@article {pmid40961345,
year = {2025},
author = {Colombi, E and Ghaly, TM and Rajabal, V and Elbourne, LDH and Gillings, M and Tetu, S},
title = {Adaptative and ancient co-evolution of integrons with Xanthomonas genomes.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001503},
pmid = {40961345},
issn = {2057-5858},
mesh = {*Integrons/genetics ; *Xanthomonas/genetics/classification ; Phylogeny ; *Evolution, Molecular ; *Genome, Bacterial ; Gene Transfer, Horizontal ; Integrases/genetics ; },
abstract = {Integrons are genetic elements that facilitate gene acquisition. They have been extensively studied in clinical bacteria, but their evolutionary role in phytopathogens remains underexplored. Here, we analysed complete genomes of Xanthomonas species to investigate the origin, distribution and functional dynamics of integrons in this genus. We found that 93% of genomes harboured integrons. The integron-integrase gene intI was predominantly located downstream of ilvD, indicating an ancestral acquisition of integrons, predating diversification within the genus. Phylogenetic analyses support vertical inheritance of intI, with the exception of rare horizontal gene transfer events, notably in Xanthomonas arboricola. Despite their widespread presence, full-length intI genes and active integron platforms are only retained in some species, especially Xanthomonas campestris, which shows high integron gene cassette variability and functional integron activity. In contrast, species such as Xanthomonas cissicola and Xanthomonas phaseoli exhibit widespread intI inactivation, likely occurring early in their divergence, leading to more stable cassette arrays and conserved integron-associated phenotypes. The number and diversity of genes within cassette arrays varied significantly by species and, to a lesser extent, by the ecological context of plant host cultivation. While most cassettes encoded proteins without a known function, those with annotated roles were associated with stress response mechanism, competitive exclusion and plant-associated functions. Together, our findings demonstrate that integrons in Xanthomonas likely originated from a single ancient acquisition event, preceding genus-wide speciation, and have co-evolved with Xanthomonas pathovars as they adapted to distinct plant hosts.},
}

*Integrons/genetics
*Xanthomonas/genetics/classification
Phylogeny
*Evolution, Molecular
*Genome, Bacterial
Gene Transfer, Horizontal
Integrases/genetics

@article {pmid40961326,
year = {2025},
author = {Nghiem, MN and Bui, DP and Ha, VTT and Tran, HT and Nguyen, DT and Vo, TTB},
title = {Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001500},
pmid = {40961326},
issn = {2057-5858},
mesh = {*Acinetobacter baumannii/genetics/isolation & purification/drug effects/classification/pathogenicity ; Vietnam ; Humans ; *Acinetobacter Infections/microbiology/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Multilocus Sequence Typing ; Phylogeny ; Whole Genome Sequencing ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Genetic Variation ; Polymorphism, Single Nucleotide ; Microbial Sensitivity Tests ; Plasmids/genetics ; Genomic Islands ; },
abstract = {Multidrug-resistant Acinetobacter baumannii poses a significant threat to hospital environments worldwide, including Vietnam. In this study, we conducted whole-genome sequencing on 30 clinical A. baumannii isolates from Hanoi to explore their genomic diversity, antibiotic resistance determinants, virulence factors and mobile genetic elements. Phylogenetic analyses, utilizing both SNP-based and multilocus sequence typing-based approaches, revealed that the isolates clustered into various sequence types (STs). Among these, ST2 and ST571 emerged as the dominant high-risk clones. The ST2 isolates exhibited a wide range of resistance genes, such as bla OXA-23, mph(E), msr(E) and armA. Additionally, they contained mobile genetic elements, including plasmids and AbaR-type resistance islands, which promote horizontal gene transfer. Virulence gene analysis showed the presence of several key determinants like ompA, adeFGH and bfmRS and quorum sensing regulators abaI and abaR, underscoring the strains' potential for persistent colonization and infection. These findings highlight the marked genomic diversity and robust resistance profiles of Vietnamese A. baumannii isolates. The predominance of ST2 and ST571, corresponding to global clones GC2 and GC1, respectively, along with frequent co-occurrence of bla OXA-23 and armA, suggests region-specific features distinct from those reported in other parts of Southeast Asia. This underscores the need for improved surveillance and targeted infection control strategies.},
}

*Acinetobacter baumannii/genetics/isolation & purification/drug effects/classification/pathogenicity
Vietnam
Humans
*Acinetobacter Infections/microbiology/epidemiology
*Drug Resistance, Multiple, Bacterial/genetics
Multilocus Sequence Typing
Phylogeny
Whole Genome Sequencing
Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Genetic Variation
Polymorphism, Single Nucleotide
Microbial Sensitivity Tests
Plasmids/genetics
Genomic Islands

@article {pmid40957209,
year = {2025},
author = {Feng, Y and Jiang, C and Zhang, W and Gong, L and Sun, L},
title = {Single and mixture toxicity effects of legacy and emerging per- and polyfluoroalkyl substances on submerged plants and epiphytic biofilms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139862},
doi = {10.1016/j.jhazmat.2025.139862},
pmid = {40957209},
issn = {1873-3336},
abstract = {Although per- and polyfluoroalkyl substances (PFASs), often referred to as "forever chemicals," pose persistent threats to aquatic ecosystems, the effects of multiple PFAS types on submerged macrophyte-biofilm symbiotic systems remain poorly understood. In this study, we systematically investigated the impacts of single and combined exposures to both legacy and emerging PFAS on submerged macrophytes, biofilms, and associated microbial risks. Our results show that the growth of Vallisneria natans was inhibited under both single and mixed PFAS stress. Photosynthetic performance and nutrient uptake in V. natans were variably affected depending on the PFAS type. Emerging PFAS were more likely to induce oxidative stress, with malondialdehyde content increasing by 36.7 % under hexafluoropropylene oxide dimer acid exposure. Notably, PFAS stress significantly altered biofilm morphology and microbial community composition, including enrichment of several human bacterial pathogens. Additionally, PFAS exposure promoted the enrichment of antibiotic resistance genes (ARGs), and the increased abundance of mobile genetic elements suggested a higher potential for horizontal gene transfer. Co-occurrence network analysis further revealed that potential ARG hosts were affected under PFAS stress.},
}

@article {pmid40957078,
year = {2025},
author = {Hernandez-Aranda, VA and Jarquin-Galvez, R and Aguilar-Benitez, G and Vega-Manriquez, DX and Vallejo-Pérez, MR and Escoto-Rodriguez, M and Winkler, R and Lara-Avila, JP},
title = {In silico analysis of secreted proteins via Sec- and Tat-pathways of Clavibacter spp. unravels functional diversity related to plant host range.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2025-0037},
pmid = {40957078},
issn = {1480-3321},
abstract = {Clavibacter genus comprises phytopathogenic and non-phytopathogenic species in a range of plant hosts. We applied structural and functional approaches for comparative genomics to unveil the adaptation of Clavibacter to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that C. tessallarius, C. zhangzhiyongii, C. capcisi, C. phaseoli depicted the more divergent species. Notably, C. nebraskensis, C. insidiosus, C. sepedonicus, Clavibacter sp. A6099, C. californiensis, and C. michiganensis formed a recent monophyletic clade. A synteny degree and genome rearrangements were noted. The functional approach based on prediction-annotation of secreted proteins via Sec and Tat pathways, and the prediction of metabolite biosynthetic potential. Regarding to Sec- and Tat-secreted proteins, we focused on carbohydrate-active enzymes (CAZymes) and expansins. The repertoire of secreted CAZymes exhibited variation related to taxonomy of Clavibacter. The predicted expansins harbored domain variability, related to horizontal gene transfer. A heterogeneous distribution-conservation of biosynthetic genetic clusters (BGCs) regarding Clavibacter phylogeny was observed. Our results suggested that farm practices of plant hosts likely influence the evolutive history of Clavibacter spp. Furthermore, Sec-, Tat-mediated secreted proteins and metabolite diversity may underpin plant-Clavibacter interactions. Biological knowledge drives sustainable strategies aimed to control plant diseases caused by Clavibacter spp.},
}

@article {pmid40956426,
year = {2025},
author = {Roy, MK and Bhattacharjee, A and Singh, AK},
title = {Bacterial type IV secretion systems and spread of antimicrobial resistance: a study of potential inhibitors to T4SS-based resistance spread.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {263},
pmid = {40956426},
issn = {1432-072X},
support = {OLP-2403 and OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; },
mesh = {*Type IV Secretion Systems/metabolism/genetics/antagonists & inhibitors ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Gram-Negative Bacteria/drug effects/genetics/metabolism ; Bacterial Proteins/metabolism/genetics ; Humans ; *Bacteria/drug effects/genetics/metabolism ; },
abstract = {Antimicrobial resistance (AMR) is a major global health threat, mainly driven by the rapid spread of resistance genes through horizontal gene transfer (HGT). The Type IV Secretion System (T4SS) acts as a crucial molecular machinery that facilitates this process, allowing bacteria to transfer DNA, effector proteins, and virulence factors. This review systematically explores the structural and functional diversity of T4SS, its role in spreading AMR, and current methods for its inhibition. T4SS consists of a multi-protein complex that spans bacterial membranes, mediating conjugative plasmid transfer, host-pathogen interactions, and bacterial competition. Key components include ATPases, pilus structures, and membrane-associated proteins that show both conserved features and species-specific adaptations. These traits enable functional specialization across Gram-positive and Gram-negative bacteria, significantly contributing to the spread of vital resistance genes like extended-spectrum β-lactamases and carbapenemases via mobile genetic elements. Several approaches have been developed to inhibit T4SS and combat AMR. Small molecules targeting ATPase activity or protein interactions are promising, as are natural phytochemicals that interfere with conjugation. Bacteriophage therapy provides another strategy by specifically targeting plasmid-carrying bacteria. Host immune responses, such as innate immune recognition and secretory immunoglobulins, also show potential to influence T4SS activity. Although progress has been made, challenges remain, especially in developing selective inhibition methods that do not harm beneficial microbiota or host cells. Future research should focus on high-resolution structural studies to support rational drug design and preclinical testing of combination therapies that include T4SS inhibitors with existing antibiotics. Gaining a deeper understanding of T4SS regulation and host-pathogen interactions will be vital for creating targeted AMR strategies that also maintain ecological balance.},
}

