics approach to detect established as well as potentially novel candidate host-adaptation genes. These findings further suggest that this strategy may be broadly applicable to the study of other opportunistic pathogens.},
}

*Pseudomonas aeruginosa/genetics/physiology/isolation & purification
*Genomics/methods
Humans
Virulence Factors/genetics
*Host Adaptation/genetics
Genome, Bacterial
Bacterial Proteins/genetics
Multigene Family
Gene Transfer, Horizontal
Pseudomonas Infections/microbiology
*Host-Pathogen Interactions/genetics

@article {pmid42835138,
year = {2026},
author = {Aguirre-Carvajal, K and Munteanu, CR and Armijos-Jaramillo, V},
title = {A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1891949},
pmid = {42835138},
issn = {2673-7647},
abstract = {INTRODUCTION: Horizontal gene transfer (HGT), the movement of genetic material between unrelated organisms, is widely recognized as an important driver of genome evolution in bacteria. In eukaryotes, however, the evolutionary impact of HGT remains debated. The identification of interkingdom HGT (iHGT) is especially challenging due to the lack of gold standard methods. While automated approaches for iHGT candidate detection exist, the interpretation of phylogenetic tree topologies into biologically meaningful evolutionary patterns has traditionally depended on expert manual inspection, a process that is subjective, difficult to reproduce, and not scalable to large datasets.

METHODS: We present a computational framework that formalizes phylogenetic tree interpretation as a supervised machine-learning problem. We define five recurrent phylogenetic patterns (iHGT, NoHGT, Limited donor evidence, Multiple major clades, and Patchy phylogeny) and developed a feature-extraction pipeline that captures taxonomic composition and phylogenetic topology through six biologically interpretable descriptors derived from unrooted gene trees. Several machine-learning algorithms were evaluated using repeated stratified cross-validation, and model interpretability was assessed through permutation importance, SHAP analysis, rule-based baselines, and feature ablation. Performance was further validated on simulated datasets, real biological iHGT candidates, and an independently annotated external dataset.

RESULTS: A Random Forest (RF) classifier achieved the best performance (AUC-ROC = 0.98; accuracy = 0.89). Topological distance and lineage-distribution features were identified as the strongest contributors to classification performance. Feature ablation and rule-based baseline comparisons demonstrated that model performance cannot be explained solely by explicit annotation rules and benefits from combining clade-composition and topology-based information. The RF classifier showed low misclassification rates on simulated and real biological datasets (7.8% and 10.43%, respectively), showed substantial agreement (69.4%) with an independently annotated external dataset, and consistently outperformed AVP (Alienness vs. Predictor), Alien Index, and HGT Index across all evaluated metrics.

CONCLUSION: These results support the use of machine learning for the automated, reproducible, and scalable classification of expert-defined phylogenetic patterns. The framework also highlights that some topologies commonly interpreted as evidence of iHGT may reflect alternative evolutionary processes, emphasizing the need for cautious and context-aware inference.},
}

@article {pmid42836310,
year = {2026},
author = {Haldar, A and Yosef, I and Goren, MG and Globus, R and Yakunina, M and Mahata, T and Qimron, U},
title = {Adaptation-coupled CRISPRi identifies antibiotic-sensitizing genes leading to a novel plasmid selection marker.},
journal = {Nucleic acids research},
volume = {54},
number = {18},
pages = {},
pmid = {42836310},
issn = {1362-4962},
support = {101248381//H2020 European Research Council/ ; 818878//H2020 European Research Council/ ; //ERC/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *CRISPR-Cas Systems ; DNA Gyrase/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Salmonella/genetics/drug effects ; Shigella/genetics/drug effects ; },
abstract = {Antibiotic resistance through horizontal gene transfer is a major challenge in microbiology and medicine. We describe a CRISPR-based screening system that couples spacer adaptation with gene repression to identify bacterial genes that sensitize bacteria to antibiotics. We used this screening system in Escherichia coli, on seven different antibiotics to select spacers that conferred resistance to them. The screen identified both known and previously unrecognized genes that modulate antibiotic susceptibility. We defined this collection of genes that sensitize bacteria to antibiotics as the 'sensitasome'. Among the identified targets were the essential genes gyrA and gyrB, whose repression increased resistance to multiple antibiotics. Some sensitization genes exhibited a clear trade-off: their repression conferred resistance to certain antibiotics while increasing susceptibility to others. Sensitasome-targeting spacers were also effective in Shigella and Salmonella, indicating that the resistance mechanism is conserved across species. Finally, we repurposed a selected spacer as a CRISPR-based antibiotic selection marker using the compact Cas12m effector. Together, these findings establish adaptation-coupled CRISPRi as a simple platform for discovering antibiotic sensitization genes and provide an environmentally safer alternative to conventional antibiotic resistance markers.},
}

