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

@article {pmid40165089,
year = {2025},
author = {Ma, Y and López-Pujol, J and Yan, D and Deng, Z and Zhou, Z and Niu, J},
title = {Complete mitochondrial genomes of the hemiparasitic genus Cymbaria (Orobanchaceae): insights into repeat-mediated recombination, phylogenetic relationships, and horizontal gene transfer.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {314},
pmid = {40165089},
issn = {1471-2164},
support = {31860106//National Natural Science Foundation of China/ ; 2019ZD008//Major Science and Technology Projects of Inner Mongolia Autonomous Region/ ; },
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Gene Transfer, Horizontal ; *Orobanchaceae/genetics/classification ; Recombination, Genetic ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Evolution, Molecular ; },
abstract = {BACKGROUND: The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica).

RESULTS: A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465 bp and 1,539,836 bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (> 1000 bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS ≤ 70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively.

CONCLUSIONS: We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.},
}

*Genome, Mitochondrial
*Phylogeny
*Gene Transfer, Horizontal
*Orobanchaceae/genetics/classification
Recombination, Genetic
RNA, Transfer/genetics
Repetitive Sequences, Nucleic Acid
Evolution, Molecular

@article {pmid40166126,
year = {2025},
author = {Zhang, Y and Zhang, B and Ahmed, I and Zhang, H and He, Y},
title = {Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica.},
journal = {Fundamental research},
volume = {5},
number = {1},
pages = {269-281},
pmid = {40166126},
issn = {2667-3258},
abstract = {Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes (ARGs). Here, we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island, Terra Nova Bay, Antarctica. Average concentrations of ARGs in intracellular DNA (iARGs) among water (3.98 × 10[6] copies/L), soil (3.41 × 10[7] copies/kg), and penguin guano (7.04 × 10[7] copies/kg) were higher than those of ARGs in extracellular DNA (eARGs) among water (1.99 × 10[4] copies/L), soil (1.75 × 10[6] copies/kg), and penguin guano (8.02 × 10[6] copies/kg). It was indicated that the transmission of ARGs across different media occurs with around 77.8% of iARGs from soil and 86.7% of iARGs from penguins observed in water, and 80.7% of iARGs and 56.7% of eARGs from penguins found in soil. Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983. Bacitracin, multidrug, and aminoglycoside resistance genes were the main ARGs among water, soil, and penguin guano. Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes, and main low-risk ARGs associated with mobile genetic elements (MGEs) were aminoglycoside resistance genes. Antibiotic-resistant bacteria (ARB) from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles. MGEs, ARB, bacterial diversities, antibiotics, and metals could explain total ARGs between water and soil. Intracellular MGEs were the most significant in-situ driver of iARGs in water, reflecting that horizontal gene transfer could facilitate the spread of ARGs in water. Penguins were important ex-situ drivers of environmental antibiotic resistome, which was linked with risky ARGs between water and soil. These findings highlight the major roles of natural drivers (e.g., MGEs and penguins) in shaping environmental antibiotic resistome in polar areas, improving our understanding of the evolution of environmental microbiome.},
}

@article {pmid40164788,
year = {2025},
author = {},
title = {Horizontal gene transfer of cold shock protein genes boosted wheat adaptation and expansion.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40164788},
issn = {2055-0278},
}

@article {pmid40162837,
year = {2025},
author = {Major, SR and Polinski, JM and Penn, K and Rodrigue, M and Harke, MJ},
title = {Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0259324},
doi = {10.1128/aem.02593-24},
pmid = {40162837},
issn = {1098-5336},
abstract = {Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.},
}

@article {pmid40161755,
year = {2025},
author = {Ratna, TA and Sharon, BM and Velin, CAB and Buttaro, BA and Palmer, KL},
title = {Factors affecting CRISPR-Cas defense against antibiotic resistance plasmids harbored by Enterococcus faecalis laboratory model strains and clinical isolates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.10.642232},
pmid = {40161755},
issn = {2692-8205},
abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive bacterium and opportunistic pathogen that acquires resistance to a wide range of antibiotics by horizontal gene transfer (HGT). The rapid increase of multidrug-resistant (MDR) bacteria including MDR E. faecalis necessitates the development of alternative therapies and a deeper understanding of the factors that impact HGT. CRISPR-Cas systems provide sequence-specific defense against HGT. From previous studies, we know that E. faecalis CRISPR-Cas provides sequence-specific anti-plasmid defense during agar plate biofilm mating and in the murine intestine. Those studies were mainly conducted using laboratory model strains with a single, CRISPR-targeted plasmid in the donor. MDR E. faecalis typically possess multiple plasmids that are diverse in sequence and may interact with each other to impact plasmid transfer and CRISPR-Cas efficacy. Here, we altered multiple parameters of our standard in vitro conjugation assays to assess CRISPR-Cas efficacy, including the number and genotype of plasmids in the donor; laboratory model strains as donor versus recent human isolates as donor; and the biofilm substrate utilized during conjugation. We found that the plasmids pTEF2 and pCF10, which are not targeted by CRISPR-Cas in our recipient, enhance the conjugative transfer of the CRISPR-targeted plasmid pTEF1 into both wild-type and CRISPR-Cas-deficient (via deletion of cas9) recipient cells. However, the effect of pTEF2 on pTEF1 transfer is much more pronounced, with a striking 6-log increase in pTEF1 conjugation frequency when pTEF2 is also present in the donor and recipients are deficient for CRISPR-Cas (compared to 4-log for pCF10). We also identified that E. faecalis Δ cas9 has altered biofilm structure and thickness relative to the wild-type strain when cultured on a plastic substrate, but equivalent growth in the agar plate biofilms widely used for conjugation studies. Overall, this study provides insight about the interplay between plasmids and CRISPR-Cas defense, opening avenues for developing novel therapeutic strategies to curb HGT among bacterial pathogens, and highlighting pTEF2 as a plasmid for additional mechanistic study.

IMPORTANCE: The emergence of MDR bacteria, including MDR E. faecalis, limits treatment options and necessitates development of alternative therapeutics. In these circumstances, bacterial CRISPR-Cas systems are being explored by the field to develop CRISPR-based antimicrobials. However, in many cases CRISPR-Cas efficacy has only been assessed using laboratory model strains. More studies are required that investigate clinical isolates, as those are the intended targets for CRISPR antimicrobials. Here, we demonstrated how the number of plasmids harbored by an E. faecalis donor strain can affect the apparent efficacy of CRISPR-Cas anti-plasmid defense in a recipient strain. Overall, our research is important to develop improved CRISPR-based antimicrobials to combat the spread and accumulation of antibiotic resistance determinants.},
}

@article {pmid40158280,
year = {2025},
author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Xiang, J and Yu, X and Liao, Q and Ai, Q and Qiu, S and Zhang, D},
title = {Strict relationship between phenotypic and plasmid-associated genotypic of multidrug-resistant Escherichia coli isolated from Taihe Black-Boned Silky Fowl farms.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105082},
doi = {10.1016/j.psj.2025.105082},
pmid = {40158280},
issn = {1525-3171},
abstract = {Taihe Black-Boned Silky Fowl (TBSF) is a unique breed in China, characterized by a high concentration of melanin deposited throughout its body. Compared to broiler chickens, many antibiotics exhibit significantly longer withdrawal periods in TBSF. Given that antibiotic exposure is widely recognized as the primary selective pressure driving the persistence and dissemination of antibiotic resistance genes (ARGs) across diverse environments, it is crucial to investigate the occurrence and prevalence of ARGs within TBSF farming systems. In this study, 34 Escherichia coli strains isolated from 22 TBSF farms were subjected to phenotypic and genotypic analyses. The isolates were tested for susceptibility to 28 antimicrobial drugs representing nine antibiotic classes to determine their antimicrobial resistance phenotypes. Draft genome sequences of these E. coli strains were obtained, and the ARGs carried by mobile genetic elements, particularly plasmids, were analyzed for their association with susceptibility phenotype. The genetic context of key ARGs in these E. coli isolates was further characterized. Network analysis was employed to investigate the correlations between ARGs, phenotypes, and drug residues. The results demonstrated that high rates of antimicrobial resistance were observed, with 100 % and 29.4 % of isolates exhibiting resistance to four or more and eight or more antibiotic classes, respectively. According to whole-genome sequencing, a total of 143 ARGs were identified. The antimicrobial resistance phenotypes were consistently correlated with the presence of corresponding ARGs in the 34 E. coli genomes. 100 % of the β-lactams antibiotics resistant mechanism could be attributed to the presence of the resistance gene blaTEM and/or blaOXA-10. Similarly, resistance to tetracyclines, chloramphenicols, aminoglycosides, and fluoroquinolones was fully explained by the presence of tetR and/or tetA, floR and/or cmlA, ant(3'')-IIa, aph(3'')-Ib, aph(6)-Id, aac(3)-IId, and aadA, and qnrS and/or mutant gyrA/parC/mdtH. The majority of these key ARGs were found to be plasmid-associated. This study verified and highlighted the prevalent horizontal gene transfer of ARGs in TBSF farms. Factors such as hygiene status, biosecurity measures, and other environmental conditions might play a more significant role than antimicrobial usage in facilitating the horizontal gene transfer of ARGs in TBSF farms. Appropriate measures should be taken to control the transmission and dissemination of these mobile genetic elements associated ARGs and prevent their entry into the human clinical environment from TBSF breeding environment.},
}

@article {pmid40155375,
year = {2025},
author = {von Rosen, T and Zdanowicz, R and El Hadeg, Y and Afanasyev, P and Boehringer, D and Leitner, A and Glockshuber, R and Weber-Ban, E},
title = {Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3042},
pmid = {40155375},
issn = {2041-1723},
support = {310030_215606//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; ETH-17 17-2//Eidgenössische Technische Hochschule Zürich (Federal Institute of Technology Zurich)/ ; },
mesh = {*Proteasome Endopeptidase Complex/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Cryoelectron Microscopy ; Protein Binding ; Mycobacterium tuberculosis/metabolism/genetics ; Models, Molecular ; Mutagenesis, Site-Directed ; Binding Sites ; Proteolysis ; Substrate Specificity ; },
abstract = {Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.},
}

*Proteasome Endopeptidase Complex/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
*Cryoelectron Microscopy
Protein Binding
Mycobacterium tuberculosis/metabolism/genetics
Models, Molecular
Mutagenesis, Site-Directed
Binding Sites
Proteolysis
Substrate Specificity

@article {pmid40154852,
year = {2025},
author = {He, L and Wang, W and Chen, H and Ma, L and Yu, L and Yang, Y and Qu, Y and Dai, P and Wang, D and Ma, X},
title = {Gene expressions of clinical Pseudomonas aeruginosa harboring RND efflux pumps on chromosome and involving a novel integron on a plasmid.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107512},
doi = {10.1016/j.micpath.2025.107512},
pmid = {40154852},
issn = {1096-1208},
abstract = {The clinical strain of Pseudomonas aeruginosa XM8 harbored multiple RND-type antibiotic efflux pump genes and a novel integron In4881 on its plasmid pXM8-2, rendering it resistant to nearly all conventional antibiotics except colistin. The resistance was primarily attributed to the inactivation of the oprD gene and overexpression of several efflux pump genes, including mexAB-oprM, mexCD-oprJ, oprN-mexFE, and mexXY. In this study, the XM8 strain was comprehensively characterized using various methods. Antimicrobial susceptibility testing was performed using the BioMerieux VITEK2 system and manual double dilution methods. Gene expression levels of efflux pump-related genes were analyzed via quantitative real-time PCR. The bacterial chromosome and plasmid were sequenced using both Illumina and Nanopore platforms, and bioinformatics tools were employed to analyze mobile genetic elements associated with antibiotic resistance. The pXM8-2 plasmid containsed multiple mobile genetic elements, including integrons (In4881, In334, In413) and transposons (Tn3, TnAs1, TnAs3). Notably, In4881 was reported for the first time in this study. The presence of these elements highlights the potential for horizontal gene transfer and further spread of antibiotic resistance. Given the strong resistance profile of the XM8 strain, effective measures should be implemented to prevent the dissemination and prevalence of such multidrug-resistant bacteria.},
}

@article {pmid40154224,
year = {2025},
author = {Hao, X and Sang, W and Li, F and Shen, L and Zhu, L and Rong, L and Jiang, D and Bai, L},
title = {Regulation of antibiotic resistance gene rebound by degrees of microecological niche occupation by microbiota carried in additives during the later phases of swine manure composting.},
journal = {Ecotoxicology and environmental safety},
volume = {294},
number = {},
pages = {118112},
doi = {10.1016/j.ecoenv.2025.118112},
pmid = {40154224},
issn = {1090-2414},
abstract = {The occupation of microecological niches (MNs) by bacteria carrying lower antibiotic resistance genes (ARGs) has been demonstrated an effective strategy for reducing ARGs in compost, thereby mitigating the associated land use risks. In this study, humus soil (HS), matured compost (MC), and their respective isolated microbial agents (HSM and MCM), which exhibit varying abundances of ARGs, were introduced as additives after the thermophilic phase to investigate their influence on ARG removal and the mechanisms underlying effective MN occupation. The addition of HS resulted in the most favorable outcomes, including the highest carbon degradation, minimized nitrogen loss, and an 83.16 % reduction in ARG abundance during the later composting stages. In comparison, ARG rebound levels were 61.77 %-285.33 % across other treatments and 729.23 % in the control. Distinct dominant bacterial genera and potential ARG-host bacterial communities were observed, which varied with different additives and contributed to MN occupation dynamics. The addition of the HS additive intensified competition among non-host bacteria, and diversified the interactions both between genes and between bacteria. These changes suppressed horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs) and altered the abundance and composition of both dominant and non-dominant potential host species. Furthermore, it shifted the relative importance of key physicochemical parameters, collectively enhancing ARG removal during composting. These findings elucidate the mechanisms by which MN adjustments contribute to ARG reduction, providing actionable insights for designing composting strategies that mitigate environmental ARG dissemination risks more effectively.},
}

@article {pmid40151755,
year = {2025},
author = {Hota, S and Patil, SR and Mane, PM},
title = {Enterococcus: Understanding Their Resistance Mechanisms, Therapeutic Challenges, and Emerging Threats.},
journal = {Cureus},
volume = {17},
number = {2},
pages = {e79628},
pmid = {40151755},
issn = {2168-8184},
abstract = {The Enterococcus species originates as non-harmful bacteria indigenous to human intestines but has transformed into severe hospital-acquired pathogens due to antimicrobial resistance (AMR). The clinical species Enterococcus faecalis and Enterococcus faecium create the most relevant infections because they appear in urinary tract infections, bloodstream infections, endocarditis, and wound infections. Enterococcus species demonstrate multiple antibiotic class resistance and resistance determinant acquisition properties that make treatment difficult for medical professionals. Vancomycin-resistant enterococci (VRE) together with high-level aminoglycoside-resistant strains and resistance to both linezolid and daptomycin have exhausted available treatment options. The review investigates the development process of Enterococcus infections by examining virulence characteristics, which involve biofilm production and defense mechanisms against the immune response and transmission of resistance genes. A thorough investigation of medical publications used Google Scholar along with PubMed and ScienceDirect and Medical Subject Headings (MeSH) as appropriate search terms. The traditional classification of Enterococcus species from historical context to modern epidemiology and pathogenesis and available treatment and test approaches are explained in this review. This section examines two categories of resistance together with their mechanisms of action with a specific focus on vancomycin resistance produced by van gene clusters as well as its prevalence trends. An examination of how horizontal gene transfer functions in transferring resistance throughout healthcare facilities is included. The paper investigates the different symptoms of enterococcal infections together with diagnostic obstacles and treatment modalities. Drug-resistant Enterococcus infections continue to increase internationally, so healthcare professionals need new therapeutic methods, better antimicrobial policies, and stronger infection prevention measures. The examination surveys Enterococcus infections through an extensive evaluation of developing resistance patterns combined with emerging intervention requirements.},
}

@article {pmid39562577,
year = {2024},
author = {Chen, Y and Wang, W and Zhang, S and Zhao, Y and Feng, L and Zhu, C},
title = {Assembly and analysis of the complete mitochondrial genome of Carya illinoinensis to provide insights into the conserved sequences of tRNA genes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28571},
pmid = {39562577},
issn = {2045-2322},
support = {32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; 32001344//the National Natural Science Foundation of China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; BK20200290//the Natural Science Foundation of Jiangsu Province, China/ ; },
mesh = {*Carya/classification/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; *RNA, Transfer/chemistry/genetics ; *Conserved Sequence ; Phylogeny ; RNA Folding ; Sequence Analysis, DNA ; Codon Usage ; RNA Editing ; Gene Transfer, Horizontal ; Fagus/genetics ; },
abstract = {Carya illinoinensis is an economically important nut tree, and its chloroplast (cp.) genome has been reported; however, its mitochondrial (mt) genome remains unknown. In the present study, we assembled the first mt genome of C. illinoinensis. The circular mt genome of C. illinoinensis is 495,205 bp long, with 37 protein-coding genes(PCGs), 24 tRNA genes, and 3 rRNA genes. All the tRNAs could be folded into typical cloverleaf secondary structures, with lengths of 58-88 bp. A conserved U-U-C-x-A-x2 consensus nucleotide sequence was discovered in the Ψ-loops of tRNA sequences. In addition, 447 dispersed repeats were detected, as well as found 482 RNA editing sites and 9,960 codons in the mt genome. Furthermore, a total of 27 DNA sequences with a length of 43,277 bp were transferred from the cp. to the mt genome, and eight integrated cp-derived genes (trnL-CAA, trnV-GAC, trnD-GUC, trnW-CCA, trnN-GUU, trnH-GUG, trnM-CAU, and rps7) were identified. We also obtained 1,086 hits, including 364.023 kp of nuclear genome sequences, that were transferred to the mt genome. To determine the evolutionary position of C. illinoinensis, we conducted a phylogenetic analysis of the mitogenomes of C. illinoinensis and 14 other taxa. The results strongly suggested that C. illinoinensis and Fagus sylvatica formed a single clade with 100% bootstrap support. This study sequenced comprehensive data on the C. illinoinensis mitochondrial genome and provided insights into the conserved sequences of tRNA genes, which could facilitate evolutionary research in other Carya trees in the future.},
}

*Carya/classification/genetics
*Genome, Mitochondrial
*Genome, Plant
*RNA, Transfer/chemistry/genetics
*Conserved Sequence
Phylogeny
RNA Folding
Sequence Analysis, DNA
Codon Usage
RNA Editing
Gene Transfer, Horizontal
Fagus/genetics

@article {pmid40151212,
year = {2025},
author = {van Almsick, VF and Sobkowiak, A and Scherff, N and Schuler, F and Oehm, JB and Böing, C and Mellmann, A and Schwierzeck, V},
title = {In-depth characterization of Klebsiella pneumoniae carbapenemase (KPC)-encoding plasmids points at transposon-related transmission of resistance genes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542828},
pmid = {40151212},
issn = {2235-2988},
mesh = {*Klebsiella pneumoniae/genetics/drug effects/enzymology ; *beta-Lactamases/genetics ; Humans ; *Plasmids/genetics ; *Klebsiella Infections/transmission/microbiology ; *DNA Transposable Elements/genetics ; *Bacterial Proteins/genetics/metabolism ; *Whole Genome Sequencing ; Germany ; Multilocus Sequence Typing ; Male ; Female ; Aged ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Tertiary Care Centers ; Cross Infection/microbiology/transmission ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genome, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing threat in healthcare systems, particularly in the management of infections in critically ill patients. This study highlights how to identify clusters and putative sharing of mobile genetic elements, such as transposons, in the hospital setting using long-read whole genome sequencing (lrWGS). The approach described here can be employed to investigate the transmission dynamics of KPC-3-positive Klebsiella pneumoniae at multiple levels, from the entire isolate down to individual plasmids and transposons. Here, a bla KPC-3 harboring transposon cluster was identified by using a Mash-based distance calculation for plasmids. This approach was used to investigate a local accumulation of KPC-3-positive Klebsiella pneumoniae on surgical and infectious disease wards of a tertiary care center in Germany over a time of six months. In total, seven patients were affected. Core genome multi-locus sequence typing analysis (cgMLST) identified two distinct genetic clusters: a sequence type (ST) 307 cluster (n = 5) and a ST101 cluster (n = 2). All isolates carried a bla KPC-3 carbapenemase. Further Mash distance-based plasmid analysis was not consistent with plasmid transfer due to genetic heterogeneity, but identified a transposon cluster across all isolates. Infection control evaluation of patient movements within their hospital admission supports a possible clonal transmission. Subsequent infection control measures, including point prevalence screening and enhanced contact precautions, successfully contained further transmissions. The study illustrates the value of in-depth plasmid analysis in understanding the transmission dynamics and epidemiology of AMR, particularly in hospital environments.},
}