*Type IV Secretion Systems/metabolism/genetics/antagonists & inhibitors
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
*Gram-Negative Bacteria/drug effects/genetics/metabolism
Bacterial Proteins/metabolism/genetics
Humans
*Bacteria/drug effects/genetics/metabolism

@article {pmid40956103,
year = {2025},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics.},
journal = {mBio},
volume = {},
number = {},
pages = {e0240925},
doi = {10.1128/mbio.02409-25},
pmid = {40956103},
issn = {2150-7511},
abstract = {UNLABELLED: Prokaryotes can acquire antivirus immunity via two fundamentally distinct types of processes: direct interaction with the virus, as in clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immunity systems, and horizontal gene transfer (HGT), which is the main route of transmission of innate immunity systems. These routes of defense evolution are not mutually exclusive and can operate concomitantly, but observations suggest that at least in some bacterial and archaeal species, one or the other route dominates the defense landscape. We hypothesized that the observed dichotomy stems from different life-history trade-offs characteristic of these organisms. To test this hypothesis, we analyzed a mathematical model of a well-mixed prokaryote population under a stochastically changing viral prevalence. Optimization of the long-term population growth rate reveals two contrasting modes of defense evolution. In stable, predictable environments, direct interaction with the virus is the optimal route of immunity acquisition. In fluctuating, unpredictable environments with a moderate viral prevalence, horizontal transfer of defense genes is preferred. In the HGT-dominant mode, we observed a universal distribution of the fraction of microbes with different immune repertoires. Under very low virus prevalence, the cost of immunity exceeds the benefits such that the optimal state of a prokaryote is complete absence of defense systems. By contrast, under very high virus prevalence, horizontal spread of defense systems dominates regardless of the stability of the virome. These findings might explain consistent but enigmatic patterns in the spread of antivirus defense systems among prokaryotes, such as the ubiquity of adaptive immunity in hyperthermophiles contrasting their patchy distribution among mesophiles.

IMPORTANCE: The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct antivirus defense systems have been discovered in prokaryotes. There are two major modes of immunity acquisition: innate immune systems spread through microbial populations via HGT, whereas adaptive-type immune systems acquire immunity via direct interaction with the virus. We developed a mathematical model to explore the short-term evolution of prokaryotic immunity and showed that in stable environments with predictable viral repertoires, adaptive-type immunity is the optimal defense strategy, whereas in fluctuating environments with unpredictable virus composition, HGT dominates the immune landscape.},
}

@article {pmid40956092,
year = {2025},
author = {Dossouvi, KM and Sambe Ba, B and Lo, G and Sellera, FP and Furlan, JPR and Culot, A and Abriat, G and Gueye, AB and Ba-Diallo, A and Dieng, A and Ly, FP and Cissé, A and Ndiaye, SML and Tine, A and Karam, F and Diagne-Samb, H and Ngom-Cisse, S and Diop-Ndiaye, H and Toure-Kane, C and Gaye-Diallo, A and Dossim, S and Mboup, S and Boye, CSB and Seck, A and Camara, M},
title = {Clinical carbapenem-resistant Enterobacterales in a University Hospital in Dakar, Senegal: genomic insights into Enterobacter hormaechei ST182 strains carrying blaNDM-5 and blaOXA-48 genes .},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0078025},
doi = {10.1128/spectrum.00780-25},
pmid = {40956092},
issn = {2165-0497},
abstract = {Senegal has witnessed the emergence and spread of carbapenem-resistant Enterobacterales (CRE), which often cause deadly infections. Accordingly, this study aimed to determine the antimicrobial susceptibility and prevalence of carbapenemases, as well as to perform a whole-genome sequence analysis of clinical CRE isolates from a university hospital in Dakar, Senegal. MALDI-TOF MS and VITEK2 systems were used for bacterial identification and antimicrobial susceptibility testing (AST). Carbapenemase- and cephalosporinase-encoding genes were screened using simplex end-point polymerase chain reaction. Whole-genome sequencing (WGS) was performed using the Illumina MiSeq platform. The CRE isolates were resistant to almost all the 34 antimicrobials tested. Nevertheless, colistin and amikacin remained active, with susceptibility rates of 96% and 71%, respectively. Only the carbapenemase genes blaOXA-48 (53.8%; 15/28) and blaNDM (35.7%; 10/28) and the cephalosporinase gene blaCMY-1 (25%; 7/28) were identified. In this context, two extensively drug-resistant Enterobacter hormaechei isolates were subjected to WGS analysis. These isolates were assigned as sequence type (ST) 182 and carried several genes related to antimicrobial resistance (AMR), metal tolerance, and virulence. An IncL/M plasmid with 61,054 bp in length was identified as carrying the blaOXA-48 gene, whereas an IncFIB(pECLA)/IncFII(pECLA)/IncX3 mutireplicon plasmid with 217,745 bp in length was detected as harboring the blaNDM-5 gene and other genes related to AMR and metal tolerance. Our study presents the first landscape of clinical CRE circulating in Senegal, along with additional genomic analysis of E. hormaechei ST182 strains, which could be useful for mitigating the burden associated with CRE in this country.IMPORTANCEThe investigation of global critical priority CRE isolates has become crucial to reduce morbidity and mortality associated with AMR. This study revealed that colistin and amikacin can be considered good alternatives for treating CRE-associated infections in Dakar. In addition, the genomic approach revealed that the CRE isolates carried both a wide resistome and virulome. Moreover, the abundance of horizontal gene transfer regions in the genomes suggests the great implications of mobile genetic elements in the spread of AMR in Dakar. Furthermore, this study reported the complete sequences of chromosomes and blaOXA-48 and blaNDM-5-carrying plasmids. Our findings are of great importance because complete genome sequences are still rarely characterized in the West African region. Finally, this study highlights the importance of strengthening genomic surveillance of CRE in sub-Saharan African countries to mitigate the burden associated with these pathogens.},
}

@article {pmid40954939,
year = {2025},
author = {Chen, J and Wang, M and Liu, H and Li, Z},
title = {Novel Substitutes of Phthalate Esters (PAEs) Promote the Propagation of Antibiotic Resistance Genes via Ferroptosis: Implication for the Environmental Safety Evaluation of PAE Substitutes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10489},
pmid = {40954939},
issn = {1520-5851},
abstract = {The horizontal transfer of antibiotic resistance genes (ARGs) has become a major threat to global public health. Recent studies have found that ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation and glutathione depletion, may play a critical role in the dissemination of ARGs among environmental microbes. Here, we demonstrated for the first time that phthalate esters (PAEs) and their substitutes significantly enhanced plasmid conjugation by triggering ferroptosis-related pathways. Classical ferroptosis-associated responses, including the hyperpolarization of the cell membrane potential, elevated production of reactive oxygen species, and heightened membrane permeability, were observed under the stress of PAEs or their substitutes. Through integrated transcriptomic and metabolomic analyses, we revealed that these compounds triggered iron dysregulation via the upregulation of iron acquisition and storage pathways while suppressing DNA replication, concurrently causing oxidative damage that stimulated the plasmid conjugation. Molecular docking simulations revealed that PAEs and their substitutes competitively disrupted the functionality of ferric uptake regulator (Fur) protein, a master controller of intracellular iron homeostasis, with superior binding affinity than its natural ligand Fe[2+]. Integrated metagenomic sequencing and homology analyses demonstrated the conservation of Fur protein across biofilm microbiota and functional implications in iron homeostasis. Structural analysis based on the characteristic molecular fingerprints of chemicals pinpointed aliphatic chains as the crucial structure responsible for enhancing ARG propagation between bacteria. Our findings uncovered a mechanism by which PAEs and their substitutes exacerbated ARG dissemination through ferroptosis-mediated conjugation, providing crucial insights for environmental risk assessment and resistance mitigation strategies.},
}