*Anti-Bacterial Agents/pharmacology
Escherichia coli/genetics/drug effects
*Plasmids/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
*CRISPR-Cas Systems
DNA Gyrase/genetics
*Clustered Regularly Interspaced Short Palindromic Repeats
Salmonella/genetics/drug effects
Shigella/genetics/drug effects

@article {pmid42836481,
year = {2026},
author = {Xie, L and Wang, L and Ma, L and Wang, J and Wu, D and Lin, A and Wang, L and Ye, M and Li, X and Zhang, T and Zhu, D},
title = {Microplastic-driven carbon availability differentiates phage-host interactions in shaping soil resistome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag258},
pmid = {42836481},
issn = {1751-7370},
abstract = {The growing prevalence of microplastics (MPs) in agroecosystem has raised significant concerns regarding their ability in facilitating the dissemination of antibiotic resistance genes (ARGs). Biodegradable and nondegradable MPs exhibited inherently different degradation rates, resulting in divergent carbon bioavailability that might trigger distinct microbial response and ARG profiles. Here, by integrating multi-omics (metagenomics, virome and metatranscriptomics) with experimental validation, we explored how microbial responses to MPs impacted ARG dissemination in a long-term field experiment. We showed that both biodegradable and nondegradable MPs significantly increased ARG abundance and transcriptional activity, differing in the drive mechanisms. Biodegradable MPs triggered bacterial oxidative stress and SOS response, increasing mobile genetic elements abundance and horizontal gene transfer of ARGs. Accordingly, increasing proportion of lysogenic phages and intensified phage-host interactions might promote ARG transduction through lysogenic conversion. In contrast, nondegradable MPs increased recalcitrant carbon, which enriched bacteria harboring genes for complex compound degradation. ARG-carrying bacteria within these taxa gained fitness advantages, facilitating their enrichment and ARG proliferation. Concurrently, phages infecting ARG-carrying bacteria encoded more auxiliary metabolic genes in complex carbohydrate metabolism, thereby enhancing host competitiveness and promoting ARG spread. In vitro validation experiments confirmed that lysogenic phages facilitated transduction of ARGs under biodegradable MPs, while phage-encoded auxiliary metabolic genes conferred growth advantages on ARG-carrying bacteria utilizing recalcitrant carbon source, consistent with conditions induced by nondegradable MPs. Our findings clarify how phages differentially impacted ARG profiles under biodegradable and nondegradable MPs, underscoring the importance of considering phage-mediated processes in assessing the risks of MPs and ARG dissemination.},
}

@article {pmid42836822,
year = {2026},
author = {Malaluan, RPP and Dy, RLV},
title = {Acquisition of novel arrays via horizontal gene transfer rewires CRISPR-mediated defense in Pseudomonas aeruginosa.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0033926},
doi = {10.1128/jb.00339-26},
pmid = {42836822},
issn = {1098-5530},
abstract = {UNLABELLED: Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems form the adaptive immunity of prokaryotes, conferring sequence-specific protection against genetic parasites. Here, we functionally characterized the type I-F CRISPR-Cas system of Pseudomonas aeruginosa ATCC 10145 (PA10145), which led us to discover the existence of an isolated CRISPR array unique to this system. Its core CRISPR-Cas system is composed of a cas operon flanked by two divergently organized arrays: CRISPR2 and CRISPR1. Meanwhile, the isolated CRISPR array, CRISPR3, was found ~1.3 million bp away from cas. The cas and three CRISPR arrays together function toward adaptive immunity, eliminating plasmids engineered with protospacer targets. If plasmids possessed an intact protospacer adjacent motif (PAM), hyperactive adaptation was stimulated in all CRISPR arrays of PA10145, whereas minimal to no adaptation was observed when the PAM was mutated. Spacer acquisition via interference-driven adaptation proceeds through strand-biased priming in PA10145. Interestingly, the isolated CRISPR3 and cas-adjacent CRISPR2 have nearly identical leader sequences, with only 3 bp mismatches. Of the 1,196 P. aeruginosa genomes analyzed, all 281 isolated arrays only occur as type I-F with similarly matching leaders to CRISPR2. Integrative conjugative elements and prophages only associate with CRISPR2 and CRISPR3, suggesting that isolated arrays might have originated from recombination events involving CRISPR2 as facilitated by these highly transmissible mobile genetic elements. Tracing evolutionary trajectories of the isolated CRISPR3 relative to cas-adjacent arrays revealed that CRISPR3 is horizontally transferred across P. aeruginosa genomes. Taken together, these results implicate the role of horizontally acquired isolated arrays in CRISPR-mediated pan-immunity as gateways to mobilize genetic memories.