*Klebsiella pneumoniae/genetics/drug effects/enzymology
*beta-Lactamases/genetics
Humans
*Plasmids/genetics
*Klebsiella Infections/transmission/microbiology
*DNA Transposable Elements/genetics
*Bacterial Proteins/genetics/metabolism
*Whole Genome Sequencing
Germany
Multilocus Sequence Typing
Male
Female
Aged
Middle Aged
Anti-Bacterial Agents/pharmacology
Tertiary Care Centers
Cross Infection/microbiology/transmission
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests
Genome, Bacterial/genetics

@article {pmid40150788,
year = {2025},
author = {Müller, GA},
title = {The Transformation Experiment of Frederick Griffith I: Its Narrowing and Potential for the Creation of Novel Microorganisms.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {40150788},
issn = {2306-5354},
abstract = {The construction of artificial microorganisms often relies on the transfer of genomes from donor to acceptor cells. This synthetic biology approach has been considerably fostered by the J. Craig Venter Institute but apparently depends on the use of microorganisms, which are very closely related. One reason for this limitation of the "creative potential" of "classical" transformation is the requirement for adequate "fitting" of newly synthesized polypeptide components, directed by the donor genome, to interacting counterparts encoded by the pre-existing acceptor genome. Transformation was introduced in 1928 by Frederick Griffith in the course of the demonstration of the instability of pneumococci and their conversion from rough, non-pathogenic into smooth, virulent variants. Subsequently, this method turned out to be critical for the identification of DNA as the sole matter of inheritance. Importantly, the initial experimental design (1.0) also considered the inheritance of both structural (e.g., plasma membranes) and cybernetic information (e.g., metabolite fluxes), which, in cooperation, determine topological and cellular heredity, as well as fusion and blending of bacterial cells. In contrast, subsequent experimental designs (1.X) were focused on the use of whole-cell homogenates and, thereafter, of soluble and water-clear fractions deprived of all information and macromolecules other than those directing protein synthesis, including outer-membrane vesicles, bacterial prions, lipopolysaccharides, lipoproteins, cytoskeletal elements, and complexes thereof. Identification of the reasons for this narrowing may be helpful in understanding the potential of transformation for the creation of novel microorganisms.},
}

@article {pmid40149106,
year = {2025},
author = {Olsen, NS and Riber, L},
title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {40149106},
issn = {2079-6382},
support = {NNF23OC0086264//Novo Nordisk Foundation/ ; },
abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.},
}

@article {pmid40149092,
year = {2025},
author = {Hernández, M and Falcó-Prieto, Á and Ugarte-Ruiz, M and Miguela-Villoldo, P and Ocampo-Sosa, A and Abad, D and Pérez-Sancho, M and Álvarez, J and Cadamuro, RD and Elois, MA and Fongaro, G and Quesada, A and González-Zorn, B and Domínguez, L and Eiros, JM and Rodríguez-Lázaro, D},
title = {Genome Analysis of 6222 Bacterial Isolates from Livestock and Food Environments in Spain to Decipher the Antibiotic Resistome.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
pmid = {40149092},
issn = {2079-6382},
support = {AGL2016-74882-C3//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to global health and the economy, with projected costs ranging from $300 billion to $1 trillion annually and an estimated 10 million deaths per year by 2050. The food chain, from primary production to retail, represents a critical entry point for antimicrobial resistant bacteria into communities. This underscores the need for a coordinated "One Health" approach, integrating efforts in animal production, environmental health, and human healthcare to address this global concern. This study aimed to characterize the global resistome in Spanish primary production by sequencing 6222 bacterial genomes from animal origin. Methods and Results: Whole genome sequencing was performed on bacterial isolates collected from various farms and analyzed using a validated bioinformatic pipeline. The analysis revealed a diverse range of bacterial species, with Enterobacteriaceae being the most prevalent family. Escherichia coli was the most common species, followed by Salmonella enterica and Pseudomonas aeruginosa. This study identified 1072 antimicrobial resistance genes coding for 43 different classes of resistance, potentially conferring resistance to 81 antimicrobials. Additionally, 79 different plasmid types were detected, highlighting the potential for horizontal gene transfer. Conclusions: The resistome analysis revealed genes conferring resistance to various antibiotic classes, as well as antiseptics, disinfectants, and efflux pump-mediated resistance. This comprehensive characterization of AMR genes circulating in bacteria from primary production provides crucial insights into the ecology of AMR in Spanish livestock.},
}

@article {pmid40149046,
year = {2025},
author = {Mitsuwan, W and Boripun, R and Saengsawang, P and Intongead, S and Boonplu, S and Chanpakdee, R and Morita, Y and Boonmar, S and Rojanakun, N and Suksriroj, N and Ruekaewma, C and Tenitsara, T},
title = {Multidrug Resistance, Biofilm-Forming Ability, and Molecular Characterization of Vibrio Species Isolated from Foods in Thailand.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antibiotics14030235},
pmid = {40149046},
issn = {2079-6382},
support = {SEAOHUN/2023-SC248//United States Agency for International Development (USAID) through the SEAOHUN 2023 One Health Research and Training (OHRT) Awards/ ; WU-CIA-03404/2024//Walailak University under the international research collaboration scheme/ ; },
abstract = {BACKGROUND: Vibrio species are common foodborne pathogens that cause gastrointestinal tract inflammation. Multidrug resistance (MDR) in Vibrio spp. is a global health concern, especially in aquaculture systems and food chain systems. This study aimed to detect Vibrio contamination in food collected from 14 markets in Nakhon Si Thammarat, Thailand, and determine their antibiotic susceptibility.

METHODS: One hundred and thirty-six food samples were investigated for Vibrio contamination. All isolates were tested for antibiogram and biofilm-forming ability. Moreover, the ceftazidime or cefotaxime resistance isolates were additionally investigated for extended-spectrum β-lactamase (ESBL) producers. The isolates were additionally examined for the presence of antibiotic resistance genes. The ESBL-suspected isolates with moderate-to-high biofilm-forming ability were further analyzed for their whole genome.

RESULTS: The prevalence of Vibrio contamination in food samples was 42.65%, with V. parahaemolyticus demonstrating the highest prevalence. Most isolates were resistant to β-lactam antibiotics, followed by aminoglycosides. The overall MDR of isolated Vibrio was 18.29%, with an average multiple antibiotic resistance (MAR) index of 16.41%. Most isolates were found to have β-lactam resistance-related genes (blaTEM) for 41.46%, followed by aminoglycoside resistance genes (aac(6')-Ib) for 18.29%. Most Vibrio showed moderate to strong biofilm-forming ability, particularly in MDR isolates (92.86%). Two ESBL-suspected isolates, one V. parahaemolyticus isolate and one V. navarrensis, were sequenced. Interestingly, V. parahaemolyticus was an ESBL producer that harbored the blaCTX-M-55 gene located in the mobile genetic element region. While V. navarrensis was not ESBL producer, this isolate carried the blaAmpC gene in the region of horizontal gene transfer event. Remarkably, the Inoviridae sp. DNA integration event was present in two Vibrio genomes.

CONCLUSIONS: These findings impact the understanding of antibiotic-resistant Vibrio spp. in food samples, which could be applied for implementing control measures in aquaculture farming and food safety plans.},
}

@article {pmid40148599,
year = {2025},
author = {Patra, M and Pandey, AK and Dubey, SK},
title = {Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {4},
pages = {114},
pmid = {40148599},
issn = {1573-0972},
support = {R/Dev./Sch./UGC Non-NET Fellowship/2023-24/72267//University Grants Commission/ ; 6031//IOE/ ; },
mesh = {*Metals, Heavy/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Soil Microbiology ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Genomics ; *Whole Genome Sequencing ; Phylogeny ; Microbial Sensitivity Tests ; Endophytes/genetics/isolation & purification ; Gene Transfer, Horizontal ; },
abstract = {The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.},
}

*Metals, Heavy/pharmacology
*Sewage/microbiology
*Drug Resistance, Multiple, Bacterial/genetics
*Soil Microbiology
*Genome, Bacterial
*Anti-Bacterial Agents/pharmacology
*Genomics
*Whole Genome Sequencing
Phylogeny
Microbial Sensitivity Tests
Endophytes/genetics/isolation & purification
Gene Transfer, Horizontal

@article {pmid40148598,
year = {2025},
author = {Wang, K and Guo, G and Bai, S and Ma, J and Zhang, Z and Xing, Z and Wang, W and Li, H and Liang, H and Li, Z and Si, X and Wang, J and Liu, Q and Xu, W and Yang, C and Song, RF and Li, J and He, T and Li, J and Zeng, X and Liang, J and Zhang, F and Qiu, X and Li, Y and Bu, T and Liu, WC and Zhao, Y and Huang, J and Zhou, Y and Song, CP},
title = {Horizontally acquired CSP genes contribute to wheat adaptation and improvement.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40148598},
issn = {2055-0278},
support = {32230079//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Although horizontal gene transfer (HGT) often facilitates environmental adaptation of recipient organisms, whether and how they might affect crop evolution and domestication is unclear. Here we show that three genes encoding cold-shock proteins (CSPs) were transferred from bacteria to Triticeae, a tribe of the grass family that includes several major staple crops such as wheat, barley and rye. The acquired CSP genes in wheat (TaCSPs) are functionally conserved in their bacterial homologues by encoding a nucleic acid-binding protein. Experimental evidence indicates that TaCSP genes positively regulate drought response and improve photosynthetic efficiency under water-deficient conditions by directly targeting a type 1 metallothionein gene to increase reactive oxygen species scavenging, which in turn contributed to the geographic expansion of wheat. We identified an elite CSP haplotype in Aegilops tauschii, introduction of which to wheat significantly increased drought tolerance, photosynthetic efficiency and grain yields. These findings not only provide major insights into the role of HGT in crop adaptation and domestication, but also demonstrate that novel microbial genes introduced through HGT offer a stable and naturally optimized resource for transgenic crop breeding and improvement.},
}

@article {pmid40146211,
year = {2025},
author = {Hornok, S and Keve, G and Tuska-Szalay, B},
title = {Transmission route-dependent genetic diversity of selected protozoan parasites as reflected by the phylogenetic analysis of the 18S rRNA gene.},
journal = {Acta veterinaria Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/004.2025.01128},
pmid = {40146211},
issn = {0236-6290},
abstract = {In this pilot study, the genetic diversity of protozoan parasites was analysed according to their different transmission routes (life cycle strategies), focusing on those species which were recently discovered or molecularly analysed for the first time in Hungary or its geographical region. The results showed that among four apicomplexan parasites (Babesia gibsoni, Cytauxzoon europaeus, Sarcocystis morae and Hepatozoon felis) the latter had the highest genetic diversity as reflected by its 18S rRNA gene sequences showing high (1.75%) maximum intraspecific pairwise distance, and also, based on its phylogenetic clustering. This is probably related to the long evolutionary history of H. felis, the absence of its intravascular division and other life cycle characteristics precluding direct transmission between hosts. On the other hand, among non-apicomplexan protozoa (Trichomonas gallinae, Pentatrichomonas hominis, Tritrichomonas foetus and Acanthamoeba castellanii), the latter proved to have the highest genetic diversity (7.73%), most likely due to its long evolutionary history, lateral gene transfer, homologous recombination and the absence of direct host-to-host dispersal. Transmission mode had a significant impact on the genetic diversity among protozoan parasites, depending on life cycle strategies and consequent frequency/chance of sexual reproduction vs binary fission. In particular, the absence of direct transmission between hosts is a common trait of H. felis and A. castellanii, contributing to their high genetic diversity.},
}

@article {pmid40142381,
year = {2025},
author = {Moriguchi, K and Nakamura, K and Takahashi, Y and Higo-Moriguchi, K and Kiyokawa, K and Suzuki, K},
title = {Genome-Wide Survey of Donor Chromosomal Genes Involved in Trans-Kingdom Conjugation via the RP4-T4SS Machinery.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
pmid = {40142381},
issn = {2076-2607},
support = {JP16K07200//Japan Society for the Promotion of Science/ ; No grant number (donation)//Consortium for the Exploration of Microbial Functions Ohsumi Frontier Science Foundation/ ; },
abstract = {Trans-kingdom conjugation (TKC)/inter-domain conjugation is a horizontal gene transfer phenomenon that transfers DNA from eubacteria to eukaryotes and archaebacteria via a type IV secretion system encoded in IncP1-type broad-host-range plasmids. Although TKC is considered a potential gene introduction tool, donor chromosomal genes that influence TKC efficiency have rarely been analyzed, hindering targeted donor breeding. To identify potential TKC-related genes on a donor chromosome, a genome-wide screening of TKC-deficient mutants was performed using a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors and a Saccharomyces cerevisiae strain as a recipient. Out of 3884 mutants, two mutants (∆aceE, ∆priA) showed a severe decrease in TKC efficiency by more than two orders of magnitude but not in bacterial conjugation. The effect on TKC efficiency by the two mutants was partly recovered by a preculture with a fresh culture medium before the TKC reaction, regardless of the presence of antibiotics. These results suggest that no single chromosomal target gene is solely responsible for universally blocking IncP1-type conjugation by impeding its function. The results also suggest the existence of an unidentified recognition or transfer mechanism distinct from bacterial conjugation, highlighting the novel roles of aceE and priA.},
}

@article {pmid40142377,
year = {2025},
author = {Pazos, C and Gualoto, M and Oña, T and Velarde, E and Portilla, K and Cabrera-García, S and Banchón, C and Dávila, G and Hernández-Alomia, F and Bastidas-Caldes, C},
title = {Molecular Detection of blaTEM and blaSHV Genes in ESBL-Producing Acinetobacter baumannii Isolated from Antarctic Soil.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
pmid = {40142377},
issn = {2076-2607},
abstract = {The phenomenon of antimicrobial resistance (AMR) in cold environments, exemplified by the Antarctic, calls into question the assumption that pristine ecosystems lack clinically significant resistance genes. This study examines the molecular basis of AMR in Acinetobacter spp. Isolated from Antarctic soil, focusing on the blaTEM and blaSHV genes associated with extended-spectrum beta-lactamase (ESBL) production; Soil samples were collected and processed to isolate Antarctic soil bacteria. Molecular detection was then conducted using polymerase chain reaction (PCR) to identify the bacteria species by 16S rRNA/rpoB and 10 different beta-lactamase-producing genes. PCR amplicons were sequenced to confirm gene identity and analyze genetic variability. Acinetobacter baumannii were identified by both microbiological and molecular tests. Notably, both the blaTEM and blaSHV genes encoding the enzymes responsible for resistance to penicillins and cephalosporins were identified, indicating the presence of resistance determinants in bacteria from extreme cold ecosystems. The nucleotide sequence analysis indicated the presence of conserved ARGs, which suggest stability and the potential for horizontal gene transfer within microbial communities. These findings emphasize that AMR is not confined to human-impacted environments but can emerge and persist in remote, cold habitats, potentially facilitated by natural reservoirs and global microbial dispersal. Understanding the presence and role of AMR in extreme environments provides insights into its global dissemination and supports the development of strategies to mitigate the spread of resistance genes in both environmental and clinical contexts.},
}

@article {pmid40141150,
year = {2025},
author = {Rendueles, C and Garay-Novillo, JN and Rau, MH and Gaspar, P and Ruiz-Masó, JÁ and Mahony, J and Rodríguez, A and Barra, JL and Del Solar, G and Martínez, B},
title = {A Plasmid-Encoded Surface Polysaccharide Partly Blocks Ceduovirus Infection in Lactococci.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
pmid = {40141150},
issn = {1422-0067},
support = {PID2020-119697RB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {*Lactococcus/genetics ; *Plasmids/genetics ; *Lactococcus lactis/genetics/virology ; Bacteriophages/genetics ; Polysaccharides, Bacterial/metabolism ; CRISPR-Cas Systems ; },
abstract = {Bacteriophages (or phages) remain the leading cause of failure in dairy fermentations. Thereby, phage-resistant Lactococcus lactis and Lactococcus cremoris dairy starters are in continuous demand. In this work, our goal was to identify phage defense mechanisms against ceduoviruses encoded by two wild isolates of dairy origin named L. lactis IPLA517 and IPLA1064. These strains were previously subjected to experimental evolution to select derivatives that are resistant to the bacteriocin Lcn972. It was observed that the Lcn972[R] derivatives became sensitive to phage infection; however, the underlying mechanism was not defined. The long-read sequencing technologies applied in this work reveal that all of the Lcn972[R] derivatives shared the loss of a 41 kb endogenous plasmid (p41) that harbors a putative exopolysaccharide (EPS) gene cluster with significant homology to one described in Lactococcus garvieae. Using a CRISPR-Cas9-based approach, p41 was selectively cured from L. lactis IPLA1064. Phage infection assays with three ceduoviruses demonstrated that curing p41 restored phage sensitivity at levels comparable to the Lcn972[R]-IPLA1064 derivatives. Phage adsorption to Δp41 cells was also increased, consistent with the hypothesis of EPS production hindering access to the phage receptor protein Pip. Our results reinforce the role of EPSs in protecting Lactococcus against phage infection, a phenomenon that is rarely reported for ceduoviruses. Moreover, the results also exemplify the likely horizontal gene transfer that can occur between L. lactis and L. garvieae in a dairy environment.},
}

*Lactococcus/genetics
*Plasmids/genetics
*Lactococcus lactis/genetics/virology
Bacteriophages/genetics
Polysaccharides, Bacterial/metabolism
CRISPR-Cas Systems

@article {pmid40135944,
year = {2025},
author = {Zheng, Y and Zhu, X and Ding, C and Chu, W and Pang, X and Zhang, R and Ma, J and Xu, G},
title = {Multidrug-resistant hypervirulent Klebsiella pneumoniae: an evolving superbug.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17460913.2025.2482478},
pmid = {40135944},
issn = {1746-0921},
abstract = {Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) combines high pathogenicity with multidrug resistance to become a new superbug. MDR-hvKP reports continue to emerge, shattering the perception that hypervirulent K. pneumoniae (hvKP) strains are antibiotic sensitive. Patients infected with MDR-hvKP strains have been reported in Asia, particularly China. Although hvKP can acquire drug resistance genes, MDR-hvKP seems to be more easily transformed from classical K. pneumoniae (cKP), which has a strong gene uptake ability. To better understand the biology of MDR-hvKP, this review discusses the virulence factors, resistance mechanisms, formation pathways, and identification of MDR-hvKP. Given their destructive and transmissible potential, continued surveillance of these organisms and enhanced control measures should be prioritized.},
}

@article {pmid40133813,
year = {2025},
author = {Huang, X and Yu, C and Lu, L},
title = {Isolation and characterization of a roseophage representing a novel genus in the N4-like Rhodovirinae subfamily distributed in estuarine waters.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {295},
pmid = {40133813},
issn = {1471-2164},
mesh = {*Phylogeny ; *Bacteriophages/genetics/isolation & purification/classification ; *Estuaries ; *Genome, Viral ; Rhodobacteraceae/genetics/virology/classification/isolation & purification ; },
abstract = {BACKGROUND: Roseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like roseophage clade, which encompasses 15 members, represents the largest clade among these roseophages. N4-like phages form a monophyletic group, classified as family Schitoviridae. And all N4-like roseophages form a unique clade within Schitoviridae and has been classified as the Rhodovirinae subfamily.