@article {pmid40953126,
year = {2025},
author = {Banerjee, S and Shende, SS and Kata, L and Lopes, RS and Praveen, S and Joshi, R and Khare, NK and Raghuram, GV and Shabrish, S and Mittra, I},
title = {Horizontally transferred cell-free chromatin particles function as autonomous 'satellite genomes' and vehicles for transposable elements within host cells.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40953126},
issn = {2050-084X},
support = {CTC-TMC//Department of Atomic Energy, Government of India/ ; },
mesh = {Animals ; Mice ; Humans ; *Chromatin/genetics/metabolism ; *DNA Transposable Elements ; *Gene Transfer, Horizontal ; NIH 3T3 Cells ; *DNA, Satellite/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Fibroblasts ; },
abstract = {Horizontal gene transfer (HGT) plays an important evolutionary role in prokaryotes, but it is less frequent in mammals. We previously reported that cell-free chromatin particles (cfChPs) - chromosomal fragments released from the billions of dying cells that circulate in human blood - are horizontally transferred to healthy cells with biological effects. However, the underlying mechanism and function of these effects remained unclear. We treated NIH3T3 mouse fibroblasts cells with cfChPs isolated from human serum and serially passaged the cells. The intracellular activities of cfChPs were analysed using chromatin fibre fluorography, cytogenetic analysis, immunofluorescence, and fluorescent in situ hybridisation. We discovered that the internalised cfChPs were almost exclusively comprised of non-coding DNA, and the disparate DNA sequences contained within them had randomly combined to form complex concatemers, some of which were multi-mega base pairs in size. The concatemers autonomously performed many functions attributable to the nuclear genome such as DNA, RNA and protein synthesis. They harboured human LINE-1 and Alu elements, with the potential to rearrange themselves within the mouse genome. Our results suggest that a cell simultaneously harbours two autonomous genome forms: one that is inherited (hereditary genome) and numerous others that are acquired (satellite genomes). The satellite genomes may have evolutionary functions given their ability to serve as vehicles for transposable elements and to generate a plethora of novel proteins. Our results also suggest that 'within-self' HGT may occur in mammals on a massive scale via the medium of cfChP concatemers that have undergone extensive and complex modifications resulting in their behaviour as 'foreign' genetic elements.},
}

Animals
Mice
Humans
*Chromatin/genetics/metabolism
*DNA Transposable Elements
*Gene Transfer, Horizontal
NIH 3T3 Cells
*DNA, Satellite/genetics/metabolism
In Situ Hybridization, Fluorescence
Fibroblasts

@article {pmid40774041,
year = {2025},
author = {Long, J and Wu, J and Xi, Y and Zhang, J and Chen, S and Yang, H and Duan, G},
title = {Association between Type IV-A CRISPR/Cas system and plasmid-mediated transmission of carbapenemase genes in Klebsiella pneumoniae.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128297},
doi = {10.1016/j.micres.2025.128297},
pmid = {40774041},
issn = {1618-0623},
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; *Bacterial Proteins/genetics ; *Klebsiella pneumoniae/genetics/enzymology/drug effects ; *CRISPR-Cas Systems/genetics ; Humans ; Klebsiella Infections/microbiology ; *Gene Transfer, Horizontal ; Genome, Bacterial ; },
abstract = {The global rise of carbapenem-producing K. pneumoniae is largely attributed to plasmid-mediated transmission of carbapenemase genes. Type IV-A CRISPR/Cas system is mainly located on plasmids in K. pneumoniae and involved in plasmid competition. However, the role of Type IV-A system in the dissemination of carbapenemase genes in K. pneumoniae remains unclear. Here, we comprehensively investigated the relationship between Type IV-A system and plasmid-mediated transmission of carbapenemase genes based on 152 K. pneumoniae clinical strains and 46226 K. pneumoniae public genomes available in NCBI database. We found that the presence of Type IV-A system was positively associated with blaNDM-1, blaNDM-5, blaOXA-48, and blaVIM-1 but negatively related to blaKPC-2, blaKPC-3,blaIMP and blaOXA-181. Additionally, plasmids carrying Type IV-A system were predominantly the vehicles of blaNDM-1 gene. Protospacer search revealed that Type IV-A system frequently matched conjugation transfer region of blaKPC-2-related IncF plasmids, especially IncFIB(K)/IncFII(K), IncFII(pHN7A8)/IncR, and IncFIB(pQil)/IncFII(K) plasmids. The prevalence of self-targeting event further highlighted the interference mechanism of transcriptional repression proposed by Type IV system. Despite frequent targeting of IncF plasmids by Type IV-A system, different types of IncF plasmids displayed varying distribution between CRISPR-positive and -negative genomes, thereby suggesting a differentiated response of Type IV-A system to IncF plasmids. Our results underscore complex interactions between Type IV-A system and plasmid-mediated carbapenemase genes, revealing its significant role in shaping the transmission dynamics of carbapenemase-encoding plasmids.},
}

*beta-Lactamases/genetics
*Plasmids/genetics
*Bacterial Proteins/genetics
*Klebsiella pneumoniae/genetics/enzymology/drug effects
*CRISPR-Cas Systems/genetics
Humans
Klebsiella Infections/microbiology
*Gene Transfer, Horizontal
Genome, Bacterial

@article {pmid40580511,
year = {2025},
author = {Ren, X and Xiao, B and Wu, M and Yang, K and Gu, P and Zhang, Z and Miao, H},
title = {Effect and mechanism of residual-chlorine on the horizontal transfer of antibiotic resistance genes of chlorine resistant bacteria in reclaimed water.},
journal = {Environmental technology},
volume = {46},
number = {23},
pages = {4667-4680},
doi = {10.1080/09593330.2025.2516055},
pmid = {40580511},
issn = {1479-487X},
mesh = {*Chlorine/pharmacology ; *Gene Transfer, Horizontal/drug effects ; *Drug Resistance, Microbial/genetics ; Water Microbiology ; Disinfectants/pharmacology ; *Bacteria/genetics/drug effects ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Microbial Sensitivity Tests ; },
abstract = {Chlorine disinfection inactivates most microbes in reclaimed water, but chlorine resistant bacteria (CRB) persist, threatening water safety and spreading antibiotic resistance genes (ARGs). ARG proliferation in reclaimed water systems risks public health, as dissemination via irrigation or urban reuse may enable environmental transmission to humans, exacerbating global antibiotic resistance. One hundred and fifty-two strains of CRB were isolated from reclaimed water in this study, and the detection rate of ARGs in those CRB was 100%, the detection rate for blTEM was 100%, followed by sul3 and tetG. Macrogenomic analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes are the dominant CRB in reclaimed water. Long-term induction with the minimum inhibitory concentration (MIC) of NaClO enhanced the resistance of CRB to both Amp and NaClO. The EPS of CRB increased 1.30- to 2.04-fold, and the elevated surface hydrophobicity may serve as a co-resistance mechanism. EPS hindered disinfectant/antibiotic penetration, while hydrophobicity reduced hydrophilic molecule adhesion and promoted bacterial aggregation, both of which contribute to the enhanced resistance of CRB. Residual chlorine dose-dependently enhances ARG conjugation via ROS-SOS, ATP, and EPS pathways, unveiling novel CRB mechanisms and urging revised disinfection to mitigate ARG spread.},
}

*Chlorine/pharmacology
*Gene Transfer, Horizontal/drug effects
*Drug Resistance, Microbial/genetics
Water Microbiology
Disinfectants/pharmacology
*Bacteria/genetics/drug effects
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Microbial Sensitivity Tests

@article {pmid40950580,
year = {2025},
author = {Panteleev, V and Kulbachinskiy, A and Gelfenbein, D},
title = {Evaluating phage lytic activity: from plaque assays to single-cell technologies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659093},
pmid = {40950580},
issn = {1664-302X},
abstract = {Bacteriophages are the most abundant biological entities on Earth, playing critical roles in microbial ecology, evolution, and horizontal gene transfer. Since the discovery of bacteriophages in the early 20th century, a wide range of techniques has been developed to study their lytic activity. This review provides a perspective on the wide range of methods for studying phage-bacteria interactions, spanning classical bulk-culture techniques and modern single-cell and high-throughput approaches. The first section covers solid culture methods relying on plaque formation phenomenon, which allow for quantification of infectious viruses, phage host-range establishment, and analysis of certain phage traits, now augmented by robotic high-throughput screening. The second section focuses on liquid culture approaches, utilizing optical density measurements, quantitative PCR, metabolic assays and cell damage assays to measure the infection dynamics. The third section details single-cell techniques, which help to dissect the heterogeneity of infection within cell populations, using microscopy, microfluidics, next-generation sequencing, and Hi-C methods. The integration of these diverse methods has greatly advanced our understanding of the molecular mechanisms of phage infection, bacterial immunity, and facilitated phage therapy development. This review is dedicated to the 110th anniversary of phage discovery and is aimed to guide researchers in selecting optimal techniques in the fast-growing field of phage biology, phage-host interactions, bacterial immunity, and phage therapy.},
}

@article {pmid40950087,
year = {2025},
author = {Moe, R and Piechowiak, KW and Håvarstein, LS and Kjos, M and Straume, D},
title = {LytF contributes to pilus extrusion during natural competence in Streptococcus sanguinis SK36.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.04.674207},
pmid = {40950087},
issn = {2692-8205},
abstract = {UNLABELLED: Streptococci may enter a physiological state called competence, during which they express a specific set of genes required for exogenous DNA uptake and its subsequent integration into the genome through homologous recombination. This process, termed natural transformation, facilitates the horizontal acquisition of genetic material, potentially conferring adaptive advantages that enhance bacterial survival under selective pressures. To make homologous DNA available in the surrounding environment, Streptococcus pneumoniae expresses a cell wall hydrolase (CbpD) that lyses and kills closely related species. This process has been coined fratricide , and the acting hydrolase a fratricin . A significant fraction of streptococcal species does not encode a CbpD-like protein, but another competence-induced peptidoglycan hydrolase LytF. It has been speculated that LytF serves the same purpose as CbpD, however, our investigations into the role of LytF in Streptococcus sanguinis revealed no evidence supporting LytF as a fratricin. Instead, we show that LytF is involved in natural transformation by promoting DNA uptake. An essential part of DNA uptake is the competence-induced type IV pilus, which facilitates DNA uptake by pulling nearby DNA toward the cell. By immunoblotting and microscopy imaging, we found that LytF increases the extracellular levels of the major pilus component ComGC, suggesting that LytF may modify peptidoglycan to promote pilus extrusion across the cell wall, thereby enhancing the efficiency of DNA uptake.