IMPORTANCE: Clustered regularly interspaced short palindromic repeat (CRISPR) arrays are typically located adjacent to cas genes, constituting the adaptive immune system. However, a substantial subset of CRISPR arrays, called isolated arrays, is found distantly located from their cognate cas operons. Despite their prevalence, the functional significance and evolutionary implications of isolated arrays have remained poorly understood. Here, we show that isolated arrays are active components of type I-F CRISPR-Cas systems in Pseudomonas aeruginosa. These arrays are continuously updated through hyperactive strand-biased primed adaptation and are transferred horizontally across P. aeruginosa, acting as conduits of immunological memory and proponents of CRISPR-mediated pan-immunity. We posit that bacterial populations mobilize these isolated arrays to maintain transferable memory in the pangenome while remaining compatible with ongoing horizontal gene transfer.},
}

@article {pmid42838283,
year = {2026},
author = {Kitagawa, H and Nakano, S and Tadera, K and Koide, S and Otake, S and Sugawara, Y and Akeda, Y and Ohnishi, M and Sugai, M and Ohge, H},
title = {Phylogenetically Distinct CC128-Related Group A Streptococcus dysgalactiae subsp. equisimilis Lineages Identified in Bacteremia Cases in Japan.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {103099},
doi = {10.1016/j.jiac.2026.103099},
pmid = {42838283},
issn = {1437-7780},
abstract = {Streptococcus dysgalactiae subsp. equisimilis (SDSE) expressing the Lancefield group A antigen is an uncommon variant that is thought to have acquired the group A carbohydrate synthesis genes through horizontal gene transfer from Streptococcus pyogenes. Its prevalence and genomic characteristics remain incompletely understood. We retrospectively investigated 48 SDSE isolates recovered from blood cultures at a tertiary care hospital in Japan, between 2010 and 2023. Lancefield grouping was performed for all isolates, and whole-genome sequencing and phylogenetic analyses were performed for the two group A SDSE isolates. Among the 48 isolates, 44 (91.7%) were group G, two (4.2%) were group A, and two (4.2%) were group C. The two group A isolates, HUSD042 and HUSD047, belonged to clonal complex 128 (CC128); HUSD042 belonged to sequence type 177 (ST177), a single-locus variant of ST128, and HUSD047 belonged to ST128. Both isolates carried the emm subtype stG485.0. Comparative genomic analysis revealed a hybrid gac/gcc carbohydrate synthesis locus, in which the central region corresponding to the group C SDSE gccF-gccK region was replaced by an S. pyogenes-derived gacF-gacL region, consistent with a previously described invasive ST128-related group A SDSE lineage. Bayesian phylogenetic analysis showed that HUSD042 clustered within a clade predominantly composed of Japanese isolates, whereas HUSD047 clustered within a clade composed mainly of isolates from the United States. These findings demonstrate the presence of phylogenetically distinct CC128-related group A SDSE lineages in Japan and highlight the genomic diversity of this rare variant. Continued genomic surveillance with broader geographic sampling and detailed epidemiological information is warranted to clarify its evolution and geographic distribution.},
}

@article {pmid42838473,
year = {2026},
author = {Artuso, I and Salaris, S and Cenere, G and Losasso, C and Scaltriti, E and Bracchi, C and Bolzoni, L and Lucarelli, C and Garcia-Fernandez, A and Di Giampietro, G and De Marchis, ML and Villa, L and Barco, L},
title = {Genomic evidence of lac operon acquisition in Salmonella Strathcona clinical isolates in Italy.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {145},
number = {},
pages = {106040},
doi = {10.1016/j.meegid.2026.106040},
pmid = {42838473},
issn = {1567-7257},
abstract = {We report six lactose-fermenting Salmonella Strathcona isolates carrying a lac operon on an IncHI2/IncHI2A plasmid. Whole-genome sequencing revealed intact lacI-lacZ-lacY and truncated lacA genes. These isolates represent the first detection of lactose-fermenting S. Strathcona, highlighting a risk of diagnostic errors due to reliance on lactose fermentation-based phenotypic identification.},
}