RESULTS: In this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggests that the newly isolated phage is a member of the Rhodovirinae subfamily and represents the sole member of a novel genus, Gonggongvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters.

CONCLUSIONS: Our work illustrates the genomic features of a novel roseophage clade among the subfamily Rhodovirinae. The AMG content of vB_DshP-R7L is under severe purification selection, which reveals their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are only detected in estuaries. Our isolation and characterization of this novel phage expands the understanding of the phylogeny, gene transfer history, and biogeography of Rhodovirinae infecting marine Roseobacteraceae.},
}

*Phylogeny
*Bacteriophages/genetics/isolation & purification/classification
*Estuaries
*Genome, Viral
Rhodobacteraceae/genetics/virology/classification/isolation & purification

@article {pmid40131635,
year = {2025},
author = {Silva, UCM and da Silva, DRC and Cuadros-Orellana, S and Moreira, LM and Leite, LR and Medeiros, JD and Felestrino, EB and Caneschi, WL and Almeida, NF and Silva, RS and Oliveira-Paiva, CA and Dos Santos, VL},
title = {Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40131635},
issn = {1678-4405},
support = {N° 477349/2013-7//CNPq/ ; N° APQ-01819-13//Fapemig/ ; },
abstract = {We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.},
}

@article {pmid40121546,
year = {2025},
author = {Wang, Q and Liu, C and Sun, Y and Li, X and Gu, W and Wang, N and Sun, S and Luo, Y},
title = {Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf045},
pmid = {40121546},
issn = {1751-7370},
abstract = {Antibiotic residues are commonly found in food. The effect of dietary exposure to veterinary antibiotics on the transmission of antibiotic resistant bacteria and antibiotic resistance genes from food to humans is unknown. We found that dietary exposure to enrofloxacin reduced microbial diversity, interactions and the immune responses, weakened the colonization resistance of the resident microbiota, and promoted the colonization of exogenous Escherichia coli K-12 MG1655 in the simulated human intestine both in vitro and in vivo experiments in mice. In addition to the growth advantages for potential most likely bacterial hosts of ARGs under enrofloxacin exposure, the dietary exposure to enrofloxacin promoted horizontal transfer of resistance plasmids and altered the simulated human gut antibiotic resistome in a time-dependent manner. Collectively, these findings demonstrated that dietary intake of enrofloxacin promoted the colonization of E. coli K-12 MG1655 in the simulated human intestine and the horizontal transfer of antibiotic resistance genes, highlighting the risk of antibiotic resistance transmission from food to humans mediated by dietary exposure to veterinary antibiotics.},
}

@article {pmid40098486,
year = {2025},
author = {Coluzzi, C and Rocha, EPC},
title = {The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range.},
journal = {Molecular biology and evolution},
volume = {42},
number = {3},
pages = {},
doi = {10.1093/molbev/msaf060},
pmid = {40098486},
issn = {1537-1719},
mesh = {*Plasmids/genetics ; *Gene Transfer, Horizontal ; *Host Specificity ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; },
abstract = {Microorganisms endure novel challenges for which other microorganisms in other biomes may have already evolved solutions. This is the case of nosocomial bacteria under antibiotic therapy because antibiotics are of ancient natural origin and resistances to them have previously emerged in environmental bacteria. In such cases, the rate of adaptation crucially depends on the acquisition of genes by horizontal transfer of plasmids from distantly related bacteria in different biomes. We hypothesized that such processes should be driven by plasmids among the most mobile and evolvable. We confirmed these predictions by showing that plasmid species encoding antibiotic resistance are very mobile, have broad host ranges, while showing higher rates of homologous recombination and faster turnover of gene repertoires than the other plasmids. These characteristics remain outstanding when we remove resistance plasmids from our dataset, suggesting that antibiotic resistance genes are preferentially acquired and carried by plasmid species that are intrinsically very mobile and plastic. Evolvability and mobility facilitate the transfer of antibiotic resistance, and presumably of other phenotypes, across distant taxonomic groups and biomes. Hence, plasmid species, and possibly those of other mobile genetic elements, have differentiated and predictable roles in the spread of novel traits.},
}

*Plasmids/genetics
*Gene Transfer, Horizontal
*Host Specificity
Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects
Evolution, Molecular
Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/genetics

@article {pmid40120959,
year = {2025},
author = {Wu, Z and Famous, M and Stoikidou, T and Bowden, FES and Dominic, G and Huws, SA and Godoy-Santos, F and Oyama, LB},
title = {Unravelling AMR dynamics in the rumenofaecobiome: insights, challenges and implications for One Health.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107494},
doi = {10.1016/j.ijantimicag.2025.107494},
pmid = {40120959},
issn = {1872-7913},
abstract = {Antimicrobial resistance (AMR) is a critical global threat to human, animal, and environmental health, exacerbated by horizontal gene transfer (HGT) via mobile genetic elements (MGEs). This poses significant challenges, that negatively impacts the sustainability of the One Health approach, hindering its long-term viability and effectiveness in addressing the interconnectedness of global health. Recent researches from livestock animals specifically ruminants indicate that culturable ruminal bacteria harbour AMR genes (ARGs) with the potential for HGT. However, these studies have predominantly focused on using the faecobiome as a proxy to the rumen microbiome or using easily isolated and culturable bacteria, overlooking the unculturable population. These unculturable microbial groups could profoundly influence the rumen resistome and AMR dynamics within livestock ecosystems, potentially holding critical insights for the advanced understanding of AMR in One Health. To address this gap, we review current research on AMR burden in livestock and propose the combined study of the rumen microbiome and faecobiome termed 'rumenofaecobiome' to enhance our understanding of AMR risks in ruminant livestock. We discuss the complexities of the rumen microbiome and the risk of AMR transmission in this microbiome in a One Health context. We summarise AMR transmission dynamics, the methodologies for assessing AMR risks in livestock and comment on future considerations for researching the impact of AMR in the rumen microbiome and the implications within the One Health framework.},
}

@article {pmid40120581,
year = {2025},
author = {Scarampi, A and Lawrence, JM and Bombelli, P and Kosmützky, D and Zhang, JZ and Howe, CJ},
title = {Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.044},
pmid = {40120581},
issn = {1879-0445},
abstract = {Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, are thought to rely on the emergence of spontaneous mutations or lateral gene transfer from a reservoir of pre-existing variants within the surrounding environment. These variants then become fixed in the population upon exposure to selective pressures. Here, we show that multiple distinct wild-type (WT) substrains of the highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly to the potent herbicide methyl viologen (MV). Genome sequencing revealed that the mutations responsible for adaptation to MV were already present prior to selection in the genomes of the unadapted parental strains at low allelic frequencies. This indicates that chromosomal polyploidy in bacteria can provide cells with a reservoir of conditionally beneficial mutations that can become rapidly enriched and fixed upon selection. MV-resistant strains performed oxygenic photosynthesis less efficiently than WTs when MV was absent, suggesting trade-offs in cellular fitness associated with the evolution of MV resistance and a possible role for balancing selection in the maintenance of these alleles under ecologically relevant growth conditions. Resistance was associated with reduced intracellular accumulation of MV. Our results indicate that genome polyploidy plays a role in the rapid adaptation of some bacteria to stressful conditions, which may include xenobiotics, nutrient limitation, environmental stresses, and seasonal changes.},
}

@article {pmid40118394,
year = {2025},
author = {Cuecas, A and Delgado, JA and Gonzalez, JM},
title = {Inferring inter-phylum gene transfer events from unique genes detected in Parageobacillus thermoglucosidasius.},
journal = {Molecular phylogenetics and evolution},
volume = {207},
number = {},
pages = {108329},
doi = {10.1016/j.ympev.2025.108329},
pmid = {40118394},
issn = {1095-9513},
abstract = {A pan-genome includes the complete pool of genes of a species including those recently acquired. The new additions of genetic material to a genome are frequently linked to horizontal gene transfer (HGT) processes and can confer adaptive advantages improving the recipient functional response and growth. Previous studies have reported that Parageobacillus have frequent DNA exchange mainly with other members of the phylum Bacillota sharing similar environments. Nevertheless, the occurrence of transfer events between phylogenetically distant microorganisms is scarcely known. In this work, based on the pan-genome of Parageobacillus thermoglucosidasius, we detected a number of unique genes within the species which were used to carry out BLAST searches to find out similar genes in distant bacteria taxa. We aimed to infer potential inter-phylum HGT events. Results suggested genetic exchanges among different phyla. Among them Actinomycetota, Pseudomonadota and the Bacteroidota/Chlorobiota group were the dominant observed phyla. Those HGT events frequently involved ATP binding cassette transporters, enzymes of the C metabolism and transcriptional regulators. Based on the frequency of these genes within specific phyla, directional HGT events could be proposed. A dominant origin of the suggested HGT events could be within the Bacillota. This exploratory analysis indicates that Bacillota are frequent exporters of DNA both within the phylum and to phylogenetically distant groups. Long-distance HGT can assist to better understand microbial evolution, the relevance of HGT processes within the prokaryotes and the genomic plasticity of microorganisms.},
}

@article {pmid40113085,
year = {2025},
author = {Ding, J and Zhang, M and Chang, J and Hu, Z and He, P and Wang, J and Feng, L},
title = {Characterization of a Multidrug-Resistant Hypovirulent ST1859-KL35 Klebsiella quasipneumoniae subsp. similipneumoniae Strain Co-harboring tmexCD2-toprJ2 and blaKPC-2.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.03.009},
pmid = {40113085},
issn = {2213-7173},
abstract = {OBJECTIVES: The rise of multidrug-resistant (MDR) Klebsiella pneumoniae is a significant public health threat. Klebsiella quasipneumoniae is often misidentified as K. pneumoniae, and its genetic and virulence traits remain underexplored. This study characterizes the genomic and phenotypic features of a K. quasipneumoniae subsp. similipneumoniae strain (KP24) .

METHODS: Antibiotic susceptibility was tested using microbroth dilution assay. Virulence was evaluated through serum killing assay and Galleria mellonella infection model. Whole genome sequencing (WGS) and bioinformatics analysis determined sequence typing, resistance profiles, and plasmid types. Conjugation assays assessed plasmid transferability, while phylogenetic analysis explored genetic relationships.

RESULTS: KP24 exhibited an MDR phenotype, including resistance to carbapenems, ceftazidime/avibactam, and tigecycline. KP24 showed significantly higher serum survival and G. mellonella lethality than ATCC700603, though it was less virulent than the hypervirulent strain NUTH-K2044. WGS identified KP24 as ST1859 and KL35, harboring the aerobactin virulence gene cluster (iucABCDiutA) and multiple resistance genes, including tmexCD2-toprJ2, blaKPC-2, blaOXA-10, blaIMP-4, and qnrS1. Notably, the tmexCD2-toprJ2 and blaKPC-2 genes were located on the same plasmid (pKP24-1) , an uncommon co-existence. Conjugation assays confirmed the independent transferability of pKP24-1 to Escherichia coli J53. Phylogenetic analysis revealed that ST1859 forms a distinct monoclade with low genetic diversity, closely related to ST334, suggesting regional expansion and potential global dissemination.

CONCLUSIONS: KP24 represents a hypovirulent yet multidrug-resistant strain of K. quasipneumoniae subsp. similipneumoniae, with a concerning combination of virulence and resistance determinants. The co-location of tmexCD2-toprJ2 and blaKPC-2 on a transferable plasmid highlights the potential for horizontal gene transfer of critical resistance mechanisms.},
}

@article {pmid40111106,
year = {2025},
author = {Kogay, R and Wolf, YI and Koonin, EV},
title = {Horizontal transfer of bacterial operons into eukaryote genomes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf055},
pmid = {40111106},
issn = {1759-6653},
abstract = {In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly, encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime, and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.},
}

@article {pmid40111082,
year = {2025},
author = {Maeda, K and Sumita, T and Nishi, O and Sushida, H and Higashi, Y and Nakagawa, H and Suzuki, T and Iwao, E and Fanani, MZ and Nishiya, Y and Iida, Y},
title = {Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism by Hansfordia pulvinata associated with horizontal gene transfer from Aspergillus species.},
journal = {mBio},
volume = {},
number = {},
pages = {e0400724},
doi = {10.1128/mbio.04007-24},
pmid = {40111082},
issn = {2150-7511},
abstract = {UNLABELLED: Leaf mold caused by the ascomycete fungus Cladosporium fulvum is a devastating disease of tomato plants. The mycoparasitic fungus Hansfordia pulvinata is an effective biocontrol agent that parasitizes C. fulvum hyphae on leaves and secretes 13-deoxyphomenone, an eremophilane-type sesquiterpene, which was also identified as a sporulation-inducing factor in Aspergillus oryzae. Here, we identified deoxyphomenone biosynthesis (DPH) gene clusters conserved in both H. pulvinata and Aspergillus section Flavi, including A. oryzae and A. flavus. Functional disruption of DPH1 orthologous genes encoding sesquiterpene cyclase in H. pulvinata, A. oryzae, and its close relative A. flavus revealed that deoxyphomenone in H. pulvinata had exogenic antifungal activity against C. fulvum and controlled endogenic sporulation in Aspergillus species. Complete DPH clusters, highly similar to those in H. pulvinata, were exclusive to Aspergillus section Flavi, while species in other Aspergillus sections contained fragmented DPH clusters. A comparative genomics analysis revealed that these DPH gene clusters share a common origin and are horizontally transferred from an ancestor of Aspergillus to H. pulvinata. Our results suggest that after horizontal transfer, H. pulvinata maintained the DPH cluster as the inhibitory effect of deoxyphomenone on spore germination and mycelial growth contributed to its mycoparasitism on the host fungus C. fulvum.

IMPORTANCE: Tomato leaf mold disease caused by C. fulvum poses a significant economic threat to tomato production globally. Breeders have developed tomato cultivars with Cf resistance genes. C. fulvum frequently evolves new races that overcome these genetic defenses, complicating control efforts. Additionally, the pathogen has developed resistance to chemical fungicides, prompting the need for sustainable alternatives like biocontrol agents. The mycoparasitic fungus H. pulvinata is crucial as an effective agent against C. fulvum. Clarifying the mechanism of mycoparasitism is significant, as it enhances its application as a biocontrol agent against plant pathogens. This study revealed how H. pulvinata produces deoxyphomenone, an antifungal compound, through horizontal gene transfer from Aspergillus species. It is hypothesized that mycoparasitism could be one of the mechanisms that facilitated horizontal gene transfer between fungi. These insights facilitate the development of eco-friendly, sustainable agricultural practices by reducing dependence on chemical fungicides and promoting natural pathogen control methods.},
}

@article {pmid40110960,
year = {2025},
author = {Xu, P and Liu, X and Ke, L and Li, K and Wang, W and Jiao, Y},
title = {The genomic insights of intertidal adaptation in Bryopsis corticulans.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70083},
pmid = {40110960},
issn = {1469-8137},
support = {2021YFA0909600//the National Key R&D Program of China/ ; 2021YFA1300403//the National Key R&D Program of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 32221001//the National Natural Science Foundation of China/ ; 32222007//the National Natural Science Foundation of China/ ; YSBR-093//CAS project for Young Scientists in Basic Research/ ; },
abstract = {Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures. Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago. Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions. Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.},
}

@article {pmid40108678,
year = {2025},
author = {Debroas, D},
title = {Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {77},
pmid = {40108678},
issn = {2049-2618},
mesh = {*Plasmids/genetics ; *Ecosystem ; *Bacteria/genetics/drug effects/classification ; Humans ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; },
abstract = {BACKGROUND: Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale.

RESULTS: This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids.

CONCLUSIONS: By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.},
}

*Plasmids/genetics
*Ecosystem
*Bacteria/genetics/drug effects/classification
Humans
*Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences/genetics
Genes, Bacterial/genetics
Drug Resistance, Microbial/genetics
Microbiota/genetics/drug effects

@article {pmid40104036,
year = {2025},
author = {Yang, SM and Gruber, A and Jiroutová, K and Richtová, J and Vancová, M and Tesařová, M and Masařová, P and Dorrell, RG and Oborník, M},
title = {Localization of heme biosynthesis in the diatom Phaeodactylum tricornutum and differential expression of multi-copy enzymes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1537037},
pmid = {40104036},
issn = {1664-462X},
abstract = {Heme is essential for all organisms. The composition and location of the pathway for heme biosynthesis, have been influenced by past endosymbiotic events and organelle evolution in eukaryotes. Endosymbioses led to temporary redundancy of the enzymes and the genes involved. Genes were transferred to the nucleus from different endosymbiotic partners, and their multiple copies were either lost or retained, resulting in a mosaic pathway. This mosaic is particularly complex in organisms with eukaryote-derived plastids, such as diatoms. The plastids of diatoms are clearly derived from red algae. However, it is not entirely clear whether they were acquired directly from a red algal ancestor or indirectly in higher-order endosymbioses. In the diatom Phaeodactylum tricornutum, most enzymes of the pathway are present in a single copy, but three, glutamyl-tRNA synthetase (GluRS), uroporphyrinogen decarboxylase (UROD) and coproporphyrinogen oxidase (CPOX), are encoded in multiple copies. These are not direct paralogs resulting from gene duplication within the lineage but were acquired horizontally during the plastid endosymbioses. While some iso-enzymes originate from the host cell, others originate either from the genome of the cyanobacterial ancestor of all plastids or from the nuclear genome of the eukaryotic ancestor of the diatom complex plastid, a rhodophyte or an alga containing rhodophyte-derived plastids, a situation known as pseudoparalogy. Using green fluorescent protein-tagged expression and immunogold labeling, we experimentally localized all enzymes of the pathway in P. tricornutum, and confirmed their localization in the plastid, with a few possible exceptions. Our meta-analyses of transcription data showed that the pseudoparalogs are differentially expressed in response to nitrate starvation, blue light, high light, high CO2, and the cell cycle. Taken together, our findings emphasize that the evolution of complex plastids via endosymbiosis has a direct impact not only on the genetics but also on the physiology of resulting organisms.},
}

@article {pmid40102781,
year = {2025},
author = {Yang, H and Gan, Y and Jiang, S and Zhu, X and Xia, Y and Gong, D and Xie, X and Gong, Y and Zhang, Y and Lei, Q and Wang, M and Li, J},
title = {Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {269},
pmid = {40102781},
issn = {1471-2164},
support = {Guizhou Education Technology [2024] No. 335//Natural Science Research Project of Guizhou Education Department in 2024/ ; (Zunyi City, Kehe HZ character (2024) No. 303)//Zunyi city Science and Technology Program project/ ; Guizhou Science and Technology Platform Talents [2021]1350-038//Zunyi Medical University 2021 Special Project for Academic New Seedling Cultivation and Innovative Exploration/ ; No. gzwjkj2019-1-123//Science and Technology Fund Project of Guizhou Health Care Commission/ ; No. [2011]57//Governor's Special Fund for Outstanding Scientific and Technological Education Talents in Guizhou Province/ ; QJJ [2023] 019//Scientific Research Program of Guizhou Provincial Department of Education/ ; },
mesh = {*Bacteroides fragilis/genetics/pathogenicity/isolation & purification ; Humans ; *Colorectal Neoplasms/microbiology/genetics/pathology ; *Tumor Microenvironment ; Genome, Bacterial ; Adaptation, Physiological/genetics ; Phylogeny ; Genomics ; Whole Genome Sequencing ; Virulence/genetics ; Enterotoxins/genetics/metabolism ; },
abstract = {BACKGROUND: The occurrence and development of colorectal cancer (CRC) is an incredibly long process that involves continuous changes in the tumor microenvironment. These constant changes may ultimately result in genetic alterations and changes in the metabolic processes of some symbiotic bacteria as a way to adapt to the changing environment. Patients with CRC exhibit an altered abundance of Bacteroides fragilis (B. fragilis) as indicated by several studies. To better understand the genomic characteristics and virulence spectrum of B. fragilis strains in tumor tissues, B. fragilis strains were isolated from tumor and paracancerous tissues of CRC patients.