IMPORTANCE: Streptococci are a significant cause of severe infections in both humans and animals. They are particularly adept at acquiring new genes through horizontal gene transfer as they can become competent for natural transformation. This allows them to quickly adapt to selective pressure and spread genes involved in virulence and antibiotic resistance. In Streptococcus sanguinis , the competence-induced peptidoglycan hydrolase LytF has been reported to stimulate natural transformation. Our study adds to the understanding of this process by demonstrating that LytF promotes extrusion of the transformation pilus required for DNA uptake.},
}

@article {pmid40950011,
year = {2025},
author = {Yang, B and Xiang, C and Li, T and Liu, B and Sinitskiy, AV and Li, J},
title = {Evolutionary Tree in Chemical Space of Natural Products.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.31.673394},
pmid = {40950011},
issn = {2692-8205},
abstract = {Natural products (NPs) are key to biological function and adaptation, with their distribution shaped by complex evolutionary and ecological forces. While it may seem reasonable to assume that closely related species produce chemically similar NPs, this assumption has not been systematically tested at a broad taxonomic scale. Here, we evaluate whether evolutionary (taxonomic) proximity correlates with chemical similarity in large-scale data from the Lotus database of NPs. We use five deep learning-based encoders, including Chemformer and SMILES Transformer, to embed NPs into a high-dimensional "chemical space." Our results demonstrate that, for flowering plants (Magnoliopsida) and conifers (Pinopsida), species separated by shorter taxonomic distances tend to produce significantly more similar NPs. Similar trends are observed for Fungi and Metazoa, albeit with some complications, possibly due to horizontal gene transfer, convergent evolution, and/or incomplete coverage in the dataset used for NPs. Our findings suggest that the evolutionary tree can be statistically recovered in a chemical space of NPs, provided that this space is constructed with appropriate deep learning techniques, and provide a new computational framework to investigate the evolutionary dynamics of secondary metabolism. These results can inform drug design strategies, for example by enabling the reconstruction of NPs from poorly studied or extinct species.},
}

@article {pmid40946852,
year = {2025},
author = {Zheng, C and Song, J and Shan, M and Qiu, M and Cui, M and Huang, C and Chen, W and Wang, J and Zhang, L and Yu, Y and Fang, H},
title = {Nutrition cycling microbiomes drive the succession of antibiotic resistome in long-term manured soils.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.09.019},
pmid = {40946852},
issn = {2090-1224},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes (ARGs) in the environment has received widespread attention. Nutrition cycling microbiomes specifically refer to microorganisms capable of mineralizing nitrogen and phosphorus, which dominate the microbial community in long-term manured soils. However, changes in nutrition cycling genes/microbiomes and the mechanisms by which these microbiomes mediate ARG transfer through vertical and horizontal gene transfer remain poorly understood.

OBJECTIVES: This study aimed to elucidate how nutrition cycling microbiomes mediate the dissemination and ecological risk of antibiotic resistance genes (ARGs) in long-term manure-amended soils.

METHODS: Here, we employed metagenomic assembly and binning to investigate the distribution of nutrition mineralization genes, nutrition cycling microbiomes, mobile genetic elements (MGEs), and ARGs in rapeseed cake, pig manure, duck manure and their corresponding long-term amended soils.

RESULTS: Long-term application of organic manures led to the dominance of nutrition cycling microbiomes associated with methanogenesis (pmoA and mmoX) and incomplete denitrification (norBC), thereby exacerbating soil nutrient loss. Nutrition cycling microbiomes, particularly Rhodanobacter and Pseudomonas, served as the primary host for ARGs and harbored multiple clinically relevant resistance genes, including MexF, ceoB, and mdtB. Notably, the abundance of ARGs in rapeseed cake and pig manure was 2.09-2.23-fold and 6.74-7.38-fold higher, respectively, than in duck manure, promoting the vertical transmission of ARGs via nutrition cycling microbiomes under long-term application. Furthermore, a significant positive correlation between nutrition mineralization genes and ARGs revealed a co-dispersal mechanism between nutrition cycling microbiomes and ARGs in long-term manured soils.

CONCLUSIONS: It is concluded that the nutrition cycling microbiome plays a more prominent role in shaping antibiotic resistome through vertical transfer in manured soils, compared to horizontal gene transfer mediated by MGEs.},
}

@article {pmid40946639,
year = {2025},
author = {Chen, H and Cheng, D and Sun, M and Zhao, S and Sheng, J and Yu, X and Li, X and Xue, G and Zou, X},
title = {Fe[0] drives tetracycline resistance genes reduction and resistance mechanism shift in activated sludge system.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127302},
doi = {10.1016/j.jenvman.2025.127302},
pmid = {40946639},
issn = {1095-8630},
abstract = {The proliferation of tetracycline antibiotic resistance genes (TC-ARGs) in wastewater treatment plants (WWTPs) poses environmental and health risks. This study investigates zero-valent iron (Fe[0]) in regulating TC-ARGs in activated sludge under co-exposure with tetracycline (TC). TC enriched tetA and tetC via efflux pump activation and horizontal gene transfer (HGT), with tetA/tetC increasing 0.19-3.57 log units and intI1 by 1-2 log units. Fe[0] addition slightly affected absolute TC-ARGs abundance in the first 40 d, with a 4.02 % decrease after 40 d, while relative abundance dropped markedly by 77.81 % and 84.87 % in the first and last 40 d, respectively; intI1 relative abundance decreased by 78.28 %. Fe[0] shifted resistance from efflux genes toward ribosomal protection (tetM/O) and enzymatic modification (tetX), reduced bioavailable TC by 39.8 %, and alleviated EPS inhibition by enhancing polysaccharide production, weakening antibiotic selection pressure. Microbial community restructuring enriched stress-tolerant taxa (e.g., Bacteroidetes). This study demonstrates that Fe[0] primarily reduces the dissemination risk of TC-ARGs by lowering their proportion in microbial genomes. These results provide new insights into optimizing the application of Fe[0] for controlling the spread of TC-ARGs in WWTPs.},
}

@article {pmid40945797,
year = {2025},
author = {Cui, L and Gao, M and Chen, J and Yan, Y and Guo, S and Ma, Y},
title = {How microbial consortium-based compound enzyme influences conjugative transfer pathway of antibiotic resistance genes?.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133305},
doi = {10.1016/j.biortech.2025.133305},
pmid = {40945797},
issn = {1873-2976},
abstract = {Microbial consortium-based compound enzyme (MCE) has been proved to be able to effectively reduce the risk of antibiotic resistance genes (ARGs) dissemination during biotransformation of food waste. However, in-depth mechanisms regarding the regulation of ARGs transfer among environmental bacteria by MCE pretreatment is remain unclear. This work analyzed the effect of MCE pretreatment on RP4 plasmid-mediated conjugative transfer of ARGs and relevant underlying mechanisms. Results showed that MCE pretreatment reduced the plasmid conjugative transfer frequency by 71% compared with the control. Meanwhile, the reduction of hydrophilic components of extracellular polymeric substances, the decrease of biofilm formation, and the disruption of intercellular contact also happened during MCE pretreatment process. In addition, ATP synthesis and bacterial motility had an effect on the plasmid replication and formation of conjugative transfer channel. These changes lead to down-regulation of the expression of conjugative transfer gene. The inhibitory effect of MCE pretreatment on plasmid conjugative transfer was confirmed in the constructed food waste model. MCE pretreatment reduced the number of pathogens, such as Escherichia-Shigella and Rothia, thereby reduced the potential risk of ARGs being disseminated among pathogens. Overall, this study reveals the key mechanism of MCE pretreatment on disrupting ARGs conjugative transfer, which may provide a crucial theoretical foundation for developing novel interventions to disrupt the environmental dissemination of ARGs in future.},
}