METHODS: The isolates were identified using 16 S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.

RESULTS: A strain of B. fragilis enterotoxin (BFT) bft1-producing ZY0302 and a non-enterotoxin-producing B. fragilis ZY0804 were isolated from cancerous and paraneoplastic tissues, respectively. Analysis based on the core and nonessential genes showed that the genomic profiles of the isolates, ZY0302 and ZY0804, differed from those of B. fragilis from other tissue sources. This core and the co-evolution of non-essential genes may be the result of their adaptation to fluctuations in the tumor microenvironment and enhancing their survival. In addition, the ZY0302 and ZY0804 genomes underwent extensive horizontal gene transfer and varying degrees of genomic rearrangements, inversions, insertions, and deletion events, which may favor the enhancement of bacteria's ability to adapt to environmental changes. For instance, the virulence factors, such as the capsular biosynthesis gene clusters and components of the type IV secretion system, acquired through horizontal gene transfer, may facilitated B. fragilis in evading immune responses and managing oxidative stress. Moreover, our analysis revealed that multiple virulence factors identified in the isolates were mainly involved in bacterial adhesion and colonization, oxidative stress, iron acquisition, and immune evasion. This observation is worth noting given that enzymes such as neuraminidase, lipase, hemolysin, protease, and phosphatase, along with genes responsible for LPS biosynthesis, which are recognized for their association with the virulence of B. fragilis, were prevalent among the isolates.

CONCLUSIONS: In summary, it is our assertion that the alterations observed in both core and nonessential genes of B. fragilis, which have been isolated from tissues of colorectal cancer patients, along with significant instances of horizontal gene transfer to the genome, are likely intended to enhance adaptation to the evolving conditions of the tumor microenvironment. This study may provide new insights into the interaction between B. fragilis and the CRC microenvironment.},
}

*Bacteroides fragilis/genetics/pathogenicity/isolation & purification
Humans
*Colorectal Neoplasms/microbiology/genetics/pathology
*Tumor Microenvironment
Genome, Bacterial
Adaptation, Physiological/genetics
Phylogeny
Genomics
Whole Genome Sequencing
Virulence/genetics
Enterotoxins/genetics/metabolism

@article {pmid40100768,
year = {2025},
author = {Chen, YW and Su, YC and Chen, WY and Wu, JH and Chen, JW and Su, SL and Chen, CS and Tsai, PF and Ko, WC and Chen, PL},
title = {Comprehensive Genomic Analysis of Antimicrobial Resistance in Aeromonas dhakensis.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2024.0212},
pmid = {40100768},
issn = {1931-8448},
abstract = {Aeromonas dhakensis is prevalent in aquatic environments in Taiwan and known for its notable antimicrobial resistance. However, comprehensive pan-genomic studies for this species in Taiwan are limited. This study analyzed 28 clinical A. dhakensis isolates using single-molecule real-time sequencing technology, coupled with diverse databases, to elucidate the whole genomes. The focus was on phylogenetic relatedness, antimicrobial resistance genes, and mobile genetic elements. Genomic analysis and multilocus sequence typing were utilized to identify A. dhakensis strains of heterogeneous origins. The detection of various β-lactamase genes (blacphA, blaimiH, blaAQU, blaOXA, blaTEM-1, blaTRU-1, and blaVEB) in clinical A. dhakensis isolates raises concern, especially considering the use of carbapenems and third-generation cephalosporins in patients with severe infections. Notably, most A. dhakensis strains carry chromosome-encoded β-lactamases, including AmpC, metallo-β-lactamase, and oxacillinase, and were susceptible to cefepime in drug susceptibility tests. A. dhakensis strains were also susceptible to aminoglycosides, fluoroquinolones, tigecycline, and trimethoprim/sulfamethoxazole. Three of the 28 A. dhakensis isolates carried plasmids containing an array of drug resistance genes, suggesting this species is likely a recipient or donor of drug resistance genes through horizontal gene transfer. Our findings provide valuable insights into the antimicrobial resistance of A. dhakensis, highlighting the medical implications of its β-lactamase diversity and its potential role in the horizontal gene transfer of drug resistance genes.},
}

@article {pmid40093628,
year = {2025},
author = {Oh, H and Choi, Y and Lee, J},
title = {Antibiotic-Resistant Salmonella in Animal Products Jeopardize Human Health.},
journal = {Food science of animal resources},
volume = {45},
number = {2},
pages = {409-428},
pmid = {40093628},
issn = {2636-0780},
abstract = {Despite the significance of antibiotics in treating bacterial infections, antibiotic resistance is continuously increasing, thus posing a significant threat. In addition to strains resistant to individual drugs, multidrug-resistant (MDR) and pandrug-resistant strains, are emerging. Salmonella, a primary cause of global foodborne illness, is often transmitted through animal products. Antibiotic treatment is crucial for immunocompromised individuals, such as older adults and patients with weakened immune systems, due to their increased susceptibility to severe effects. MDR Salmonella, which can arise following antibiotic use in food animals, may transfer to humans, leading to significant health challenges. The emergence of Salmonella strains resistant to carbapenems, often considered a last-resort antibiotic class, is particularly concerning. Salmonella neutralizes antibiotics through mechanisms, such as horizontal gene transfer via plasmids, efflux/influx system regulation, and enzyme production that deactivate or alter antibiotics. The rise of megaplasmids in Salmonella is particularly alarming, as it may enable resistance to a broader range of antibiotics. This review summarizes the current state of the growing threat of MDR Salmonella and underscores the urgent need for a coordinated response.},
}

@article {pmid40092036,
year = {2025},
author = {Balta, I and Lemon, J and Gadaj, A and Cretescu, I and Stef, D and Pet, I and Stef, L and McCleery, D and Douglas, A and Corcionivoschi, N},
title = {The interplay between antimicrobial resistance, heavy metal pollution, and the role of microplastics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550587},
pmid = {40092036},
issn = {1664-302X},
abstract = {Environmental pollution with heavy metals (HMs) and microplastics (MPs) could enhance the global health challenge antimicrobial resistance (AMR). Herein, we explore the complicated mechanics of how HMs, MPs, and AMR are interlinked within microbial ecosystems, as well as the co-selection and cross-resistance mechanisms. Unlike antibiotics, HMs have influenced microbial evolution for billions of years, promoting resistance mechanisms that predate antibiotic resistance genes (ARGs). At the same time, this conundrum is further complicated by the pervasive spread of MPs in the aquatic and terrestrial environments, acting as substrates for bacterial pathogenic biofilms and accelerates the horizontal gene transfer (HGT) of ARGs and heavy metal resistance genes (MRGs). This review highlights that HMs such as lead (Pb), mercury (Hg), arsenic (As), chromium (Cr), cadmium (Cd), and nickel (Ni) have persistently selected for resistance traits through efflux systems and genetic co-regulation. Together, these interactions are amplified by MPs that create genetic exchange hotspots due to biofilm formation. These dynamics are modulated by organic matter, which serves both as a nutrient source and a mediator of HM bioavailability, directly influencing ARG abundance. Soil and water ecosystems, including riverine systems and landfill leachate, are reservoirs for ARGs and ARG-MRG combinations, with notable contributions originating from anthropogenic activities. This review also emphasizes the urgent need for integrated environmental and public health strategies to mitigate pollutant-driven AMR. This work seeks to approach HMs and MPs as synergistic drivers of AMR such that both HMs and MPs are upstream (causes) levers, a foundation from which future research on sustainable environmental management practices and health policy (One Health Approach), aimed at curbing the spread of resistance determinants can proceed.},
}

@article {pmid40090954,
year = {2025},
author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E},
title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2595},
pmid = {40090954},
issn = {2041-1723},
support = {2018-02835//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2019-03482//Vetenskapsrådet (Swedish Research Council)/ ; 2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; },
abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/drug effects
Humans
*Phylogeny
Wastewater/microbiology
Genome, Bacterial
Animals
Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/genetics
Microbiota/genetics/drug effects
Genes, Bacterial
Metagenome
Drug Resistance, Bacterial/genetics

@article {pmid40090302,
year = {2025},
author = {Wang, J and Hu, Y and An, L and Wang, J and Wu, F and Gu, J and Wang, X and Tiedje, JM},
title = {An efficient strategy for bdd electrode drive electro-catalysis triggering active species on lincomycin and antibiotic resistance genes removal: Electron transfer based on calculation modeling.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137915},
doi = {10.1016/j.jhazmat.2025.137915},
pmid = {40090302},
issn = {1873-3336},
abstract = {Identifying the degradation pathway and the final by-products is essential, as their ecological risks are pertinent to the advancement of this technology and its potential application in practical environmental pollution treatment. Elucidating the reaction mechanisms of the degradation system represents the most effective strategy for controlling this process. This study thoroughly revealed that indirect oxidation predominates throughout the electrochemical system, while direct oxidation serves a significant auxiliary role under the synergistic influence. It elucidates the critical importance of electron transfer behavior at the electrode surface for pollutant degradation and unveil potential mechanisms underlying primary degradation reactions via integrating charge density differences and Bader atomic charge analysis. In situ electrochemical infrared spectroscopy (In situ EC-FTIR) and density functional calculation (DFT) were used to analyze the final by-product generation path. It further elucidated the correlation between antibiotic resistance gene (ARGs) and binding strength among base pairs. The oxidative stress process of antibiotic resistance bacteria (ARB) was explained in detail. To comprehensively assess the impact of electrochemical treatment on environmental microbial communities, combined horizontal gene transfer (HGT) experiments were conducted to confirm that electrolytically treated wastewater does not induce ecological stress effects on microorganisms. Finally, a small cyclic electrochemical system was employed to evaluate both ecological impacts and economic benefits associated with wastewater treatment, thereby providing a novel theoretical framework for this domain.},
}

@article {pmid40086311,
year = {2025},
author = {Pereira, AP and Almeida-Santos, AC and Duarte, B and Antunes, P and Peixe, L and Freitas, AR and Novais, C},
title = {Insights towards the impact of subinhibitory chlorhexidine on antimicrobial susceptibility and horizontal gene transfer in Enterococcus faecium.},
journal = {The Science of the total environment},
volume = {972},
number = {},
pages = {179064},
doi = {10.1016/j.scitotenv.2025.179064},
pmid = {40086311},
issn = {1879-1026},
abstract = {Enterococcus faecium, a human and animal commensal broadly distributed in the environment, is currently one of the most challenging multidrug-resistant (MDR) healthcare-associated pathogens worldwide. It is often exposed to chlorhexidine (CHX), a broad-spectrum antiseptic, extensively used in healthcare, domestic, and food production settings, and a diffused polluter. However, the impact of gradients of CHX concentrations, including at subinhibitory levels, on E. faecium adaptation to various antimicrobials remains unclear. Our study aimed to explore the effects of subinhibitory CHX concentrations on biocides and antibiotics susceptibility as well as in the transfer of clinically relevant antibiotic resistance genes among E. faecium (n = 11) from diverse sources and clonal backgrounds. Serial exposure to increasing CHX concentrations resulted in strain-specific MICCHX and MBCCHX changes among six E. faecium studied. These strains presented different CHX genotypes, namely the P102H mutation in DNA-binding response regulator ChtR in two strains showing twofold increased MICCHX and/or MBCCHX, and an absent EfrEF transporter in a strain exhibiting increased CHX susceptibility after exposure. Whole-genome comparison between parental and CHX-adapted strains found no alterations in genes with a recognized role in CHX reduced susceptibility. Additionally, in a different assay, subinhibitory CHX exposure enhanced the transfer (up to 12.5-fold) of vancomycin or linezolid resistance genes among most E. faecium strains tested, except one lacking a functional EfrEF transporter. Our data suggest that subinhibitory CHX concentrations could have a role in Enterococcus adaptation to CHX and in the spread of antibiotic resistance through horizontal transfer events. Further investigation is warranted to elucidate the underlying mechanisms driving these phenomena in E. faecium, ensuring the continued effectiveness of both CHX and antibiotics, and safeguarding Public Health.},
}

@article {pmid40083414,
year = {2025},
author = {Shi, G and Dai, Y and Zhou, D and Chen, M and Zhang, J and Bi, Y and Liu, S and Wu, Q},
title = {An alignment- and reference-free strategy using k-mer present pattern for population genomic analyses.},
journal = {Mycology},
volume = {16},
number = {1},
pages = {309-323},
pmid = {40083414},
issn = {2150-1203},
abstract = {Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-genome alignments. K-mer decomposition is an alternative to graph-based pangenomes. However, how to directly use k-mers for the population genetic analyses is unknown. Here, we developed a novel strategy that uses the variants of k-mer count in the genome for population analyses. To test the effectivity of this method, we compared it directly to the SNP-based method on the analysis of population structure and genetic diversity of 267 Saccharomyces cerevisiae strains within two simulated datasets and a real sequence dataset. The population structure identified with k-mers recapitulates that obtained using SNPs, indicating the effectiveness of k-mer-based approach, and higher genetic diversity within real dataset supported k-mers contained more genetic variants. Based on k-mer frequency, we found not only SNP but also some insertion/deletion and horizontal gene transfer (HGT) fragments related to the adaptive evolution of S. cerevisiae. Our study creates a framework for the alignment- and reference-free (ARF) method in population genetic analyses, which will be more pronounced in the species with no complete genome or highly diverged species.},
}

@article {pmid40081886,
year = {2025},
author = {Muleshkova, T and Bazukyan, I and Papadimitriou, K and Gotcheva, V and Angelov, A and Dimov, SG},
title = {Exploring the Multifaceted Genus Acinetobacter: the Facts, the Concerns and the Oppoptunities the Dualistic Geuns Acinetobacter.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2411043},
doi = {10.4014/jmb.2411.11043},
pmid = {40081886},
issn = {1738-8872},
mesh = {*Acinetobacter/genetics/classification/isolation & purification ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genetic Variation ; Phylogeny ; Humans ; Biodegradation, Environmental ; Acinetobacter Infections/microbiology ; },
abstract = {In recent years, the research community has been interested in members of the Acinetobacter genus mainly because of their role as causative agents of nosocomial infections. However, this rich-in-species genus has been proven to play a significant role in several biotechnological processes, such as bioremediation and fermented foods production. To partially fill the lack of information on Acinetobacter's dualistic nature, in this review, based on literature data, we attempt to summarize the available information on the different roles the members of the genus play by considering their genetic constitution and metabolic properties. We analyzed reports of genetic divergence between the pathogenic and non-pathogenic species and isolates, which can be explained by their high adaptability to the different ecological niches. In turn, this adaptability could result from intrinsic genetic variability due to mechanisms of horizontal genetic transfer, as well as high mutability determined by the expression of error-prone DNA polymerases. Yet, we concluded that further studies are needed, especially whole-genome sequencing of non-pathogenic isolates, which for the moment are relatively scarce.},
}

*Acinetobacter/genetics/classification/isolation & purification
*Gene Transfer, Horizontal
Genome, Bacterial
Genetic Variation
Phylogeny
Humans
Biodegradation, Environmental
Acinetobacter Infections/microbiology

@article {pmid40079731,
year = {2025},
author = {Elmarghani, ED and Pettersson, JH and Atterby, C and Hickman, RA and Seng, S and San, S and Osbjer, K and Magnusson, U and Mourkas, E and Järhult, JD},
title = {Genomic insights into extended-spectrum β-lactamase- and plasmid-borne AmpC-producing Escherichia coli transmission between humans and livestock in rural Cambodia.},
journal = {Journal of medical microbiology},
volume = {74},
number = {3},
pages = {},
pmid = {40079731},
issn = {1473-5644},
mesh = {Humans ; Cambodia/epidemiology ; *beta-Lactamases/genetics ; Animals ; *Escherichia coli/genetics/isolation & purification/drug effects/classification/enzymology ; *Escherichia coli Infections/transmission/epidemiology/microbiology/veterinary ; *Plasmids/genetics ; *Livestock/microbiology ; *Phylogeny ; *Bacterial Proteins/genetics ; *Rural Population ; Male ; Female ; Adult ; Middle Aged ; Whole Genome Sequencing ; Feces/microbiology ; Multilocus Sequence Typing ; Young Adult ; Anti-Bacterial Agents/pharmacology ; Child ; Adolescent ; },
abstract = {Introduction. The global spread of extended-spectrum cephalosporinase-producing Escherichia coli (producing extended-spectrum β-lactamase or plasmid-borne AmpC, hereafter ESC-Ec) is a major public health concern. Whilst extensively studied in high-income countries, the transmission pathways between humans and animals in low- and middle-income countries (LMICs) remain unclear. In rural Cambodia, the asymptomatic carriage and transmission dynamics of ESC-Ec between humans and animals living in close proximity are poorly understood, highlighting the need for targeted research in this area.Gap statement. An enhanced understanding of the genetic epidemiology of ESC-Ec can enable mitigation strategies to reduce the burden of disease and drug-resistant infections in LMIC settings.Aim. This study aimed to investigate the genetic relatedness and genotypic antibiotic resistance profiles of ESC-Ec strains from humans and livestock in rural Cambodia and to identify patterns of antimicrobial resistance (AMR) gene transmission between hosts and across households and villages.Methodology. Faecal samples were collected from 307 humans and 285 livestock in 100 households in or near Kampong Cham Province in rural Cambodia. From these samples, 108 ESC-Ec strains were subjected to whole-genome sequencing. Core genome MLST (cgMLST) and phylogenetic analysis determined genetic relationships between strains. All strains were screened for the presence of antibiotic resistance genes and plasmids.Results. Human and livestock isolates were assigned to six phylogroups, with phylogroup A being the most common (56.5%). MLST identified 50 sequence types (STs), 17 of which were shared between humans and animals, with ST155 being the most prevalent. cgMLST revealed 97 distinct cgMLST sequence types (cgST), indicating strain sharing between humans and animals. Additionally, AMR gene analysis showed widespread resistance, with genes from the bla CTX-M group detected in 84.2% of isolates. Notably, AMR genes such as aph(3'')-Ib-sul2 co-occurred in 50% of isolates. Finally, plasmid analysis identified IncF plasmids in 75.9% of isolates, likely facilitating AMR gene transmission across hosts.Conclusions. Our findings demonstrate that ESC-Ec strains and their AMR genes are transmitted between humans and livestock in rural Cambodia, likely driven by both clonal spread and plasmid-mediated horizontal gene transfer. These results highlight the urgent need for antimicrobial stewardship and infection control strategies to mitigate the spread of multidrug-resistant pathogens in both human and animal populations.},
}

Humans
Cambodia/epidemiology
*beta-Lactamases/genetics
Animals
*Escherichia coli/genetics/isolation & purification/drug effects/classification/enzymology
*Escherichia coli Infections/transmission/epidemiology/microbiology/veterinary
*Plasmids/genetics
*Livestock/microbiology
*Phylogeny
*Bacterial Proteins/genetics
*Rural Population
Male
Female
Adult
Middle Aged
Whole Genome Sequencing
Feces/microbiology
Multilocus Sequence Typing
Young Adult
Anti-Bacterial Agents/pharmacology
Child
Adolescent

@article {pmid40078948,
year = {2024},
author = {Zhou, Z and Chen, H},
title = {Evaluating human exposure to antibiotic resistance genes.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {98-100},
pmid = {40078948},
issn = {2590-0536},
abstract = {Antibiotic resistance is an escalating global concern, leading to millions of annual fatalities. Antibiotic resistance genes (ARGs) present in bacteria equip them to withstand the effects of antibiotics. Intra- and interspecific ARGs transmission through horizontal gene transfer further exacerbates resistance dissemination. The presence of ARGs in the environment heightens the probability of human exposure via direct inhalation, ingestion, or contact with polluted air, food, or water, posing substantial biosafety and health hazards. Consequently, ARGs represent a critical focal point in public health and environmental safety and are classified as emerging contaminants. This perspective underscores the necessity to assess ARG exposure within the One Health framework and to accord greater attention to the mitigation strategies and tactics associated with ARGs.},
}

@article {pmid39932282,
year = {2025},
author = {Karki, S and Aylward, FO},
title = {Evolution of ubiquitin, cytoskeleton, and vesicular trafficking machinery in giant viruses.},
journal = {Journal of virology},
volume = {99},
number = {3},
pages = {e0171524},
doi = {10.1128/jvi.01715-24},
pmid = {39932282},
issn = {1098-5514},
support = {2141862//National Science Foundation (NSF)/ ; },
mesh = {*Evolution, Molecular ; *Cytoskeleton/metabolism/virology ; *Ubiquitin/metabolism/genetics ; *Giant Viruses/genetics/metabolism ; Viral Proteins/metabolism/genetics ; Phylogeny ; Genome, Viral ; Gene Transfer, Horizontal ; DNA Viruses/genetics/metabolism ; },
abstract = {Members of the phylum Nucleocytoviricota, which include "giant viruses" known for their large physical dimensions and genome lengths, are a diverse group of dsDNA viruses that infect a wide range of eukaryotic hosts. The genomes of nucleocytoviruses frequently encode eukaryotic signature proteins (ESPs) such as RNA- and DNA-processing proteins, vesicular trafficking factors, cytoskeletal components, and proteins involved in ubiquitin signaling. Despite the prevalence of these genes in many nucleocytoviruses, the timing and number of gene acquisitions remains unclear. While the presence of DNA- and RNA-processing proteins in nucleocytoviruses likely reflects ancient gene transfers, the origins and evolutionary history of other proteins are largely unknown. In this study, we examined the distribution and evolutionary history of a subset of viral-encoded ESPs (vESPs) that are widespread in nucleocytoviruses. Our results demonstrate that most vESPs involved in vesicular trafficking were acquired multiple times independently by nucleocytoviruses at different time points after the emergence of the eukaryotic supergroups, while viral proteins associated with cytoskeletal and ubiquitin system proteins exhibited a more complex evolutionary pattern exhibited by both shallow and deep branching viral clades. This pattern reveals a dynamic interplay between the co-evoluton of eukaryotes and their viruses, suggesting that the viral acquisition of many genes involved in cellular processes has occurred both through ancient and more recent horizontal gene transfers. The timing and frequency of these gene acquisitions may provide insight into their role and functional significance during viral infection.IMPORTANCEThis research is pertinent for understanding the evolution of nucleocytoviruses and their interactions with eukaryotic hosts. By investigating the distribution and evolutionary history of viral-encoded eukaryotic signature proteins, the study reveals gene transfer patterns, highlighting how viruses acquire genes that allow them to manipulate host cellular processes. Identifying the timing and frequency of gene acquisitions related to essential cellular functions provides insights into their roles during viral infections. This work expands our understanding of viral diversity and adaptability, contributing valuable knowledge to virology and evolutionary biology, while offering new perspectives on the relationship between viruses and their hosts.},
}

*Evolution, Molecular
*Cytoskeleton/metabolism/virology
*Ubiquitin/metabolism/genetics
*Giant Viruses/genetics/metabolism
Viral Proteins/metabolism/genetics
Phylogeny
Genome, Viral
Gene Transfer, Horizontal
DNA Viruses/genetics/metabolism

@article {pmid39879767,
year = {2025},
author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH},
title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137206},
doi = {10.1016/j.jhazmat.2025.137206},
pmid = {39879767},
issn = {1873-3336},
mesh = {*Microalgae/genetics/drug effects/metabolism ; *Extracellular Polymeric Substance Matrix/metabolism ; *Bacteria/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.},
}

*Microalgae/genetics/drug effects/metabolism
*Extracellular Polymeric Substance Matrix/metabolism
*Bacteria/genetics/drug effects/metabolism
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Drug Resistance, Microbial/genetics
Gene Transfer, Horizontal
Wastewater/microbiology
Drug Resistance, Bacterial/genetics

@article {pmid39874760,
year = {2025},
author = {Liu, Y and Shan, X and Liu, C and Chen, H},
title = {Microcosm experiments deciphered resistome coalescence, risks and source-sink relationship of antibiotic resistance in the soil irrigated with reclaimed water.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137398},
doi = {10.1016/j.jhazmat.2025.137398},
pmid = {39874760},
issn = {1873-3336},
mesh = {*Agricultural Irrigation ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Soil/chemistry ; Gene Transfer, Horizontal ; },
abstract = {Reclaimed water is widely used in agriculture irrigation to alleviate water scarcity, whereas the dissemination of antibiotic resistance genes (ARGs) in the soil it introduces has attracted widespread attention. Currently, few studies have systematically elucidated the coalescence of the resistome originating from reclaimed water with the soil's native community. Also, the effects and mechanisms of irrigation on the dissemination of ARGs in soils have yet to be demonstrated. To address this gap, microcosm experiments have been conducted in this study to decipher the resistome coalescence, risks and source-sink relationship of ARGs in soils irrigated with reclaimed water. The results show 237 ARGs, 55 mobile genetic elements (MGEs) and 28 virulence factors were identified in the irrigated soils. Irrigation increased the abundance and diversity of ARGs in the soil by introducing antibiotic-resistant bacteria, altering the microbial community and facilitating horizontal transfer of ARGs via MGEs, and ultimately exacerbated resistome risks in the environment. Relatively, a larger volume of irrigation water led to a more complex propagation network of the resistome. Source apportionment analysis suggested reclaimed water contributed less than 15 % of ARGs in the irrigated soils, whereas its contribution proportion increased with a larger volume of irrigation water.},
}

*Agricultural Irrigation
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Bacteria/genetics/drug effects
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Soil/chemistry
Gene Transfer, Horizontal

@article {pmid40078945,
year = {2024},
author = {Zhai, W and Wang, Y and Sun, H and Fu, B and Zhang, Q and Wu, C and Shen, J and Liu, D and Wang, Y},
title = {Epidemiology and genetic characterization of tet(X4)-positive Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from raw meat in Chengdu City, China.},
journal = {Biosafety and health},
volume = {6},
number = {2},
pages = {116-124},
pmid = {40078945},
issn = {2590-0536},
abstract = {The rapid spread of mobile tigecycline resistance presents a significant public health threat, particularly with the increasing prevalence of tet(X4)-positive Enterobacterales across various species. This study aimed to investigate the epidemic features and transmission dynamics of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) through the analysis of 206 raw meats, including pork (n = 182), beef (n = 16), duck (n = 5), and chicken (n = 3). These samples were collected from schools, markets, and restaurants in Chengdu City, China. A total of 25 isolates were obtained from 13 administrative regions. All isolates exhibited resistance to tetracycline, tigecycline, ampicillin, chloramphenicol, and florfenicol. Over half of the isolates also demonstrated resistance to streptomycin (80 %), sulfamethoxazole/trimethoprim (72 %), ciprofloxacin (64 %), and ampicillin/sulbactam (56 %). Among these strains, 14 distinct sequence types (STs) were identified, revealing evidence of inter-regional clonal spread, notably among 9 K. pneumoniae ST3393. Phylogenetic analysis revealed the presence of two K. pneumoniae ST5 closely resembling hypervirulent K. pneumoniae from Jiangsu. Importantly, 12 isolates were capable of transferring tigecycline resistance to Escherichia coli J53. Further plasmid analysis showed that the tet(X4)-harboring plasmids in K. pneumoniae could be classified into four types, primarily belonging to the IncFIA(HI1)/HI1A/HI1B hybrid plasmid (n = 16) and IncFII plasmid (n = 7), which significantly contributed to the cross-species dissemination of tet(X4). In summary, this study highlights the prevalence of MDR tet(X4)-positive K. pneumoniae in Chengdu, driven predominantly by clonal expansion and plasmid-mediated horizontal gene transfer. These findings emphasize the importance of continuous surveillance of tet(X4)-positive K. pneumoniae in raw meat and the implementation of effective measures to control their spread.},
}

@article {pmid40076423,
year = {2025},
author = {Aguirre-Carvajal, K and Cárdenas, S and Munteanu, CR and Armijos-Jaramillo, V},
title = {Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
pmid = {40076423},
issn = {1422-0067},
support = {PRG.BIO.23.14.01//Universidad de Las Américas/ ; },
mesh = {*Gene Transfer, Horizontal ; *Phylogeny ; *Ascomycota/genetics ; Evolution, Molecular ; Proteome/genetics ; },
abstract = {Horizontal gene transfer (HGT) is a significant source of diversity in prokaryotes and a key factor in their genome evolution. Although similar processes have been postulated for eukaryotes, the validity of HGT's impact remains contested, particularly between long-distance-related organisms like those from different kingdoms. Among eukaryotes, the fungal subphylum Pezizomycotina has been frequently cited in the literature for experiencing HGT events, with over 600 publications on the subject. The proteomes of 421 Pezizomycotina species were meticulously examined to identify potential instances of interkingdom HGT. Furthermore, the phylogenies of over 275 HGT candidates previously reported were revisited. Manual scrutiny of 521 anomalous phylogenies revealed that only 1.5% display patterns indicative of interkingdom HGT. Moreover, novel interkingdom HGT searches within Pezizomycotina yielded few new contenders, casting doubt on the prevalence of such events within this subphylum. Although the detailed examination of phylogenies suggested interkingdom HGT, the evidence for lateral gene transfer is not conclusive. The findings suggest that expanding the number of homologous sequences could uncover vertical inheritance patterns that have been misclassified as HGT. Consequently, this research supports the notion that interkingdom HGT may be an extraordinary occurrence rather than a significant evolutionary driver in eukaryotic genomes.},
}

*Gene Transfer, Horizontal
*Phylogeny
*Ascomycota/genetics
Evolution, Molecular
Proteome/genetics

@article {pmid40078307,
year = {2024},
author = {Salman, S and Umar, Z and Xiao, Y},
title = {Current epidemiologic features and health dynamics of ESBL-producing Escherichia coli in China.},
journal = {Biosafety and health},
volume = {6},
number = {1},
pages = {40-49},
pmid = {40078307},
issn = {2590-0536},
abstract = {Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) are widespread in China, with occurrences documented in humans, animals, and the environment. The dissemination of ESBL-producing E. coli is likely facilitated by the widespread use of antibiotics in human and animal agriculture, the presence of antibiotic-resistant bacteria (ARBs) in animal feces, and close human-animal interactions. Plasmids, particularly those belonging to incompatibility (Inc) group, such as IncF, IncI, and IncH families, play a vital role in facilitating the horizontal gene transfer of ESBL genes across various sectors, from humans to animals and the environment. IS26 and IS1 elements also significantly influences the mobilization and evolution of antibiotic-resistance genes (ARGs), contributing to the spread of ESBL-producing E. coli. bla CTX-M-14, bla CTX-15, and bla CTX-M-55 are prevalent in ESBL-producing E. coli across the three domains and are often found in conjunction with other ARGs. Considering these challenges, it is imperative to take proactive measures to prevent the further spread of ARBs. This includes the judicious and responsible use of antibiotics and efforts to minimize contact with animal feces. Sector-specific strategies should be developed to effectively educate and engage relevant personnel in tackling this multifaceted problem. These efforts are vital to combat the dissemination of ESBL-producing E. coli and preserve public health.},
}

@article {pmid40075357,
year = {2025},
author = {Donkor, ES and Odoom, A and Osman, AH and Darkwah, S and Kotey, FCN},
title = {A systematic review and meta-analysis on antibiotic resistance genes in Ghana.},
journal = {BMC medical genomics},
volume = {18},
number = {1},
pages = {47},
pmid = {40075357},
issn = {1755-8794},
support = {D43 TW012487/TW/FIC NIH HHS/United States ; D43TW012487//the Fogarty International Center of the National Institutes of Health through the Research and Capacity Building in Antimicrobial Resistance in West Africa (RECABAW) Training Programme/ ; },
mesh = {Ghana ; Humans ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; },
abstract = {BACKGROUND: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources.

METHODS: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis.

RESULTS: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was blaCTX-M, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by blaTEM (19.5% [95% CI: 9.7-29.3]), and blaSHV (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for blaNDM to 10.3% (95% CI: 1.9-18.7) for blaOXA. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources.

CONCLUSION: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.},
}

Ghana
Humans
Animals
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects
Genes, Bacterial

@article {pmid40073489,
year = {2025},
author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC},
title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.},
journal = {Water research},
volume = {279},
number = {},
pages = {123463},
doi = {10.1016/j.watres.2025.123463},
pmid = {40073489},
issn = {1879-2448},
abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.},
}

@article {pmid40072588,
year = {2025},
author = {Zeng, Q and Liu, Q and Pu, Y and Gong, P and Li, Y and Sun, Y and Hao, Y and Yang, Q and Wu, Y and Yang, B and Shi, S and Gong, Z},
title = {Impacts of Naphthenic Acids (NAs) Exposure on Soil Bacterial Community and Antibiotic Resistance Genes (ARGs) Dissemination.},
journal = {Current microbiology},
volume = {82},
number = {5},
pages = {188},
pmid = {40072588},
issn = {1432-0991},
support = {2022-MS-311//Natural Science Foundation of Liaoning Province/ ; JYTMS20231059//Basic Scientific Research Project of Education Department of Liaoning Province/ ; H2022011//Horizontal Scientific Research Project (Microbial-enhanced treatment of petroleum hydrocarbon pollutants: Technical and engineering demonstration)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/drug effects/classification/metabolism ; *Carboxylic Acids/metabolism/pharmacology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Denitrification ; Reactive Oxygen Species/metabolism ; Microbiota/drug effects/genetics ; Nitrification/drug effects ; },
abstract = {Naphthenic acids (NAs) are indigenous and complex components in petroleum. In the context of increasing global energy demand, the increasing extraction of fossil resources leads to increased environmental release of NAs, resulting in various environmental risks. However, the impact of NAs exposure on soil microorganisms remains still unclear. This study constructed a microcosm system to explore bacterial community structure and function, biological risk generation, and the mechanism of antibiotic resistance genes (ARGs) dissemination under NAs exposure. After 28 days of NAs stimulation, the denitrifying bacteria were enriched and the abundance of genes related to nitrogen cycle was up-regulated, enhancing nitrification and denitrification. Meanwhile, NAs stimulated the production of extracellular polymeric substances (EPS) and the accumulation of reactive oxygen species (ROS), as well as activated the glutathione antioxidant system. Furthermore, the cell metabolic, repair, and transfer regulatory pathways were enhanced under NAs exposure. The networks of ARGs with genera and mobile genetic elements (MGEs) indicated that NAs exposure promoted the enrichment of ARGs in hosts, the selective accumulation of MGEs, and the induction of horizontal gene transfer (HGT) of ARGs. This study will provide valuable perspectives of interactions between NAs and its microecological environment, as well as ARGs transfer mechanisms.},
}

*Soil Microbiology
*Bacteria/genetics/drug effects/classification/metabolism
*Carboxylic Acids/metabolism/pharmacology
*Gene Transfer, Horizontal
Genes, Bacterial
Drug Resistance, Bacterial/genetics
Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Denitrification
Reactive Oxygen Species/metabolism
Microbiota/drug effects/genetics
Nitrification/drug effects

@article {pmid40071515,
year = {2025},
author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY},
title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10879},
pmid = {40071515},
issn = {1520-5851},
abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.},
}

@article {pmid40069391,
year = {2025},
author = {Huang, YX and Rao, HY and Su, BS and Lv, JM and Lin, JJ and Wang, X and Xu, LN and Kong, XD and Sun, Y},
title = {The pan-genome of Spodoptera frugiperda provides new insights into genome evolution and horizontal gene transfer.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {407},
pmid = {40069391},
issn = {2399-3642},
support = {32100355, 32100352, 31871964//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Spodoptera/genetics ; Animals ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; *Genome, Insect ; Genetic Variation ; },
abstract = {Spodoptera frugiperda is a common and severely damaging agricultural pest. In-depth analysis of its population genomics and transcriptomics is crucial for providing references for pest control efforts. This study, focused on the extensive variation in the genome size of S. frugiperda, constructed its pan-genome and identified 1.37 Gb of non-reference sequences, highlighting significant genetic variation within the population. Analysis of Long Terminal Repeat (LTR) Presence/Absence Variation (PAV) suggests that LTR alterations may be one of the driving factors for genome size variation. Additionally, population gene PAV analysis revealed that variable genes are enriched in functions like acetyltransferase activity, which might be associated with detoxification, implying diverse selection pressures related to detoxification in different S. frugiperda populations. Moreover, 19 horizontal gene transfer (HGT) acquired genes were identified in the reference genome used in this study, which responded to 16 different treatments. Notably, three HGT-acquired genes (SFR02618, SFR05248, and SFR05249) co-expressed with heat shock protein family and responded under treatments with Avermectin and Cypermethrin. This may indicate their involvement in a detoxification mechanism coordinated with heat shock proteins. These results offering new insights into its genomic evolution and the potential functions of HGT-acquired genes.},
}

*Spodoptera/genetics
Animals
*Gene Transfer, Horizontal
*Evolution, Molecular
*Genome, Insect
Genetic Variation

@article {pmid40069285,
year = {2025},
author = {Masuyer, G and Taverner, A and MacKay, J and Lima Marques, AR and Wang, Y and Hunter, T and Liu, K and Mrsny, RJ},
title = {Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {413},
pmid = {40069285},
issn = {2399-3642},
mesh = {*Exotoxins/chemistry/metabolism/genetics ; *Bacterial Toxins/chemistry/metabolism/genetics ; *Pseudomonas aeruginosa Exotoxin A ; *ADP Ribose Transferases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Virulence Factors/chemistry/metabolism/genetics ; Amino Acid Sequence ; Humans ; Models, Molecular ; Phylogeny ; Bacterial Proteins/chemistry/metabolism/genetics ; },
abstract = {Mono-ADP-ribosyl transferase (mART) proteins are secreted virulence factors produced by several human pathogens, the founding member being diphtheria toxin (DT). Pseudomonas aeruginosa can also secrete a mART toxin, known as exotoxin A (PE), but with an organization of its three functional domains (receptor, translocation, and enzymatic elements) that is opposite to DT. Two additional PE-like toxins (PLTs) have been identified from Vibrio cholerae and Aeromonas hydrophila, suggesting more PLT family members may exist. Database mining discovered six additional putative homologues, considerably extending this group of PLTs across a wide range of bacterial species. Here, we examine sequence and structural information for these new family members with respect to previously identified PLTs. The X-ray crystal structures of four new homologues show the conservation of critical features responsible for structure and function. This study shows the potential of these newly described toxins for the development of novel drug delivery platforms. Additionally, genomic analysis suggests horizontal gene transfer to account for the wide distribution of PLTs across a range of eubacteria species, highlighting the need to monitor emerging pathogens and their virulence factors.},
}

*Exotoxins/chemistry/metabolism/genetics
*Bacterial Toxins/chemistry/metabolism/genetics
*Pseudomonas aeruginosa Exotoxin A
*ADP Ribose Transferases/chemistry/metabolism/genetics
Crystallography, X-Ray
Virulence Factors/chemistry/metabolism/genetics
Amino Acid Sequence
Humans
Models, Molecular
Phylogeny
Bacterial Proteins/chemistry/metabolism/genetics

@article {pmid40066988,
year = {2025},
author = {Mašlaňová, I and Kovařovic, V and Botka, T and Švec, P and Sedláček, I and Šedo, O and Finstrlová, A and Neumann-Schaal, M and Kirstein, S and Schwendener, S and Staňková, E and Rovňáková, K and Petráš, P and Doškař, J and Perreten, V and Pantůček, R},
title = {Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0165224},
doi = {10.1128/aem.01652-24},
pmid = {40066988},
issn = {1098-5336},
abstract = {Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376[T] = CCM 8659[T] = DSM 111350[T]) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.},
}