@article {pmid40945439,
year = {2025},
author = {Wang, W and Yang, W and Jiang, L and Yao, C and Zhang, Z and Xu, M and Yan, X and Qian, X},
title = {Applications of Oxford Nanopore Technology in the analysis of antibiotic resistance genes: A review.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139824},
doi = {10.1016/j.jhazmat.2025.139824},
pmid = {40945439},
issn = {1873-3336},
abstract = {Antibiotic misuse has led to the rapid expansion of the antibiotic resistance gene (ARGs) pool, making antimicrobial resistance (AMR) a major global health threat. The efficient identification of ARGs and the development of strategies to control AMR have become research hotspots. However, the Next-generation sequencing (NGS) has many limitations in ARGs identification, hindering our understanding of their genetic context. This review uses Oxford Nanopore Technology (ONT) as an example to summarize the advantages and application prospects of the third-generation sequencing technologies in the migration and transmission of ARGs. By analyzing 12 sets of NGS - ONT datasets, this review demonstrates the strengths and limitations of ONT from multiple perspectives, including the identification of ARGs, key pathogens, plasmids, viruses, and horizontal gene transfer events, and provides detailed analytical workflows. It offers comprehensive analytical approaches and application insights for ARGs research based on ONT, highlighting the importance and necessity of the third-generation sequencing technologies in studying the prevalence and transmission of ARGs in complex environments.},
}

@article {pmid40943202,
year = {2025},
author = {Pruss, A and Kobylińska, D and Fijałkowski, K and Masiuk, H and Kwiatkowski, P},
title = {Evaluation of Colistin Susceptibility of Klebsiella pneumoniae Strains Exposed to Rotating Magnetic Field.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178281},
pmid = {40943202},
issn = {1422-0067},
abstract = {Klebsiella pneumoniae, due to its capacity to produce numerous virulence factors and form biofilms, is one of the most significant etiological agents of nosocomial infections. The extensive and often unwarranted use of antibiotic therapy has driven the emergence of various mutations, adaptive mechanisms, and horizontal gene transfer among K. pneumoniae strains, resulting in resistance to most beta-lactam antibiotics, carbapenems, and the last-resort drug-colistin. A promising alternative or adjunctive treatment is the application of rotating magnetic fields (RMFs). The present study aimed to evaluate changes in colistin susceptibility among 20 extended-spectrum beta-lactamases (ESBLs) and 20 K. pneumoniae carbapenemase (KPC)-positive K. pneumoniae strains isolated from hospital infections following exposure to RMF at frequencies of 5 and 50 Hz. Exposure to RMF at 5 Hz resulted in decreased colistin minimum inhibitory concentration (MIC) values in over half of the tested (ESBLs) and (KPC)-positive strains. Additionally, RMF at 50 Hz reduced colistin MIC values in 30% of (ESBL)-positive and 40% of (KPC)-positive strains. Therefore, in the future, RMF may be developed as a supportive therapeutic strategy to improve the efficacy of antibiotics in the treatment of infections caused by multidrug-resistant (MDR) pathogens, including colistin-resistant K. pneumoniae.},
}

@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}

@article {pmid40934669,
year = {2025},
author = {Osti, JF and Pereira Leal, RM and de Souza, AJ and Paulon Rezende, LG and Viana, DG and Andreote, FD and Mendonça, RS and Jakelaitis, A and Regitano, JB},
title = {Complex interplay between composted manure application, metal contamination, and antibiotic resistance genes profile under tropical field conditions.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109783},
doi = {10.1016/j.envint.2025.109783},
pmid = {40934669},
issn = {1873-6750},
abstract = {Manure applications in agricultural soils are a major driver of antibiotic resistance gene (ARG) dissemination, yet long-term effects of composted manure applications under tropical real field conditions remain unclear. This study assessed how successive composted manure applications influence soil physicochemical attributes, bacteriome and resistome profiles in the Brazilian Cerrado, including one site with naturally high heavy metal content. Across all sites, multidrug resistance genes were most abundant, followed by macrolide-lincosamide-streptogramin (MLS), tetracycline, β-lactam and glycopeptides resistance, aligning with predominance of Actinomycetota and Pseudomonadota as key ARG hosts. Manure increased soil pH and available phosphorus (P), with pH significantly shaping bacterial communities and pH and P the resistome in uncontaminated sites (2 and 3). However, in the metal-rich site (1), Cu was the dominant driver. Manure increased ARG richness and changed resistome structure but did not affect clinically relevant genes or resistome diversity. Metal resistance genes (MRGs), particularly for Cu and Zn, strongly influenced resistome dynamics, highlighting co-selection. Integrons integrase genes (intl) abundance increased in metal-depleted but not in metal-rich soils. While composting appears to mitigate ARG spread, particularly for clinically relevant genes, the high antibiotic use in livestock, large manure volumes, and potential for ARG persistence in tropical soils highlight the need for further research on manure treatment strategies and ARG fate in these environments. Environmental Implication. Our study highlights the environmental risks of antibiotic resistance gene (ARG) dissemination in tropical agricultural soils, emphasizing the role of manure application and heavy metal contamination in shaping soil resistome. While composted manure increased bacterial diversity and ARG richness, it did not significantly impact clinically relevant genes and resistome diversity, suggesting that composting may help mitigate ARG spread but does not eliminate it. Metals were the dominant drivers of ARG selection in the contaminated site, underscoring the role of co-selection mechanisms in maintaining resistance. However, manure applications increased integrons abundance, raising concerns about horizontal gene transfer and potential ARG proliferation into pathogens. These findings stress the urgent need for improved manure management policies in Brazil, where high antibiotic use in livestock and large manure volumes pose significant environmental and public health risks. Developing sustainable manure treatment strategies and monitoring ARG persistence are essential to limit antibiotic resistance proliferation in tropical agricultural ecosystems.},
}

@article {pmid40933520,
year = {2025},
author = {Habib, I and Mohamed, MI and Lakshmi, GB and Al Marzooqi, HM and Afifi, HS and Shehata, MG and Elbediwi, M},
title = {First detection and genomic analysis of mcr-1-positive Salmonella Infantis isolated from a broiler production system in the United Arab Emirates.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1592955},
doi = {10.3389/fvets.2025.1592955},
pmid = {40933520},
issn = {2297-1769},
abstract = {This study reports the first detection of mcr-1.1-mediated colistin resistance in Salmonella enterica serovar Infantis from a commercial broiler farm in the United Arab Emirates (UAE). Two S. infantis isolates (SAL_93 and SAL_94) were recovered from caecal droppings and characterized using whole-genome sequencing (WGS). Genomic analysis revealed a single-nucleotide polymorphism (SNP) difference between them, confirming their close epidemiological relationship. Both isolates belonged to multilocus sequence type 32 and exhibited multidrug resistance (MDR), including resistance to colistin (MIC = 4 mg/L) and ciprofloxacin (MIC = 0.5 mg/L). Notably, the mcr-1.1 gene was detected on a conjugative IncX4 plasmid. Additionally, the isolates harbored a large (275,043 bp) conjugative IncFIB plasmid carrying multiple AMR genes, including aadA1, sul1, tet(A), qacEdelta1. Bioinformatic analysis showed a high identity for globally reported mcr-1.1-carrying IncX4 plasmids. The investigation of virulence-associated factors in the studied isolates identified 162 potential virulence-related genes. These included genes linked to the type 3 secretion system, specifically those encoded by pathogenicity island-1 (SPI-1). However, multiple genes linked to the second type 3 secretion system, encoded by SPI-2, were absent in all isolates. These findings suggest a potential risk of horizontal gene transfer in poultry production. Given these risks, the UAE's recent ban on colistin in veterinary medicine marks a crucial step in mitigating AMR transmission within a One Health framework.},
}

@article {pmid40933131,
year = {2025},
author = {Braun, SD and Reinicke, M and Diezel, C and Müller, E and Frankenfeld, K and Schumacher, T and Arends, H and Monecke, S and Ehricht, R},
title = {High-throughput screening of monoclonal antibodies against carbapenemases using a multiplex protein microarray platform.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650094},
doi = {10.3389/fmicb.2025.1650094},
pmid = {40933131},
issn = {1664-302X},
abstract = {INTRODUCTION: Carbapenemase-producing bacteria undermine the efficacy of carbapenems, a class of last-resort antibiotics used primarily to treat infections caused by multidrug-resistant Gram-negative pathogens. Carbapenemases are among the most alarming antimicrobial resistance mechanisms because they inactivate all β-lactam antibiotics leaving clinicians with few or no therapeutic options. The genes encoding these enzymes are typically located on mobile genetic elements (MGE), which facilitate rapid horizontal gene transfer among different bacterial species. These MGE's often additionally carry toxin-antitoxin systems that promote long-term persistence in bacterial populations. Carbapenem-resistant Enterobacteriaceae (CRE) often colonize the gastrointestinal tract without symptoms, serving as silent reservoirs for further dissemination. Infections caused by CRE are associated with high morbidity and mortality and are frequently resistant to multiple drug classes. Given the urgent clinical need for rapid diagnostics, immunochromatographic assays represent a promising and urgently needed approach for economic and available point-of-care detection. However, the development of such assays is often hindered by the time-consuming process of identifying high-affinity antibody pairs.

METHODS: To accelerate this process, we evaluated a protein microarray platform as a high-throughput screening tool to identify optimal monoclonal antibody (mAb) pairs targeting the most clinically relevant carbapenemases. Monoclonal antibodies derived from hybridoma libraries and commercial sources were spotted in triplicates and tested in a single experiment against lysates from reference strains expressing the carbapenemase enzymes KPC, NDM, IMP, VIM, OXA-23/48/58, and MCR-1, an enzyme conferring resistance to colistin. Signal intensities were quantified, and diagnostic performance was assessed across four thresholds.

RESULTS: A cut-off > 0.2 yielded the best balance, with approximately 61% balanced accuracy and ≥99% specificity. Around 22% of tested antibodies showed strong, reproducible reactivity. For several targets-such as KPC, IMP, VIM, OXA-58, and MCR-1-100% sensitivity was achieved. The array allowed simultaneous mapping of cross-reactivity, a key advantage over conventional ELISA workflows.

DISCUSSION: Our findings confirm that protein-based microarrays offer a robust, efficient platform for antibody pair selection, reducing reagent use while accelerating assay development. The validated antibody pairs are directly applicable to ELISA or lateral flow test formats and provide a strong foundation for next-generation diagnostics capable of detecting an evolving panel of carbapenemases in clinical settings.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929971,
year = {2025},
author = {Wang, Y and Han, Y and Li, L and Liu, J and Tian, H},
title = {Airborne human-associated ARGs in municipal wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139766},
doi = {10.1016/j.jhazmat.2025.139766},
pmid = {40929971},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) in bioaerosols pose significant health hazards to humans because of their inhalability. Municipal wastewater treatment plants (MWTPs) are one of the typical sources of bioaerosol generation. However, there is a lack of clear understanding of human-associated ARGs (HA-ARGs) in bioaerosols from MWTPs. This study focused on airborne HA-ARGs in a typical MWTP. The results found that 331 HA-ARGs were identified in bioaerosols, dominated by multidrug, aminoglycoside, β-lactam, macrolide, lincosamide, and streptogramin genes. The detected abundances of the airborne HA-ARGs were 5.77-2.12E+ 03 transcripts per kilobase million (TPM), 202.36-3.17E+ 09 copies/ngDNA, and 4.42-4.92E+ 06 copies/m[3]air. The greatest abundances were detected mainly in the sludge dewatering house and in the summer and winter. HA-ARGs were mainly propagated and amplified by vertical gene transfer (VGT) and horizontal gene transfer (HGT). Proteobacteria, Actinobacteria, and Bacteroidetes were bacteria that had a strong co-occurrence with airborne HA-ARGs in VGT. Plasmids and transposases were the dominant mobile genetic elements in HGT. The analysis of co-occurrence network showed that VGT was identified as the main pathway for the spread and amplification of airborne HA-ARGs, with an average contribution of 85.38 %. These results provide a theoretical basis for potential risk assessment and reduction of airborne HA-ARGs in MWTPs.},
}

@article {pmid40929802,
year = {2025},
author = {Yang, KY and Sun, YF and Liang, YS and Li, H and Qi, MX and Wang, Z and Ramos Aguila, LC and Cai, LQ and Li, HS and Pang, H},
title = {Horizontally transferred NADAR genes contribute to immune defense of ladybird beetles against bacterial infection.},
journal = {Insect biochemistry and molecular biology},
volume = {184},
number = {},
pages = {104397},
doi = {10.1016/j.ibmb.2025.104397},
pmid = {40929802},
issn = {1879-0240},
abstract = {Horizontal gene transfer (HGT) is now widely recognized as an important mechanism contributing to host immunity and adaptation. Ladybird beetles, with their diverse diets and habitats, encounter a broad spectrum of microbial threats, making effective immune responses critical for their survival. However, the immune roles of HGT-acquired genes in ladybirds remain largely unexplored. To address this gap, we investigated HGT of a NADAR (NAD- and ADP-ribose-associated) domain-containing gene from microorganisms to insects. Phylogenetic analyses revealed that NADAR genes in ladybird beetles form a well-supported clade nested within a larger group composed primarily of bacterial sequences, providing strong evidence for an HGT origin. Sampling across 69 ladybird species suggests that NADAR genes originated in the Coccinellidae family and were subsequently retained or duplicated across ladybird genomes, indicating their functional importance. Using the ladybird Cryptolaemus montrouzieri as a model, we observed that the expression levels of CmNADAR1 and CmNADAR2 were significantly upregulated in response to bacterial infection. Immune challenges combined with RNA interference targeting NADAR genes led to reduced survival rates and marked necrosis in intestinal tissues, compared to controls exposed to either bacterial infection or dsRNA alone. Together, our results demonstrate that NADAR genes in ladybird beetles were acquired through horizontal gene transfer and contribute to immune defense against bacterial infection.},
}

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40928248,
year = {2025},
author = {Hourigan, D and Field, D and Murray, E and Sugrue, I and O'Connor, PM and Hill, C and Ross, RP},
title = {Nisin-like biosynthetic gene clusters are widely distributed across microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0154525},
doi = {10.1128/mbio.01545-25},
pmid = {40928248},
issn = {2150-7511},
abstract = {Bacteriocins are antimicrobial peptides/proteins that can have narrow or broad inhibitory spectra and remarkable potency against clinically relevant pathogens. One such bacteriocin that is extensively used in the food industry and with potential for biotherapeutic application is the post-translationally modified peptide, nisin. Recent studies have shown the impact of nisin on the gastrointestinal microbiome, but relatively little is known of how abundant nisin production is in nature, the breadth of existing variants, and their antimicrobial potency. Whether or not nisin production and immunity are widespread in gut microbiomes could be a deciding factor in determining the suitability of nisin as a prospective therapeutic for human and/or animal infections. Here, we used publicly available data sets to determine the presence of widespread and diverse nisin biosynthetic gene clusters (nBGCs) across the biosphere. We show that 30% of these nBGCs are predicted to be located on mobile genetic elements, with some found in pathogenic bacteria. Furthermore, we highlight evidence of horizontal gene transfer of nBGCs between genera, including Streptococcus suis, Enterococcus hirae, and Staphylococcus aureus. In all, we describe 107 novel nisin-like peptides. Five representatives were heterologously expressed and all exhibited antimicrobial activity. We further characterized nisin VP, a novel natural nisin variant produced by Velocimicrobium porci isolated from the porcine gut. The peptide has a completely novel hinge region "AIQ" not detected in other nisin variants to date. While nisin VP could be induced by nisin A, the latter could not be induced by nisin VP.IMPORTANCEOur research reveals the heretofore underappreciated presence of diverse and widespread nisin-like biosynthetic gene clusters in microbiomes across the globe. Notably, different clusters share similar biosynthetic machinery but differ in sequence, suggesting gene transfer and adaptation. We identify >100 new nisin-like variants, including several in species not previously known to produce nisin. This emphasizes the widespread dissemination of nisin-like gene clusters and the diversity of novel core peptides with biotherapeutic potential. These findings point to a role for nisin in microbial competition in microbiomes. We heterologously expressed nine nisin variants, five of which are completely novel peptides, using the nisin A biosynthetic machinery and confirmed that all exhibited antimicrobial activity.},
}

@article {pmid40927181,
year = {2025},
author = {Ziemann, M and Mitrofanov, A and Stöckl, R and Alkhnbashi, OS and Backofen, R and Hess, WR},
title = {Analysis of tracrRNAs reveals subgroup V2 of type V-K CAST systems.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqaf020},
pmid = {40927181},
issn = {2633-6693},
abstract = {Clustered regularly interspaced palindromic repeats (CRISPR)-associated transposons (CAST) consist of an integration between certain class 1 or class 2 CRISPR-Cas systems and Tn7-like transposons. Class 2 type V-K CAST systems are restricted to cyanobacteria. Here, we identified a unique subgroup of type V-K systems through phylogenetic analysis, classified as V-K_V2. Subgroup V-K_V2 CAST systems are characterized by an alternative tracrRNA, the exclusive use of Arc_2-type transcriptional regulators, and distinct differences in the length of protein domains in TnsB and TnsC. Although the occurrence of V-K_V2 CAST systems is restricted to Nostocales cyanobacteria, it shows signs of horizontal gene transfer, indicating its capability for genetic mobility. The predicted V-K_V2 tracrRNA secondary structure has been integrated into an updated version of the CRISPRtracrRNA program available on GitHub under https://github.com/BackofenLab/CRISPRtracrRNA/releases/tag/2.0.},
}

@article {pmid40925947,
year = {2025},
author = {Smyth, C and Leigh, RJ and Do, TT and Walsh, F},
title = {Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {78},
pmid = {40925947},
issn = {2731-8745},
support = {Grant 2019-W-PhD-14//Irish Environmental Protection Agency/ ; Grant 2019-W-PhD-14//Irish Environmental Protection Agency/ ; PHD_3//The Kathleen Lonsdale Institute for Human Health Research, Maynooth University/ ; PHD_3//The Kathleen Lonsdale Institute for Human Health Research, Maynooth University/ ; },
abstract = {Plasmids facilitate antimicrobial resistance (AMR) gene spread via horizontal gene transfer, yet the mobility of genes in wastewater treatment plant (WWTP) resistomes remains unclear. We sequenced 173 circularised plasmids transferred from WWTP effluent into Escherichia coli and characterised their genetic content. Multiple multidrug-resistant plasmids were identified, with a significant number of mega-plasmids (>100 kb). Almost all plasmids detected existed with other plasmids i.e. as communities rather than lone entities. These plasmid communities enabled non-AMR plasmids to survive antimicrobial selection by co-existing with resistant partners. Our data demonstrates the highly variable nature of plasmids in addition to their capacity to carry mobile elements and genes within these highly variable regions. The impact of these variations on plasmid ecology, persistence, and transfer requires further investigation. Plasmid communities warrant exploration across biomes, as many non-resistant plasmids escape elimination by co-existing with AMR plasmids in the same bacterial host, representing a previously unrecognised survival strategy.},
}