@article {pmid40066273,
year = {2025},
author = {Han, B and Feng, C and Jiang, Y and Ye, C and Wei, Y and Liu, J and Zeng, Z},
title = {Mobile genetic elements encoding antibiotic resistance genes and virulence genes in Klebsiella pneumoniae: important pathways for the acquisition of virulence and resistance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1529157},
pmid = {40066273},
issn = {1664-302X},
abstract = {Klebsiella pneumoniae is an opportunistic pathogen primarily associated with nosocomial infections, characterized by a propensity for multi-drug resistance and the potential evolution into hypervirulent strains. Based on its phenotypic and genotypic characteristics, K. pneumoniae can be classified into two types: classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). The spread of mobile genetic elements (MGEs) in K. pneumoniae has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP) and carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP). The emergence of CR-hvKP is particularly concerning due to its multidrug resistance, high pathogenicity, and increased transmissibility. This review summarizes the types of MGEs present in K. pneumoniae, the mechanisms of horizontal gene transfer (HGT) mediated by these mobile elements, their roles in the dissemination of antibiotic resistance genes (ARGs) and virulence genes, and the relationships among MGEs that resemble Russian dolls or exhibit hybrid characteristics. Additionally, the clinical treatment and epidemiological characteristics of CR-hvKP are discussed. Given the high variability and transmissibility of MGEs, continuous monitoring and control of the variation and transmission of such genetic material in K. pneumoniae should be prioritized.},
}

@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}

*Geminiviridae/genetics
*Recombination, Genetic
Software
Algorithms
Sequence Alignment
Genome, Viral
Evolution, Molecular
Computational Biology/methods
Phylogeny

@article {pmid40063617,
year = {2025},
author = {Gaona, M and Corral, J and Sánchez Osuna, M and Campoy, S and Barbé, J and Pérez-Varela, M and Aranda, J},
title = {Reciprocal regulation between Acinetobacter baumannii and Enterobacter cloacae AdeR homologs: implications for antimicrobial resistance and pathogenesis.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315428},
pmid = {40063617},
issn = {1932-6203},
mesh = {*Enterobacter cloacae/genetics/drug effects/pathogenicity ; *Acinetobacter baumannii/genetics/drug effects/pathogenicity ; *Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/pharmacology ; Animals ; Drug Resistance, Bacterial/genetics ; Promoter Regions, Genetic ; Microbial Sensitivity Tests ; Virulence/genetics ; Mice ; Membrane Transport Proteins ; },
abstract = {Acinetobacter baumannii and Enterobacter cloacae are phylogenetically distant Gram-negative bacterial pathogens that represent significant challenges in healthcare settings due to their remarkable ability to acquire antimicrobial resistance. This study investigates one of the most important efflux pump systems in A. baumannii, AdeABC-AdeRS, and identifies homologous components in E. cloacae. By constructing isogenic knockout mutants, we show that the AdeB pump component and the AdeR regulator are significant for antimicrobial resistance and pathogenicity in A. baumannii. Through in silico predictions, we identify homologs of AdeB and AdeR (ECL_01758 and ECL_01761, respectively) in E. cloacae. Notably, we demonstrate that while the inactivation of the E. cloacae gene encoding the AdeB protein does not impact on pathogenesis and only alters colistin susceptibility, a knockout mutant of the gene encoding the AdeR regulator significantly affects susceptibility to various antimicrobial classes, motility, and virulence. Additionally, we demonstrate that the AdeR regulators of A. baumannii and E. cloacae can functionally substitute for each other both in vitro and in vivo conditions. Electrophoretic mobility shift assays reveal that these regulators are capable of binding to the promoter regions of each other's species, where similar DNA motifs are present. Furthermore, cross-complementation tests show that the affected phenotypes in each species can be restored interchangeably. Moreover, phylogenomic analysis of previously published E.cloacae genomes and reconstructrion of ancestral states through the phylogenetic trees of the adeB and adeR genes suggest that these homologs are more likely derived from a common ancestor rather than through recent horizontal gene transfer. The findings of this work highlight that conserved regulatory functions concerning efflux pump expression can be maintained across species despite evolutionary divergence and open new perspectives for the control of bacterial infections.},
}

*Enterobacter cloacae/genetics/drug effects/pathogenicity
*Acinetobacter baumannii/genetics/drug effects/pathogenicity
*Bacterial Proteins/genetics/metabolism
Gene Expression Regulation, Bacterial
Anti-Bacterial Agents/pharmacology
Animals
Drug Resistance, Bacterial/genetics
Promoter Regions, Genetic
Microbial Sensitivity Tests
Virulence/genetics
Mice
Membrane Transport Proteins

@article {pmid40061860,
year = {2025},
author = {Zhang, S and Yang, J and Abbas, M and Yang, Q and Li, Q and Liu, M and Zhu, D and Wang, M and Tian, B and Cheng, A},
title = {Threats across boundaries: the spread of ESBL-positive Enterobacteriaceae bacteria and its challenge to the "one health" concept.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496716},
pmid = {40061860},
issn = {1664-302X},
abstract = {β-lactam antibiotics are essential medications for treating human diseases. The spread of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) exists globally in multiple reservoirs and the natural environment and poses an immense threat to public health. Plasmid incompatibility groups, such as IncFIA, IncI1, IncY, IncFIB, IncN, IncFIC, IncX4, IncB/O/K/Z, IncHI1/2, and IncA/C, which exist in humans, animals, and the environment, carrying bla CTX-M, bla TEM, and bla SHV genes. The ISEcp1 upstream and orf477 downstream of bla CTX-M genes, as well as other mobile genetic elements (MGEs) such as IS903 and IS26, are involved in capturing and mobilizing antibiotic-resistant genes (ARGs). The bla CTX-M-15 gene is the most common among all discussed reservoirs. The environmental reservoir and propagation mode of ESBL-PE are increasing and difficult to control. The reasons include but are not limited to bacterial adaptability and horizontal gene transfer (HGT) mediated by MGEs and plasmids. Conjugation is a pathway of HGT that is almost uncontrollable. MGEs and plasmids such as Tn3, IS1380 families, IncI1, IncK, and IncN are facilitating HGT of bla CTX-M genes. This review highlights the need to monitor trends in antimicrobial resistance (AMR) in the natural environment. Therefore, policies such as antibiotic management plans, training for healthcare providers and/or patients, cautious use of antibiotics, the need for epidemiological networks, pre-travel consultations, World Health Organization (WHO) infection control and biosafety guidelines, and other intervention measures are considered desirable.},
}

@article {pmid40058530,
year = {2025},
author = {Smykal, V and Tobita, H and Dolezel, D},
title = {Evolution of circadian clock and light-input pathway genes in Hemiptera.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104298},
doi = {10.1016/j.ibmb.2025.104298},
pmid = {40058530},
issn = {1879-0240},
abstract = {Circadian clocks are timekeeping mechanisms that help organisms anticipate periodic alterations of day and night. These clocks are widespread, and in the case of animals, they rely on genetically related components. At the molecular level, the animal circadian clock consists of several interconnected transcription-translation feedback loops. Although the clock setup is generally conserved, some important differences exist even among various insect groups. Therefore, we decided to identify in silico all major clock components and closely related genes in Hemiptera. Our analyses indicate several lineage-specific alterations of the clock setup in Hemiptera, derived from gene losses observed in the complete gene set identified in the outgroup, Thysanoptera, which thus presents the insect lineage with a complete clock setup. Nilaparvata and Fulgoroidea, in general, lost the (6-4)-photolyase, while all Hemiptera lost FBXL3, and several lineage-specific losses of dCRY and jetlag were identified. Importantly, we identified non-canonical splicing variants of period and m-cry genes, which might provide another regulatory mechanism for clock functioning. Lastly, we performed a detailed reconstruction of Hemiptera's light input pathway genetic repertoire and explored the horizontal gene transfer of cryptochrome-DASH from plant to Bemisia. Altogether, this inventory reveals important trends in clock gene evolution and provides a reference for clock research in Hemiptera, including several lineages of important pest species.},
}

@article {pmid40056814,
year = {2025},
author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M},
title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.},
journal = {Chemosphere},
volume = {376},
number = {},
pages = {144296},
doi = {10.1016/j.chemosphere.2025.144296},
pmid = {40056814},
issn = {1879-1298},
abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.},
}

@article {pmid40056564,
year = {2025},
author = {Singh, H and Bagra, K and Dixit, S and Singh, AK and Singh, G},
title = {Association of infrastructure and operations with antibiotic resistance potential in the dairy environment in India.},
journal = {Preventive veterinary medicine},
volume = {239},
number = {},
pages = {106497},
doi = {10.1016/j.prevetmed.2025.106497},
pmid = {40056564},
issn = {1873-1716},
abstract = {The dairy industry in developing countries is often associated with inappropriate use of antibiotics and the subsequent contamination of the environment with co-selectors of antibiotic resistance. However, the specific factors in dairy farm environments that influence antibiotic resistance levels and the subsequent exposure risks to farm workers are unknown. We examined the link between the infrastructure and operations of the dairy farm and the antibiotic resistance potential in India, which is the highest producer and consumer of dairy products globally. We sampled sixteen dairy farms in the Dehradun district, India, that varied in their herd size, infrastructure, and operational features during winter, summer, and monsoon. We collected samples of dung, manure, wastewater, manure-amended, and control soil from these farms. We quantified six antibiotic resistance genes (ARGs) (sul1, sul2, parC, mcr5, ermF, and tetW), an integron integrase gene cassette (intI1), and 16S rRNA gene copies as an indicator for total bacterial count. We observed that the infrastructure and the operations of the dairy farms were significantly associated with antibiotic resistance potential in the dairy environment. For example, with increased ventilation and exposure to external weather, the levels of sul2 (x͂=10[-1.63]) and parC (x͂=10[-4.24]) in manure increased. When farmers administered antibiotics without veterinary consultation, the relative levels of intI1 (x͂=10[-2.36]), sul2 (x͂=10[-1.58]), and tetW (x͂=10[-3.04]) in manure were lower than the cases where professional advice was sought. Small-scale farms had lower relative ARG levels than medium- and large-scale farms, except for mcr5 (x͂=10[-3.98]) in wastewater. In different sample types, the relative ARG levels trended as manure-amended soil (x͂=10[-2.34]) > wastewater (x͂=10[-2.90])> manure (x͂=10[-3.39])> dung (x͂=10[-2.54]). ARGs correlated with the marker for horizontal gene transfer, intI1, which exacerbates overall antibiotic resistance levels. Exposure assessment showed that the agriculture farm workers working in manure-amended agriculture farms are exposed to higher antibiotic resistance potential than dairy farm workers, who manually handle dung. Our study showed that the link between the dairy infrastructure (ventilation and floor type) and operations (scale of operation and veterinary consultation) and the antibiotic resistance potential in the dairy farm environment was statistically significant. This knowledge paves the way for designing interventions that can minimize the antibiotic resistance potential on dairy farms and in affected environments and thus reduce the public health burden of antibiotic-resistant infections in the dairy industry and dairy workers in India.},
}

@article {pmid40056523,
year = {2025},
author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y},
title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137804},
doi = {10.1016/j.jhazmat.2025.137804},
pmid = {40056523},
issn = {1873-3336},
abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.},
}

@article {pmid40056518,
year = {2025},
author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S},
title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137870},
doi = {10.1016/j.jhazmat.2025.137870},
pmid = {40056518},
issn = {1873-3336},
abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.},
}

@article {pmid40052062,
year = {2025},
author = {Liu, Y and Liu, L and Wang, X and Shao, M and Wei, Z and Wang, L and Li, B and Li, C and Luo, X and Li, F and Zheng, H},
title = {Microplastics enhance the prevalence of antibiotic resistance genes in mariculture sediments by enriching host bacteria and promoting horizontal gene transfer.},
journal = {Eco-Environment & Health},
volume = {4},
number = {1},
pages = {100136},
pmid = {40052062},
issn = {2772-9850},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) pose significant challenges to the One Health framework due to their intricate and multifaceted ecological and environmental impacts. However, the understanding of how MP properties influence ARG prevalence in mariculture sediments remains limited. Herein, the polystyrene (PS) and polyvinyl chloride (PVC) MPs with different sizes (20-120 μm and 0.5-2.0 mm) were selected to evaluate their impacts and underlying mechanisms driving ARGs dissemination. The results showed that PS and PVC MPs increased the relative abundance of ARGs by 1.41-2.50-fold and 2.01-2.84-fold, respectively, compared with control, particularly high-risk genes. The polymer type effect was identified as more influential than the size effect in driving the sediment resistome evolution. PVC shifted the microbial community assembly from stochastic to deterministic processes, thus enriching ARG host pathogens. Furthermore, the highly hydrophobic PS not only recruited the host bacteria colonization but also facilitated ARG exchange within the plastisphere. The exogenous additives released by PVC (e.g., heavy metals, bisphenol A, and tridecyl ester) and the particles synergistically promoted ARG conjugative transfer by inducing oxidative stress and enhancing cell membrane permeability. These findings revealed how MPs characteristics facilitated the spread of ARGs in marine benthic ecosystems, underscoring the importance of mitigating MPs pollution to maintain mariculture ecosystem health, prevent zoonotic diseases, and balance global mariculture with ecological health.},
}

@article {pmid40051841,
year = {2025},
author = {Vivekanandan, KE and Kumar, PV and Jaysree, RC and Rajeshwari, T},
title = {Exploring molecular mechanisms of drug resistance in bacteria and progressions in CRISPR/Cas9-based genome expurgation solutions.},
journal = {Global medical genetics},
volume = {12},
number = {2},
pages = {100042},
pmid = {40051841},
issn = {2699-9404},
abstract = {Antibiotic resistance in bacteria is a critical global health challenge, driven by molecular mechanisms such as genetic mutations, efflux pumps, enzymatic degradation of antibiotics, target site modifications, and biofilm formation. Horizontal gene transfer (HGT) further accelerates the spread of resistance genes across bacterial populations. These mechanisms contribute to the emergence of multidrug-resistant (MDR) strains, rendering conventional antibiotics ineffective. Recent advancements in CRISPR/Cas9-based genome editing offer innovative solutions to combat drug resistance. CRISPR/Cas9 enables precise targeting of resistance genes, facilitating their deletion or inactivation, and provides a potential method to eliminate resistance-carrying plasmids. Furthermore, phage-delivered CRISPR systems show promise in selectively killing resistant bacteria while leaving susceptible strains unaffected. Despite challenges such as efficient delivery, off-target effects, and potential bacterial resistance to CRISPR itself, ongoing research and technological innovations hold promise for using CRISPR-based antimicrobials to reverse bacterial drug resistance and develop more effective therapies. These abstract highlights the molecular mechanisms underlying bacterial drug resistance and explores how CRISPR/Cas9 technology could revolutionize treatment strategies against resistant pathogens.},
}

@article {pmid40051073,
year = {2025},
author = {Saranya, SV and Prathiviraj, R and Chellapandi, P},
title = {Mobilome-Mediated Speciation: Genomic Insights Into Horizontal Gene Transfer in Methanosarcina.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70013},
doi = {10.1002/jobm.70013},
pmid = {40051073},
issn = {1521-4028},
support = {//The authors express their gratitude to the Science and Engineering Research Board, Ministry of Science and Technology, Government of India (EEQ/2020/000095), and RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS) for their financial support. Funded by Department of Science and Technology, Ministry of Science and Technology, India, Science and Engineering Research Board, Grant/Award Number EEQ/2020/000095. Ministry of Education, India, Rashtriya Uchchatar Shiksha Abhiyan, RUSA 2.0: Biological Science, Government of India (12/BDU/RUSA/TRP/BS)./ ; },
abstract = {Speciation in prokaryotes is often driven by complex genetic exchanges such as horizontal gene transfer (HGT), which facilitates genomic divergence and adaptation. In this study, we inferred the evolutionary transitions of the mobilome (plasmids, transposons, and phages) between Methanosarcina and bacteria in driving speciation within the Methanosarcina genus. By conducting evolutionary and phylogenetic analyses of Methanosarcina acetivorans, M. barkeri, M. mazei, and M. siciliae, we identified key mobilome elements acquired through HGT from distantly related bacterial species. These mobile genetic elements have shaped genomic plasticity, enabling Methanosarcina to adapt to diverse environmental niches and potentially facilitating lineage divergence. The acquisition of mobilome-associated genes involved in antibiotic resistance, DNA repair, and stress responses suggests their significant role in the ecological speciation of Methanosarcina. Overall, we hypothesized that their mobile genetic element might have been acquired from distantly related bacteria by HGT and subsequently established as new functional homologs in the present lineage. This study provides insight into how mobilome-mediated gene flow contributes to genomic divergence and speciation within microbial populations, highlighting the broader significance of mobilome in microbial evolution and speciation processes.},
}

@article {pmid40051064,
year = {2025},
author = {Saranya, SV and Chellapandi, P},
title = {Convergent Evolution of Coenzyme Metabolism in Methanosarcina mazei: Insights Into Primitive Life and Metabolic Adaptations.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70015},
doi = {10.1002/jobm.70015},
pmid = {40051064},
issn = {1521-4028},
support = {//This paper was supported by Science and Engineering Research Board, Ministry of Science and Technology, Government of India and RUSA 2.0: Biological Science, Government of India./ ; },
abstract = {The convergent evolution of coenzyme metabolism in methanogens provides critical insights into primitive life and metabolic adaptations. This study investigated the molecular evolution and functional dynamics of eight coenzymes and cofactors in Methanosarcina mazei, a model methanogen essential for methane production and energy conservation in anaerobic environments. Phylogenetic and genetic diversity analyses of the 706 protein sequences revealed conserved evolutionary trajectories interspersed with lineage-specific adaptations driven by gene duplication, horizontal gene transfer, and selective pressures. Key findings included the purifying selection of methanofuran (Tajima's D = -2.9589) and coenzyme A (Tajima's D = -2.8555), indicating the conservation of critical metabolic functions. The coenzyme B biosynthesis pathway showed balanced selection (Tajima's D = 2.38602), reflecting its evolutionary plasticity. Phylogenetic analyses linked coenzyme F420 biosynthetic enzymes closely to Methanosarcina horonobensis, while coenzyme F430 enzymes highlighted prokaryotic specialization distinct from their eukaryotes. Coenzyme M biosynthetic genes have demonstrated unique evolutionary connections with species across domains, such as Methanothermobacter thermautotrophicus and Gekko japonicus, emphasizing their broad adaptive significance. These evolutionary trajectories reveal how M. mazei optimized its metabolic pathways to thrive in extreme anaerobic environments, bridging ancient metabolic systems from the Last Universal Common Ancestor with contemporary ecological adaptations.},
}

@article {pmid40050512,
year = {2025},
author = {Chacón, RD and Ramírez, M and Suárez-Agüero, D and Pineda, APA and Astolfi-Ferreira, CS and Ferreira, AJP},
title = {Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry.},
journal = {Current microbiology},
volume = {82},
number = {4},
pages = {173},
pmid = {40050512},
issn = {1432-0991},
support = {Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; fellowship 1D//Conselho Nacional de Pesquisa e Desenvolvimento Tecnológico/ ; },
mesh = {Animals ; Brazil ; *Salmonella/genetics/drug effects/classification/pathogenicity ; *Poultry/microbiology ; *Salmonella Infections, Animal/microbiology ; Virulence/genetics ; *Anti-Bacterial Agents/pharmacology ; *Serogroup ; *Poultry Diseases/microbiology ; *Genome, Bacterial ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Phylogeny ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Genomics ; },
abstract = {Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.},
}

Animals
Brazil
*Salmonella/genetics/drug effects/classification/pathogenicity
*Poultry/microbiology
*Salmonella Infections, Animal/microbiology
Virulence/genetics
*Anti-Bacterial Agents/pharmacology
*Serogroup
*Poultry Diseases/microbiology
*Genome, Bacterial
*Virulence Factors/genetics
*Drug Resistance, Bacterial/genetics
Phylogeny
Whole Genome Sequencing
Microbial Sensitivity Tests
Genomics

@article {pmid39826686,
year = {2025},
author = {Fu, Y and Morris, FC and Pereira, SC and Kostoulias, X and Jiang, Y and Vidor, C and Williams, G and Srikhanta, Y and Macesic, N and Yu, Y and Lyras, D and Peleg, AY},
title = {Mechanisms of blaIMP-4 dissemination across diverse carbapenem-resistant clinical isolates.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {189-194},
doi = {10.1016/j.jgar.2025.01.003},
pmid = {39826686},
issn = {2213-7173},
mesh = {*Plasmids/genetics ; *beta-Lactamases/genetics/metabolism ; Humans ; *Carbapenems/pharmacology ; *Microbial Sensitivity Tests ; *Acinetobacter/genetics/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; Klebsiella/genetics/drug effects/enzymology ; Enterobacter/genetics/drug effects/isolation & purification/enzymology ; Bacterial Proteins/genetics/metabolism ; Conjugation, Genetic ; Serratia marcescens/genetics/drug effects/enzymology/isolation & purification ; Victoria ; DNA Transposable Elements ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVE: The IMP-4 carbapenemase is an endemic cause of carbapenem resistance in the Asia-Pacific region. Our aim was to determine the dissemination mechanism of the blaIMP-4 gene.