@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {16},
number = {9},
pages = {e0113425},
doi = {10.1128/mbio.01134-25},
pmid = {40793781},
issn = {2150-7511},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; },
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*DNA Transposable Elements
Feces/microbiology
Ecuador
Metagenomics
Child
Child, Preschool
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Female
Gene Transfer, Horizontal
Male
Plasmids/genetics

@article {pmid40923893,
year = {2025},
author = {Reyes Gamas, K and Seamons, TR and Dysart, MJ and Fang, L and Chappell, J and Stadler, LB and Silberg, JJ},
title = {Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00313},
pmid = {40923893},
issn = {2161-5063},
abstract = {Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNAs that store information within user-defined sets of microbes in environmental communities for gene transfer studies.},
}

@article {pmid40919919,
year = {2025},
author = {Luo, Y and Srinivas, A and Guidry, C and Bull, C and Haney, CH and Hamilton, C},
title = {GacA regulates symbiosis and mediates lifestyle transitions in Pseudomonas.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0027725},
doi = {10.1128/msphere.00277-25},
pmid = {40919919},
issn = {2379-5042},
abstract = {Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the brassicacearum/corrugata/mediterranea (BCM) subclade of Pseudomonas fluorescens, including Pseudomonas species N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. Pseudomonas sp. N2E2 is a plant commensal and contains genes encoding biosynthetic enzymes for the antifungal compound 2,4-diacetylphloroglucinol (DAPG). In contrast, Pseudomonas sp. N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)- and syringopeptin (SYP)-like toxins from the plant pathogen Pseudomonas syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant-pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle. Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.IMPORTANCEEmerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer (HGT) aids in the acquisition of novel genes that facilitate adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT. These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. This work provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.},
}

@article {pmid40916842,
year = {2025},
author = {Oo, G and Low, WW and Yong, M and Stanton, TD and Ayuni, NN and Bifani, P and Wyres, KL and Gan, YH},
title = {Anti-plasmid defense in hypervirulent Klebsiella pneumoniae involves Type I-like and Type IV restriction modification systems.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2558877},
doi = {10.1080/22221751.2025.2558877},
pmid = {40916842},
issn = {2222-1751},
abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) and classical multidrug-resistant (MDR) strains belong to distinct lineages and hvKp are typically characterized by hypermucoid capsules that have been shown to limit horizontal gene transfer (HGT), including plasmid acquisition. However, the convergence of hypervirulence and MDR is increasingly common worldwide. When we profiled 127 antibiotic-susceptible hvKp strains, we found that most (86%) are highly permissive to plasmid transfer despite their capsules. In the few strains that showed low permissiveness, we identified two restriction modification (RM) systems: the Type IV restriction system McrBC that targets bacteriophage, and a unique Type I RM system. Both systems effectively inhibit plasmid uptake in recipient strains. Further analysis reveals that L-arginine and spermidine metabolism regulates the Type I-like RM system through S-adenosyl methionine. Strains lacking these RM systems were highly receptive to plasmids, and clinical isolates worldwide often lack these systems, correlating with their antibiotic resistance. Collectively, our study provides the first report on the susceptibility of hvKp strains to plasmid transfer and evidence of unusual RM systems restricting plasmid acquisition. It reveals an arms race between plasmids evolving to bypass RM systems and host strains developing new defenses. This dynamic and the rarity of these RM systems help explain the emergence of MDR hvKp strains in clinical settings driven by antibiotic pressure.},
}

@article {pmid40914064,
year = {2025},
author = {Zhang, K and Gao, J and Zhang, J and Wang, Y and Wang, H and Guo, Y and Lu, T},
title = {Preservatives induced succession of microbial communities and proliferation of resistance genes within biofilm and plastisphere in sulfur autotrophic denitrification system.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139750},
doi = {10.1016/j.jhazmat.2025.139750},
pmid = {40914064},
issn = {1873-3336},
abstract = {Methylparaben (MeP), Benzethonium chloride (BZC) and microplastics (MPs) as emerging contaminants are frequently detected in the environment. Furthermore, MPs can be colonized by microorganisms to form a unique ecological niche known as the "plastisphere". In this study, three biofilm-based sulfur autotrophic denitrification (SAD) reactors were established, which were exposed to 0.5-5 mg/L MeP and BZC individually and in combination, while polyamide 6 bags were added to cultivate plastisphere within the three SAD systems. The results found that BZC had a more serious inhibition effect than MeP. Besides, MeP mitigated the toxicity of BZC on SAD, and the observed inhibition gradually diminished over time. The incorporation of preservatives significantly changed the microbial community structures and induced the proliferation of resistance genes (RGs) in both biofilm and plastisphere. Enrichment of functional bacterium like Thiobacillus and the colonization of pathogenic bacterium like Desulfovibrio were found in plastisphere. The proliferation of intracellular RGs in biofilm might drive the recovery of SAD performance. In addition, mobile genetic elements were recognized as the key drivers of horizontal gene transfer responsible for the dissemination of RGs. This research guided the efforts to control the risks associated with preservatives and MPs in wastewater treatment.},
}

@article {pmid40904109,
year = {2025},
author = {Clabby, T and Tesson, F and Gaborieau, B and Bernheim, A},
title = {Why do bacteria accumulate antiphage defence systems?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240082},
pmid = {40904109},
issn = {1471-2970},
support = {//MSDAVENIR/ ; //Pasteur Institute/ ; /ERC_/European Research Council/International ; },
mesh = {*Bacteria/classification/genetics/immunology/virology ; *Bacteriophages/genetics/physiology ; Ecology ; CRISPR-Cas Systems ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; *Phage Therapy ; },
abstract = {While it is well established that bacterial genomes encode multiple and diverse antiphage systems, the reasons for their co-occurrence and their heterogeneous distribution remain debated. This review examines why bacteria accumulate antiphage systems and how this influences phage-bacteria interactions, particularly in the context of phage therapy. Two main hypotheses may explain this phenomenon: (i) the pan-immunity hypothesis, which suggests that defence system accumulation provides protection against phage predation at the community level, and (ii) mobile genetic element (MGE) competition, where defence systems primarily protect intra-bacterial MGEs against other ones rather than the bacterial host itself. The ecological context also influences the distribution of antiphage systems, with defencee accumulation shaping phage-bacteria interactions in diverse communities but playing a lesser role at the species level, potentially explaining why multiple defences do not strongly limit phage host range in therapeutic settings. Finally, we address the challenges in understanding the drivers shaping the distribution of defence systems across bacterial genomes (expressions, costs, etc.) and their implications for elucidating the ecological role of defence systems and optimizing phage therapy strategies.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}

*Bacteria/classification/genetics/immunology/virology
*Bacteriophages/genetics/physiology
Ecology
CRISPR-Cas Systems
Gene Transfer, Horizontal
Interspersed Repetitive Sequences
*Phage Therapy

@article {pmid40914062,
year = {2025},
author = {Zhang, B and Hu, X and Guo, Z and Qu, J and He, Y and Han, L and Kou, J and Yu, H and Lian, J and Zhang, Y},
title = {In-situ remediation efficiency and mechanism of tylosin contaminated soil with biochar immobilized degrading enzyme.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139483},
doi = {10.1016/j.jhazmat.2025.139483},
pmid = {40914062},
issn = {1873-3336},
abstract = {Residues of veterinary antibiotics such as tylosin in soils can induce selective pressure on indigenous soil microbes and increase the dissemination risk of antibiotic resistance genes (ARGs) by horizontal gene transfer (HGT), which poses a serious threat to both soil and public health. While conventional bioremediation methods face challenges in efficiency and stability, enzyme-based approaches offer promising alternatives. This study developed a novel biochar-immobilized tylosin-degrading enzyme (BIE) system to simultaneously address tylosin contamination and antibiotic resistance gene (ARG) proliferation in agricultural soils. Using HPLC-MS, qPCR, and 16S rRNA sequencing, we comprehensively evaluated tylosin degradation kinetics, ARG dynamics, and microbial community responses during BIE treatment towards tylosin-contaminated soil. The results revealed the remarkable degradation efficiency of tylosin (99.85 %) by BIE within 7 days. In addition, after 20 days of BIE treatment, the relative abundances of ARGs and mobile gene elements (MGEs) significantly decreased by 11.63-100 % depending on the specific gene which favored the recovery of soil bacterial community diversity. Mechanistic studies revealed that biochar synergistically enhanced enzyme stability and provided protective microenvironments, enabling efficient lactone bond hydrolysis and tylosin detoxification. These findings establish biochar-immobilized degrading enzyme technology as a sustainable solution for dual challenges of antibiotic persistence and resistance spread in contaminated soils. Future research should focus on field validation, large-scale application protocols, and long-term ecological impacts to facilitate practical implementation of this innovative approach.},
}