METHODS: Twelve representative Australian IMP-4 clinical isolates from The Alfred Hospital (Victoria, Australia) were characterised using antimicrobial susceptibility testing, with their genome and plasmid assemblies analysed. The conjugation efficiencies of different plasmids were investigated using filter mating with four recipient strains across two species.

RESULTS: Selected IMP-4 isolates included six species and four genera (Enterobacter, Klebsiella, Serratia, and Acinetobacter), whereby isolates of the same species belonged to the same sequence type and were closely related. Four IMP-4 plasmid types were noted: IncHI2A types 1 and 2 (Klebsiella spp. and Enterobacter hormaechei, respectively), IncC (Serratia marcescens and Klebsiella pneumoniae), and a novel type in Acinetobacter pittii. Sequence homology was observed across all plasmids at the blaIMP-4 location, termed Region I, with IS26 on IncHI2A, and IS5075 and Tn3 resistance gene cassettes present on IncC plasmids. Genomic rearrangements mediated by IS26 or Tn3 and IS5075 were identified in Region I of plasmids from the same Inc type. The plasmids of each Inc type were capable of conjugative transfer with varying efficiency. IncH12A plasmids and K. pneumoniae IncC displayed higher transfer efficiencies than other plasmids examined in this study when using the recipient E. coli strain J53 (with conjugation efficiencies of 1.17×10[-2] to 5.02×10[-5], P < 0.001).

CONCLUSIONS: Clonal spread, Inc type, homologous region, and insertion sequences are important mobility factors in the dissemination and evolution of blaIMP-4 plasmids.},
}

*Plasmids/genetics
*beta-Lactamases/genetics/metabolism
Humans
*Carbapenems/pharmacology
*Microbial Sensitivity Tests
*Acinetobacter/genetics/drug effects/isolation & purification
Anti-Bacterial Agents/pharmacology
Klebsiella pneumoniae/genetics/drug effects/isolation & purification
Klebsiella/genetics/drug effects/enzymology
Enterobacter/genetics/drug effects/isolation & purification/enzymology
Bacterial Proteins/genetics/metabolism
Conjugation, Genetic
Serratia marcescens/genetics/drug effects/enzymology/isolation & purification
Victoria
DNA Transposable Elements
Gene Transfer, Horizontal

@article {pmid39701446,
year = {2025},
author = {Long, X and Lin, F and Tang, B and Miao, F and Li, Z and Shen, Y and Yang, H and Ma, J},
title = {Acinetobacter indicus Coharboring Tet(X6) and blaNDM-1 Isolated From Slaughterhouse Waste.},
journal = {Journal of global antimicrobial resistance},
volume = {41},
number = {},
pages = {1-7},
doi = {10.1016/j.jgar.2024.12.004},
pmid = {39701446},
issn = {2213-7173},
mesh = {*beta-Lactamases/genetics ; *Acinetobacter/genetics/drug effects/isolation & purification ; *Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Abattoirs ; Animals ; Drug Resistance, Multiple, Bacterial/genetics ; Plasmids/genetics ; DNA Transposable Elements ; Whole Genome Sequencing ; Acinetobacter Infections/microbiology ; Gene Transfer, Horizontal ; },
abstract = {OBJECTIVES: Acinetobacter indicus is an important pathogen of nosocomial infection. The purpose of this study was to analyze the resistance and transmission of A. indicus strain AIBD14 isolated from slaughterhouse environment.

METHODS: A total of 96 environmental samples were collected from slaughterhouse. The antimicrobial susceptibility test was carried out by microbroth dilution method and E-test. Whole genome sequencing and bioinformatics analysis of the AIBD14 were performed, then S1-PFGE and southern blot verified the location of blaNDM-1 and tet(X6).

RESULTS: The AIBD14 is resistant to meropenem but susceptibility to tigecycline, and coharboring blaNDM-1 and tet(X6). The blaNDM-1 is located on the pAIBD14-NDM-1 that cannot be transferred by conjugation. Specifically, blaNDM-1 is located on the transposon Tn125, and blaNDM-1 can be transferred to other species with the help of transposon. The genetic background of blaNDM-1 is "ISAba125-blaNDM-1-bleMEL-dsbD-cutA-groES-groEL-insE-ISAba125". pAIBD14-NDM-1 is classified into the GR31 plasmid based on the homology of the repB. Meanwhile, there are two XerC/D-like binding sites on the plasmid, which can mediate the transfer of resistance genes. The tet(X6) gene is located on the chromosome of AIBD14, its downstream is accompanied by the neglected macrolide resistance gene estT, and there is a single copy of the insertion element ISCR2 around tet(X6) as the genetic background "ISAba4-IS3-hp-hp-tet(X6)-estT-guaA-ISCR2".

CONCLUSIONS: This is the first report of the coexistence of tet(X6) and blaNDM-1 in the A. indicus, and it has the risk of horizontal transfer across multiple species. So strict monitoring the multiple-resistant bacteria in the industrial chain is necessary based on the "One Heath".},
}

*beta-Lactamases/genetics
*Acinetobacter/genetics/drug effects/isolation & purification
*Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
*Abattoirs
Animals
Drug Resistance, Multiple, Bacterial/genetics
Plasmids/genetics
DNA Transposable Elements
Whole Genome Sequencing
Acinetobacter Infections/microbiology
Gene Transfer, Horizontal

@article {pmid40048953,
year = {2025},
author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y},
title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178989},
doi = {10.1016/j.scitotenv.2025.178989},
pmid = {40048953},
issn = {1879-1026},
abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.},
}

@article {pmid40045656,
year = {2025},
author = {Zhang, M and Zhao, X and Ren, X},
title = {Research Progress on the Mechanisms of Algal-Microorganism Symbiosis in Enhancing Large-Scale Lipid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c11580},
pmid = {40045656},
issn = {1520-5118},
abstract = {Microalgae, characterized by their exceptional lipid content, rapid growth, and robust adaptability, represent a promising biological resource. In natural and engineered ecosystems, microalgae engage in intricate symbiotic relationships with diverse microorganisms, a dynamic interplay essential for ecological resilience and metabolic optimization. This review examines the role of symbiotic microorganisms in microalgal growth and lipid accumulation, with particular emphasis on the biological regulatory mechanisms that govern these processes. These include nutrient exchange, phytohormone-mediated growth stimulation, cofactors, and quorum-sensing-driven community coordination. The review highlights how these microbial interactions facilitate optimal lipid production by enhancing metabolic pathways, thereby improving the efficiency of lipid accumulation in microalgae. Furthermore, the review investigates horizontal gene transfer as an evolutionary driver that fortifies algal-microbial consortia against environmental stressors, enabling robust performance in fluctuating conditions. The integration of these biological insights holds transformative potential for advancing next-generation bioenergy platforms, where algal-microbial systems could play a pivotal role in enhancing biofuel production, wastewater treatment, and sustainable agriculture.},
}

@article {pmid40043931,
year = {2025},
author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ},
title = {Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121282},
doi = {10.1016/j.envres.2025.121282},
pmid = {40043931},
issn = {1096-0953},
abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.},
}

@article {pmid40038805,
year = {2025},
author = {Diricks, M and Maurer, FP and Dreyer, V and Barilar, I and Utpatel, C and Merker, M and Wetzstein, N and Niemann, S},
title = {Genomic insights into the plasmidome of non-tuberculous mycobacteria.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {19},
pmid = {40038805},
issn = {1756-994X},
support = {2004//German Cystic Fibrosis Association Mukoviszidose e.V/ ; EXC 2167//The Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy Precision Medicine in Inflammation/ ; },
mesh = {*Plasmids/genetics ; *Nontuberculous Mycobacteria/genetics ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Phylogeny ; Mycobacterium Infections, Nontuberculous/microbiology ; },
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are a diverse group of environmental bacteria that are increasingly associated with human infections and difficult to treat. Plasmids, which might carry resistance and virulence factors, remain largely unexplored in NTM.

METHODS: We used publicly available complete genome sequence data of 328 NTM isolates belonging to 125 species to study gene content, genomic diversity, and clusters of 196 annotated NTM plasmids. Furthermore, we analyzed 3755 draft genome assemblies from over 200 NTM species and 5415 short-read sequence datasets from six clinically relevant NTM species or complexes including M. abscessus, M. avium complex, M. ulcerans complex and M. kansasii complex, for the presence of these plasmids.

RESULTS: Between one and five plasmids were present in approximately one-third of the complete NTM genomes. The annotated plasmids varied widely in length (most between 10 and 400 kbp) and gene content, with many genes having an unknown function. Predicted gene functions primarily involved plasmid replication, segregation, maintenance, and mobility. Only a few plasmids contained predicted genes that are known to confer resistance to antibiotics commonly used to treat NTM infections. Out of 196 annotated plasmid sequences, 116 could be grouped into 31 clusters of closely related sequences, and about one-third were found across multiple NTM species. Among clinically relevant NTM, the presence of NTM plasmids showed significant variation between species, within (sub)species, and even among strains within (sub)lineages, such as dominant circulating clones of Mycobacterium abscessus.

CONCLUSIONS: Our analysis demonstrates that plasmids are a diverse and heterogeneously distributed feature in NTM bacteria. The frequent occurrence of closely related putative plasmid sequences across different NTM species suggests they may play a significant role in NTM evolution through horizontal gene transfer at least in some groups of NTM. However, further in vitro investigations and access to more complete genomes are necessary to validate our findings, elucidate gene functions, identify novel plasmids, and comprehensively assess the role of plasmids in NTM.},
}

*Plasmids/genetics
*Nontuberculous Mycobacteria/genetics
*Genome, Bacterial
*Genomics/methods
Humans
Phylogeny
Mycobacterium Infections, Nontuberculous/microbiology

@article {pmid40036335,
year = {2025},
author = {Bergman, S and Birk, C and Holmqvist, E},
title = {ProQ prevents mRNA degradation through inhibition of poly(A) polymerase.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
doi = {10.1093/nar/gkaf103},
pmid = {40036335},
issn = {1362-4962},
support = {2016-03656//Swedish Research Council/ ; ICA16-0021//Swedish Foundation for Strategic Research/ ; },
mesh = {*Salmonella typhimurium/genetics/pathogenicity ; *Bacterial Proteins/metabolism/genetics ; *Polynucleotide Adenylyltransferase/metabolism/genetics ; *Sigma Factor/metabolism/genetics ; *RNA Stability ; *RNA, Messenger/metabolism/genetics ; *Biofilms/growth & development ; *Gene Expression Regulation, Bacterial ; RNA-Binding Proteins/metabolism/genetics ; 3' Untranslated Regions/genetics ; Polyadenylation ; },
abstract = {The RNA-binding protein ProQ interacts with many transcripts in the bacterial cell. ProQ binding is associated with increased messenger RNA (mRNA) levels, but a mechanistic explanation for this effect has been lacking. In Salmonella Typhimurium, ProQ affects key traits associated with infection, including motility and intracellular survival. However, the direct links between ProQ activity and these phenotypes are not well understood. Here, we demonstrate that ProQ promotes biofilm formation, another virulence-associated phenotype. This effect is strictly dependent on sigma factor RpoS. ProQ increases both RpoS protein and rpoS mRNA levels, but neither affects rpoS transcription nor translation. The rpoS mRNA is a ProQ target, and expression of the rpoS 3'UTR alone is strongly dependent on ProQ. RpoS expression becomes independent of ProQ in strains lacking poly(A) polymerase I (PAPI), indicating that ProQ protects against 3' end-dependent decay. Indeed, purified ProQ inhibits PAPI-mediated polyadenylation at RNA 3' ends. Finally, PAPI is required for ProQ's effect on expression of genes involved in biofilm, motility, osmotic stress, and virulence, indicating that inhibition of polyadenylation is a general function of ProQ.},
}

*Salmonella typhimurium/genetics/pathogenicity
*Bacterial Proteins/metabolism/genetics
*Polynucleotide Adenylyltransferase/metabolism/genetics
*Sigma Factor/metabolism/genetics
*RNA Stability
*RNA, Messenger/metabolism/genetics
*Biofilms/growth & development
*Gene Expression Regulation, Bacterial
RNA-Binding Proteins/metabolism/genetics
3' Untranslated Regions/genetics
Polyadenylation

@article {pmid40035762,
year = {2025},
author = {Raymond, JA},
title = {A horizontally transferred bacterial gene aids the freezing tolerance of Antarctic bdelloid rotifers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2421910122},
doi = {10.1073/pnas.2421910122},
pmid = {40035762},
issn = {1091-6490},
support = {OPP-9814294//National Science Foundation (NSF)/ ; OPP-088000//National Science Foundation (NSF)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Freezing ; Animals ; *Rotifera/genetics ; Genes, Bacterial ; Antifreeze Proteins/genetics/metabolism ; },
abstract = {Bdelloid rotifers are well known for their abilities to survive long periods of freezing as well as acquire foreign genes. Recently sequenced genomes of some bdelloid rotifers in England were found to encode several proteins similar to ice-binding proteins (IBPs) that are usually associated with freeze-thaw tolerance. Here, I describe bdelloid rotifers inhabiting an algal patch in Antarctica that have multiple homologs of these genes. Structures of the proteins predicted by AlphaFold show that they are well designed for ice-binding and a recombinant protein made for one of them showed strong ice-binding activity. The existence of multiple copies of these proteins is another characteristic of IBPs. Furthermore, multiple bdelloid rotifers in the algal patch were revived in less than an hour after storage at -25 °C for 24 y, an apparent record for laboratory-controlled studies. Several characteristics of these genes point to bacteria as their source: sequence homology, absence of introns, and a structural peculiarity so far found only in bacteria. The remarkable freezing tolerance of bdelloid rotifers can thus be at least partially attributed to horizontally acquired bacterial genes encoding IBPs.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Freezing
Animals
*Rotifera/genetics
Genes, Bacterial
Antifreeze Proteins/genetics/metabolism

@article {pmid40035521,
year = {2025},
author = {Kanakapura Sundararaj, B and Goyal, M and Samuelson, J},
title = {Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0094824},
doi = {10.1128/msphere.00948-24},
pmid = {40035521},
issn = {2379-5042},
abstract = {Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.},
}

@article {pmid40032822,
year = {2025},
author = {Biller, SJ and Ryan, MG and Li, J and Burger, A and Eppley, JM and Hackl, T and DeLong, EF},
title = {Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2126},
pmid = {40032822},
issn = {2041-1723},
support = {OCE-2049004//National Science Foundation (NSF)/ ; OCE-2304066//National Science Foundation (NSF)/ ; 917971//Simons Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Extracellular Vesicles/metabolism ; *Ecosystem ; Seawater/microbiology/virology ; Interspersed Repetitive Sequences ; Viruses/genetics/metabolism ; },
abstract = {Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). The information enclosed within these structures represents a substantial portion of the HGT potential available in planktonic ecosystems, but whether some genes might be preferentially transported through one type of nanoparticle versus another is unknown. Here we use long-read sequencing to compare the genetic content of EVs and VLPs from the oligotrophic North Pacific. Fractionated EV-enriched and VLP-enriched subpopulations contain diverse DNA from the surrounding microbial community, but differ in their capacity and encoded functions. The sequences carried by both particle types are enriched in mobile genetic elements (MGEs) as compared with other cellular chromosomal regions, and we highlight how this property enables novel MGE discovery. Examining the Pelagibacter mobilome reveals >7200 distinct chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.},
}

*Gene Transfer, Horizontal
*Extracellular Vesicles/metabolism
*Ecosystem
Seawater/microbiology/virology
Interspersed Repetitive Sequences
Viruses/genetics/metabolism

@article {pmid40032228,
year = {2025},
author = {Jiang, Z and Zeng, J and Wang, X and Yu, H and Yue, L and Wang, C and Chen, F and Wang, Z},
title = {Biodegradable microplastics and dissemination of antibiotic resistance genes: an undeniable risk associated with plastic additives.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125952},
doi = {10.1016/j.envpol.2025.125952},
pmid = {40032228},
issn = {1873-6424},
abstract = {Biodegradable plastics (BDPs) represent a promising alternative to conventional plastics; however, the release of microplastics (MPs) during degradation necessitates an urgent investigation into their biological effects. The potential risks associated with MPs and additives released from BDPs, particularly in facilitating the dissemination of antibiotic resistance genes (ARGs), remain largely unknown. This study aims to investigate the effects of polylactic acid (PLA) MPs and their common plasticizer, dibutyl phthalate (DBP), on the horizontal gene transfer (HGT) of ARGs using conjugative transfer and transformation model systems. The viability of Escherichia coli (E. coli) cells after exposure to PLA MPs (0.01, 0.1, 1, and 10 mg L[-1]), DBP (0.01, 0.1, 1, and 10 μg L[-1]) alone, or in combination (1 mg L[-1] PLA MPs + 1 μg L[-1]DBP) remained unaffected. Exposure to PLA MPs at environmentally relevant concentrations did not promote the HGT of ARGs. However, the addition of DBP significantly enhanced the transfer frequency by 1.5-1.8 folds compared to exposure to PLA MPs alone. The accelerated dissemination of ARGs was primarily attributed to the elevated levels of reactive oxygen species (by 26.2%), increased membrane permeability (by 19.4%), and the up-regulation of genes involved in mating pair formation (by 1.6-3.8 folds) and DNA translocation (by 1.5-3.4 folds). These findings underscore the critical role of additives and highlight the potential accumulative effects associated with prolonged exposure to high concentrations of PLA MPs, which should be considered for a comprehensive risk assessment of BDPs.},
}

@article {pmid40029705,
year = {2025},
author = {Hong, J and Xue, W and Wang, T},
title = {Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40029705},
issn = {2050-084X},
support = {12401660//National Natural Science Foundation of China/ ; HSE499011086//Shenzhen Institue of Synthetic Biology Scientific Research Program/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Bacteria/genetics ; Models, Theoretical ; Microbial Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Ecosystem ; },
abstract = {Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.},
}

*Gene Transfer, Horizontal
*Microbiota/genetics
Bacteria/genetics
Models, Theoretical
Microbial Interactions/genetics
Interspersed Repetitive Sequences/genetics
Ecosystem

@article {pmid40027803,
year = {2025},
author = {Christman, ND and Dalia, AB},
title = {The molecular basis for DNA-binding by competence T4P is distinct in Gram-positive and Gram-negative species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.17.638644},
pmid = {40027803},
issn = {2692-8205},
abstract = {UNLABELLED: Competence type IV pili (T4P) are bacterial surface appendages that facilitate DNA uptake during horizontal gene transfer by natural transformation. These dynamic structures actively extend from the cell surface, bind to DNA in the environment, and then retract to import bound DNA into the cell. Competence T4P are found in diverse Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA-binding by diderm competence T4P has been the recent focus of intensive study, relatively little is known about DNA-binding by monoderm competence T4P. Here, we use Streptococcus pneumoniae as a model system to address this question. Competence T4P likely bind to DNA via a tip-associated complex of proteins called minor pilins, and recent work highlights a high degree of structural conservation between the minor pilin tip complexes of monoderm and diderm competence T4P. In diderms, positively charged residues in one minor pilin, FimT, are critical for DNA-binding. We show that while these residues are conserved in ComGD, the FimT homolog of monoderms, they only play a minor role in DNA uptake for natural transformation. Instead, we find that two-positively charged residues in the neighboring minor pilin, ComGF (the PilW homolog of monoderms), play the dominant role in DNA uptake for natural transformation. Furthermore, we find that these residues are conserved in other monoderms, but not diderms. Together, these results suggest that the molecular basis for DNA-binding has either diverged or evolved independently in monoderm and diderm competence T4P.

AUTHOR SUMMARY: Diverse bacteria use extracellular structures called competence type IV pili (T4P) to take up DNA from their environment. The uptake of DNA by T4P is the first step of natural transformation, a mode of horizontal gene transfer that contributes to the spread of antibiotic resistance and virulence traits in diverse clinically relevant Gram-negative (diderm) and Gram-positive (monoderm) bacterial species. While the mechanism of DNA binding by competence T4P in diderms has been an area of recent study, relatively little is known about how monoderm competence T4P bind DNA. Here, we explore how monoderm competence T4P bind DNA using Streptococcus pneumoniae as a model system. Our results indicate that while monoderm T4P and diderm T4P likely have conserved structural features, the DNA-binding mechanism of each system is distinct.},
}

@article {pmid40027742,
year = {2025},
author = {Tabatabaee, Y and Zhang, C and Arasti, S and Mirarab, S},
title = {Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.20.639320},
pmid = {40027742},
issn = {2692-8205},
abstract = {UNLABELLED: Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT) can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to ILS. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both GDL and ILS. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extends it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for HGT, we show that CASTLES-Pro maintains relatively high accuracy under high rates of random HGT.

CODE AVAILABILITY: CASTLES-Pro is implemented inside the software package ASTER, available at https://github.com/chaoszhang/ASTER .

DATA AVAILABILITY: The datasets and scripts used in this study are available at https://github.com/ytabatabaee/CASTLES-Pro-paper .},
}

@article {pmid40027631,
year = {2025},
author = {Schmidt, H and Raphael, BJ},
title = {The tree labeling polytope: a unified approach to ancestral reconstruction problems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.14.638328},
pmid = {40027631},
issn = {2692-8205},
abstract = {MOTIVATION: Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction - a solution to the small parsimony problem - can be efficiently found using the dynamic programming algorithms of Fitch-Hartigan and Sankoff. Ancestral reconstruction is important in many applications including inferring the routes of metastases in cancer, deriving the transmission history of viruses, determining the direction of cellular differentiation in organismal development, and detecting recombination and horizontal gene transfer in phylogenetic networks. However, most of these applications impose additional global constraints on the reconstructed ancestral states, which break the local structure required in the recurrences of Fitch-Hartigan and Sankoff.

RESULTS: We introduce an alternative, polyhedral approach to ancestral reconstruction problems using the tree labeling polytope , a geometric object whose vertices represent the feasible ancestral labelings of a tree. This framework yields a polynomial-time linear programming algorithm for the small parsimony problem . More importantly, the tree labeling polytope facilitates the incorporation of additional constraints that arise in modern ancestral reconstruction problems. We demonstrate the utility of our approach by deriving mixed-integer programming algorithms with a small number of integer variables and strong linear relaxations for three such problems: the parsimonious migration history problem, the softwired small parsimony problem on phylogenetic networks, and the convex recoloring problem on trees. Our algorithms outperform existing state-of-the-art methods on both simulated and real datasets. For instance, our algorithm scales to trace routes of cancer metastases in trees with thousands of leaves, enabling the analysis of large trees generated by recent single-cell sequencing technologies. On a mouse model of metastatic lung adenocarcinoma, the tree labeling polytope allows us to infer simpler migration histories compared to previous results.

AVAILABILITY: Python implementations of the algorithms provided in this work are available at: github.com/raphael-group/tree-labeling-polytope .},
}

@article {pmid40024690,
year = {2025},
author = {Wajima, T and Tanaka, E and Uchiya, KI},
title = {Unique and Ingenious Mechanisms Underlying Antimicrobial Resistance and Spread of Haemophilus influenzae.},
journal = {Biological & pharmaceutical bulletin},
volume = {48},
number = {3},
pages = {205-212},
doi = {10.1248/bpb.b23-00640},
pmid = {40024690},
issn = {1347-5215},
mesh = {*Haemophilus influenzae/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Haemophilus Infections/drug therapy/microbiology ; *Drug Resistance, Bacterial/genetics ; Animals ; },
abstract = {Antimicrobial resistance (AMR) is a serious global concern. AMR pathogens are found in hospitals and communities. Haemophilus influenzae is a common pathogen associated with community-acquired infections. H. influenzae infections are usually treated with β-lactams, macrolides, and quinolones. However, the drug-resistant strains have emerged. The resistance mechanisms of H. influenzae are complex but are roughly characterized by the acquisition of a mutation in antimicrobial-targeting genes and exogenous resistant genes. Generally, the former cannot be transferred horizontally to a susceptible strain. However, several studies have demonstrated that, in the case of H. influenzae, both the former and the latter can be transferred horizontally. In this review, we provide an overview of the bacterial features and antimicrobial resistance of H. influenzae. We also summarize the unique and ingenious antimicrobial resistance mechanisms used by this pathogen based on the findings of recent studies. These are expected to facilitate the understanding of AMR pathogens in the community and develop strategies to combat infections.},
}

*Haemophilus influenzae/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
*Haemophilus Infections/drug therapy/microbiology
*Drug Resistance, Bacterial/genetics
Animals

@article {pmid40023817,
year = {2025},
author = {Shao, Y and Chen, M and Cai, J and Doi, Y and Chen, M and Wang, M and Zeng, M and Guo, Q},
title = {Cefotaxime-Resistant Neisseria meningitidis Sequence Type 4821 Causing Fulminant Meningitis.},
journal = {Emerging infectious diseases},
volume = {31},
number = {3},
pages = {591-595},
doi = {10.3201/eid3103.241493},
pmid = {40023817},
issn = {1080-6059},
mesh = {Humans ; *Cefotaxime/therapeutic use/pharmacology ; *Neisseria meningitidis/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Child, Preschool ; *Meningitis, Meningococcal/microbiology/drug therapy ; Microbial Sensitivity Tests ; China ; Male ; Drug Resistance, Bacterial ; },
abstract = {We explored the role of commensal Neisseria in the emergence of third-generation cephalosporin-resistant N. meningitidis. Cefotaxime resistance-conferring penA795 was prevalent among commensal Neisseria isolates in Shanghai, China, and was acquired by a serogroup C quinolone-resistant sequence type 4821 N. meningitidis, Nm507, causing fulminant meningitis in an unvaccinated 2-year-old child.},
}

Humans
*Cefotaxime/therapeutic use/pharmacology
*Neisseria meningitidis/genetics/drug effects
*Anti-Bacterial Agents/pharmacology/therapeutic use
Child, Preschool
*Meningitis, Meningococcal/microbiology/drug therapy
Microbial Sensitivity Tests
China
Male
Drug Resistance, Bacterial

@article {pmid40019366,
year = {2025},
author = {Hu, Y and Gong, C and Yang, Z and Han, H and Tian, T and Yang, X and Xie, W and Wang, S and Wu, Q and Zhou, X and Turlings, TCJ and Guo, Z and Zhang, Y},
title = {Functional Divergence of Plant-Derived Thaumatin-Like Protein Genes in Two Closely Related Whitefly Species.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502193},
doi = {10.1002/advs.202502193},
pmid = {40019366},
issn = {2198-3844},
support = {2021YFD1400600//National Key R & D Program of China/ ; GZB20240839//Postdoctoral Fellowship Program of CPSF/ ; Y2023XK15//Central Public-interest Scientific Institution Basal Research Fund/ ; Y2024XK01//Central Public-interest Scientific Institution Basal Research Fund/ ; //Beijing Key Laboratory for Pest Control and Sustainable Cultivation of Vegetables/ ; //Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences/ ; 788949//European Research Council Advanced/ ; CARS-23//Earmarked Fund for China Agriculture Research System/ ; 2024M753572//China Postdoctoral Science Foundation/ ; 32221004//National Natural Science Foundation of China/ ; },
abstract = {The recent discovery that various insects have acquired functional genes through horizontal gene transfer (HGT) has prompted numerous studies into this puzzling and fascinating phenomenon. So far, horizontally transferred genes are found to be functionally conserved and largely retained their ancestral functions. It evidently has not yet been considered that horizontally transferred genes may evolve and can contribute to divergence between species. Here, it is first showed that the genomes of the two widespread and agriculturally important whiteflies Trialeurodes vaporariorum and Bemisia tabaci both contain a plant-derived thaumatin-like protein (TLP) gene, but with highly distinct functions in these closely related pests. In T. vaporariorum, TLP has maintained a function similar to that of the plant donor, acting as an antimicrobial protein to resist fungal infection; but in sharp contrast, in B. tabaci, TLP has evolved into an effector that suppresses plant defense responses. These findings reveal an as-yet undescribed scenario of cross-species functional differentiation of horizontally transferred genes and suggest that the HGT-mediated evolutionary novelty can contribute to ecotypic divergence and even speciation.},
}

@article {pmid40013789,
year = {2025},
author = {Jin, M and Rouxel, O and Quintin, N and Geslin, C},
title = {Molecular piracy in deep-sea hydrothermal vent: phage-plasmid interactions revealed by phage-FISH in Marinitoga piezophila.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0230624},
doi = {10.1128/aem.02306-24},
pmid = {40013789},
issn = {1098-5336},
abstract = {UNLABELLED: Prokaryotes and mobile genetic elements (MGEs, such as viruses and plasmids) interact extensively, leading to horizontal gene transfer (HGT) and consequent microbial evolution and diversity. However, our knowledge of the interactions between MGEs in deep-sea hydrothermal ecosystems is limited. In this study, we adapted a phage-fluorescence in situ hybridization (phage-FISH) approach to visualize and quantify the dynamics of phage-plasmid interactions in an anaerobic, thermophilic deep-sea bacterium, Marinitoga piezophila. Notably, our results revealed that plasmid signals were detected in viral particles released from lysed cells, indicating that mitomycin C not only induced plasmid replication but also its packaging into phage particles. Further analysis of the DNA content in purified virions showed that the phage capsids incorporated plasmid DNA even without induction, and the majority of capsids (up to 70%) preferentially packaged plasmid DNA rather than viral DNA after induction. Therefore, this study provided direct evidence of molecular piracy in the deep-sea hydrothermal ecosystem, highlighting the important roles of selfish MGEs in virus-host interactions and HGT in extreme marine environments.

IMPORTANCE: Deep-sea hydrothermal vents are hotspots for microbes. Several studies revealed that virus-mediated horizontal gene transfer (HGT) in deep-sea hydrothermal vent ecosystems may be crucial to the survival and stability of prokaryotes in these extreme environments. However, little is known about the interaction between viruses and other mobile genetic elements (MGEs, such as plasmids), and how their interactions influence virus-mediated HGT in these ecosystems. In this study, we adapted a phage-fluorescence in situ hybridization approach to directly monitor the dynamics of phage-plasmid-host interactions at the single-cell level in the Marinitoga piezophila model. Interestingly, our results indicate that plasmid DNA could not only be induced by mitomycin C to a great extent but also hijacked viral assembly machinery to facilitate its propagation and spread. Therefore, the data presented here imply that the interaction between the viruses and other MGEs could play profound roles in virus-host interaction and virus-mediated HGT in the deep-sea hydrothermal ecosystem.},
}

@article {pmid40012781,
year = {2025},
author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J},
title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492128},
pmid = {40012781},
issn = {1664-302X},
abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.},
}

@article {pmid39898629,
year = {2025},
author = {Huang, S and Wei, DD and Hong, H and Chen, S and Fan, L-P and Huang, Q-S and Du, F-L and Xiang, T-X and Li, P and Zhang, W and Wan, L-G and Liu, Y},
title = {Capture of mobile genetic elements following intercellular conjugation promotes the production of ST11-KL64 CR-hvKP.},
journal = {Microbiology spectrum},
volume = {13},
number = {3},
pages = {e0134724},
doi = {10.1128/spectrum.01347-24},
pmid = {39898629},
issn = {2165-0497},
support = {82102411, 32370195, 82260403//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/metabolism ; *Klebsiella Infections/microbiology ; *Conjugation, Genetic ; *Plasmids/genetics ; Humans ; *Interspersed Repetitive Sequences ; Virulence/genetics ; Gene Transfer, Horizontal ; Animals ; Whole Genome Sequencing ; Mice ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification ; },
abstract = {UNLABELLED: Sequence type (ST)11 carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) can cause life-threatening infections and is therefore of global concern. Despite its importance, the evolutionary history and mechanism for the emergence of ST11 CR-hvKP are unclear. In recent years, the detection rate of ST11 CR-hvKP has increased in a teaching hospital. Based on its clonal transmission, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. Research had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). This is the first demonstration that plasmid recombination in vitro has led to the formation of ST11 CR-hvKP strains. The clinical setting is a multi-factorial and multi-selection pressure environment that may stimulate the evolution of conjugant strains in the transition period to local strains in the stable period, and surveillance is urgently needed for infection control.

IMPORTANCE: The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) heralded the onset of a new and rapidly worsening public health disaster on a global scale. More attention has been paid to its evolutionary history and mechanism, which currently remains unclear. In this study, a conjugation experiment was performed between a hvKP strain AP8555 and a ST11 CRKP strain, resulting in two ST11 CR-hvKP strains. We had confirmed that the virulence plasmid pAP855 was horizontally transferred to the CRKP strain to form the conjugant S270-Tc, which was recombined by mobile genetic elements to evolve into the conjugant S270-Tc-R. The S270-Tc-R had high virulence, high plasmid stability, and greater adaptability. Interestingly, it had high homology to clinically prevalent ST11 CR-hvKP strains using pulsed-field gel electrophoresis and whole-genome sequencing.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/metabolism
*Klebsiella Infections/microbiology
*Conjugation, Genetic
*Plasmids/genetics
Humans
*Interspersed Repetitive Sequences
Virulence/genetics
Gene Transfer, Horizontal
Animals
Whole Genome Sequencing
Mice
Anti-Bacterial Agents/pharmacology
Carbapenems/pharmacology
Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification

@article {pmid40010677,
year = {2025},
author = {Lapadula, WJ and Cañadas, MG and Ayub, MJ},
title = {Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum.},
journal = {Gene},
volume = {948},
number = {},
pages = {149356},
doi = {10.1016/j.gene.2025.149356},
pmid = {40010677},
issn = {1879-0038},
abstract = {Ribosome-inactivating proteins (RIPs) are rRNA N-glycosylases (EC 3.2.2.22) that depurinate an adenine residue from the conserved alpha-sarcin/ricin loop in rRNA, blocking protein synthesis. In previous research, we demonstrated that whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci), mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti), and flies of Sciaroidea superfamily (e.g., Contarinia nasturtii) acquired these genes via three independent horizontal gene transfer events. The temporal expression profiles analyzed in mosquitoes and flies are consistent with the expected for immune effector molecules of insects. Notably, in A. aegypti, we found that these genes contribute to immunity. In whiteflies, codon analysis suggests that RIP genes have evolved under the influence of natural selection. Public transcriptomic experiments have shown that these genes are expressed in the adult stage of B. tabaci. Despite computational findings supporting RIP genes functionality in whiteflies, no experimental studies have been conducted. Furthermore, there is currently no publicly available RNA-seq data evaluating gene expression throughout ontogeny in the Aleyrodidae family. In this work, we experimentally demonstrated the presence of these foreign genes in the genome of Trialeurodes vaporariorum. We quantified their expression across the life cycle stages of this species and analyzed their untranslated regions. The results obtained contribute to a deeper understanding of the biological roles that these ribotoxin encoding genes may play in whiteflies and other insects.},
}

@article {pmid40010597,
year = {2025},
author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z},
title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {371},
number = {},
pages = {125923},
doi = {10.1016/j.envpol.2025.125923},
pmid = {40010597},
issn = {1873-6424},
abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.},
}

@article {pmid40008406,
year = {2025},
author = {Heida, A and Hamilton, MT and Gambino, J and Sanderson, K and Schoen, ME and Jahne, MA and Garland, J and Ramirez, L and Quon, H and Lopatkin, AJ and Hamilton, KA},
title = {Population Ecology-Quantitative Microbial Risk Assessment (QMRA) Model for Antibiotic-Resistant and Susceptible E. coli in Recreational Water.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07248},
pmid = {40008406},
issn = {1520-5851},
abstract = {Understanding and predicting the role of waterborne environments in transmitting antimicrobial-resistant (AMR) infections are critical for public health. A population ecology-quantitative microbial risk assessment (QMRA) model is proposed to evaluate urinary tract infection (UTI) development due to recreational waterborne exposures to Escherichia coli (E. coli) and antibiotic-resistant extended-spectrum β-lactamase-producing (ESBL) E. coli. The horizontal gene transfer (HGT) mechanism of conjugation and other evolutionary factors were modeled separately in the environment and the gut. Persistence/dilution dominated HGT in the environment; however, HGT highly impacted predicted ESBL populations in the body. Predicted disability life year (DALY) risks from exposure to ESBL E. coli at concentrations consistent with US recreational water criteria were less than the 10[-6] pppy benchmark value but greater than the susceptible E. coli DALY risks associated with a UTI health outcome. However, the prevailing susceptible dose-response relationship may underestimate ESBL risk if HGT rates in vivo approach those reported in vitro. A sensitivity analysis demonstrated that DALY values, E. coli/ESBL concentrations, and exposure parameters were influential on predicted risks. The model is a preliminary tool to begin the expansion of the QMRA paradigm to explore the impacts of evolutionary changes in AMR risk assessment.},
}

@article {pmid40007369,
year = {2025},
author = {Li, S and Liu, Y and Zhang, Y and Huang, P and Bartlam, M and Wang, Y},
title = {Stereoselective behavior of naproxen chiral enantiomers in promoting horizontal transfer of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137692},
doi = {10.1016/j.jhazmat.2025.137692},
pmid = {40007369},
issn = {1873-3336},
abstract = {Antibiotic resistance poses a global threat to public health, with recent studies highlighting the role of non-antibiotic pharmaceuticals in the transmission of antibiotic resistance genes (ARGs). This study provides insights into the comprehensive profile, horizontal gene transfer potential, hosts, and public health risks associated with antibiotic resistomes in river ecosystems exposed to chiral naproxen (NAP). Our findings demonstrate that NAP stress selectively enriches ARGs and mobile genetic elements (MGEs), thereby bolstering bacterial resistance to specific antibiotics. Importantly, the spatial variation of NAP chiral enantiomers influences the enantioselective response of bacterial communities to antibiotics. While (S)-NAP and (R)-NAP exhibit differing degrees of horizontal transfer potential, (S/R)-NAP notably facilitates microbial aggregation and DNA transport via type IV secretion system (T4SS)-related functional genes, promoting the conjugation of sul1. Moreover, (S/R)-NAP promotes the horizontal transfer of ARGs by stimulating ROS production and altering cell membrane permeability. Chiral NAP exposure induces pathogens to acquire ARGs and accelerates the proliferation of Burkholderia. ARG-Rank analysis indicates that the health risk posed by (R)-NAP exposure surpasses that of (S)-NAP, with the highest risk observed when both enantiomers are present. This study elucidates the horizontal transfer and transmission mechanisms of ARGs under chiral NAP stress, underscoring the potential health hazards associated with NAP chiral enantiomers.},
}