@article {pmid40914041,
year = {2025},
author = {Zhang, J and Li, W and Zhang, X and Wang, X and Guo, X and Bai, C and Lv, L},
title = {Higher chlorine dosage does not consistently enhance antibiotic resistance mitigation in the Cl2-UV process.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124534},
doi = {10.1016/j.watres.2025.124534},
pmid = {40914041},
issn = {1879-2448},
abstract = {Health problems arising from antibiotic resistance are a global concern. The Cl2-UV disinfection process has shown potential for controlling antibiotic resistance in water; however, the influence of disinfectant dosage on its effectiveness remains insufficiently understood. Can antibiotic resistance be controlled by simply increasing the disinfectant dosage? This study demonstrated that higher disinfectant levels improved antibiotic resistance gene (ARG) removal, with certain ARGs reaching 1.82 log removal under conventional conditions. Nevertheless, higher disinfectant dosages also led to an increase in the relative abundance of multidrug resistance genes (MRGs), aminoglycoside resistance genes (AmRGs), and fosmidomycin resistance genes (FRGs). Correlation analysis of ARGs with mobile genetic elements (MGEs) and ARG-host bacteria indicated that this enrichment was primarily driven by enhanced horizontal gene transfer (HGT). Notably, increases in UV fluence and chlorine dose had distinct impacts on the total relative abundance of ARGs: higher UV fluence reduced total relative abundance, whereas higher chlorine dose increased it. These contrasting trends are likely linked to differences in the dominant HGT pathways under each condition. Greater UV fluence tended to promote conjugative transfer among surviving bacteria, while higher chlorine dosages more effectively facilitated natural transformation. Considering both the absolute and relative abundances of ARGs, along with calculated health-risk indices for each treatment condition, the findings indicated that increasing UV fluence is more effective for controlling ARGs in water. These results provide valuable insights for optimizing the Cl2-UV disinfection process to better manage antibiotic resistance in aquatic environments.},
}

@article {pmid40911574,
year = {2025},
author = {Chang, ACG and Amaral, MWW and Greenwood, M and Ikudaisi, C and Li, J and Hamsher, SE and Miller, S and Kociolek, P},
title = {Evolutionary dynamics in plastomes and mitogenomes of diatoms.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331749},
pmid = {40911574},
issn = {1932-6203},
mesh = {*Diatoms/genetics/classification ; *Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; Pseudogenes ; },
abstract = {Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling, contributing significantly to photosynthesis and serving as fundamental components in aquatic ecosystems. Recent advancements in genomic sequencing have shed light on their evolutionary dynamics, revealing evolutionary complex genomes influenced by symbiotic relationships and horizontal gene transfer events. By analyzing publicly available sequences for 120 plastomes and 70 mitogenomes, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. Gene losses and pseudogenes were more frequently observed in plastomes compared with mitogenomes. Overall, gene losses were particularly abundant in the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp. Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC, ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost repeatedly across several diatom taxa. Analysis of nucleotide substitution rates indicated that, in general, mitogenomes were evolving at a more rapid rate compared to plastomes. This is contrary to what was observed in synteny analyses, where plastomes exhibited more structural rearrangements than mitogenomes, with the exception of the genus Coscinodiscus and one group of species within Thalassiosira.},
}

*Diatoms/genetics/classification
*Genome, Mitochondrial/genetics
*Evolution, Molecular
Phylogeny
Pseudogenes

@article {pmid40911283,
year = {2025},
author = {Liu, Y and Wang, X},
title = {Post-translational Modifications of the Nucleoid Protein H-NS: Sites, Mechanisms, and Regulatory Cues.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf045},
pmid = {40911283},
issn = {1574-6976},
abstract = {Histone-like nucleoid structuring protein H-NS plays a pivotal role in orchestrating bacterial chromatin and regulating horizontal gene transfer (HGT) elements. In response to environmental signals, H-NS undergoes dynamic post-translational modifications (PTMs) that resemble the epigenetic codes of eukaryotic histones. This review explores how environmental cues regulate PTMs at specific sites within distinct domains of H-NS, thereby modulating its oligomerization and DNA-binding capabilities to reprogram bacterial responses. Notably, HGT elements commonly encode counter-silencing factors, including PTM-modifying enzymes, that counteract H-NS repression. We propose that combinatorial PTM patterns on H-NS form the bacterial histone-like epigenetic code, regulating the expression of HGT elements. Collectively, these interactions establish a sophisticated network of silencing and counter-silencing mechanisms that drive bacterial genome evolution.},
}

@article {pmid40910769,
year = {2025},
author = {Vandierendonck, J and Valcek, A and Nguyen, VS and Vertommen, D and Malhotra-Kumar, S and De Greve, H and Loris, R},
title = {Isolation and characterization of bacteriophages from clinical enterohemorrhagic Escherichia coli strains.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0059725},
doi = {10.1128/spectrum.00597-25},
pmid = {40910769},
issn = {2165-0497},
abstract = {Temperate bacteriophages play a pivotal role in the biology of their bacterial host. Of particular interest are bacteriophages infecting enterohemorrhagic E. coli (EHEC) due to their significant contribution to the pathogenicity of its host, most notably by encoding the key virulence factor of this pathogen, the Shiga toxin. To better understand the role of EHEC phages on the functionality of its host, we isolated eight temperate phages from clinical EHEC isolates and characterized their genomic composition, morphology, and receptor targeting. Morphological analysis identified one long-tailed siphophage, targeting the OmpC receptor for host recognition, whereas the other seven phages are short-tailed podophages and target the essential BamA protein. Genomic characterization revealed significant variations between the long- and short-tailed phages. Five of the eight isolated phages encode the potent Shiga toxin. Comparative analysis displays the typical lambdoid mosaicism, indicative of horizontal gene transfer driving evolution. These findings provide insights into the genetic and morphologic diversity and receptor specificity of EHEC phages, highlighting their role in the evolution and pathogenicity of clinical EHEC strains.IMPORTANCECharacterizing bacteriophages from clinical EHEC isolates is crucial in understanding the mechanisms underlying bacterial evolution and virulence. Despite the clinical relevance of EHEC bacteriophages, they remain underexplored, and particularly phage receptors are often not characterized. Studying temperate EHEC phages is essential in the development of strategies to address the global burden of these foodborne infections. Notably, identifying the phage receptors is critical in unraveling the specific interaction between phage and host. Knowledge of the phage receptors can provide insights into the mechanisms of phage infection, host range, and bacterial resistance and is fundamental in the design of targeted therapies like new antimicrobials, phage therapy, or prevention of those infections.},
}

@article {pmid40910370,
year = {2025},
author = {Stepanauskas, R and Brown, JM and Arasti, S and Mai, U and Gavelis, G and Pachiadaki, M and Bezuidt, O and Munson-McGee, JH and Chang, T and Biller, SJ and Berube, PM and Mirarab, S},
title = {Net rate of lateral gene transfer in marine prokaryoplankton.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf159},
pmid = {40910370},
issn = {1751-7370},
abstract = {Lateral gene transfer is a major evolutionary process in Bacteria and Archaea. Despite its importance, lateral gene transfer quantification in nature using traditional phylogenetic methods has been hampered by the rarity of most genes within the enormous microbial pangenomes. Here, we estimated lateral gene transfer rates within the epipelagic tropical and subtropical ocean using a global, randomized collection of single amplified genomes and a non-phylogenetic computational approach. By comparing the fraction of shared genes between pairs of genomes against a lateral gene transfer-free model, we show that an average cell line laterally acquires and retains ~13% of its genes every 1 million years. This translates to a net lateral gene transfer rate of ~250 genes L-1 seawater day-1 and involves both "flexible" and "core" genes. Our study indicates that whereas most genes are exchanged among closely related cells, the range of lateral gene transfer exceeds the contemporary definition of bacterial species, thus providing prokaryoplankton with extensive genetic resources for lateral gene transfer-based adaptation to environmental stressors. This offers an important starting point for the quantitative analysis of lateral gene transfer in natural settings and its incorporation into evolutionary and ecosystem studies and modeling.},
}

@article {pmid40907314,
year = {2025},
author = {Chu, WC and Wu, YX and Liu, FF},
title = {Bio-based microplastics as vectors of resistance genes under combined pressure of antibiotics and heavy metals in marine environment.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139698},
doi = {10.1016/j.jhazmat.2025.139698},
pmid = {40907314},
issn = {1873-3336},
abstract = {In this study, we investigated the characteristics of biofilm formation on petroleum-based polyethylene (PE) and bio-based polylactic acid (PLA) microplastics, the structure of bacterial communities, and the enrichment and transfer of related resistance genes in marine environments. We examined these factors under varying concentrations of the heavy metal zinc (Zn) and the sulfadiazine (SDZ), both individually and in combination, and analyzed the underlying mechanisms and interrelationships. The results indicated that PE surface was more conducive to bacterial colonization and biofilm stabilization. Conversely, the prolonged combined exposure to SDZ and Zn promoted the growth of PLA biofilm. Bacterial communities within the biofilms responded to external stresses through oxidative stress responses, alterations in extracellular polymeric substances, shifts in the relative abundance of specific microbial taxa, and adjustments in metabolic pathways. These adaptations positively influenced the enrichment and transfer of resistance genes. Under experimental conditions, PLA microplastics were more likely than PE to serve as carriers of resistance genes in marine environments. Zn promoted the spread of resistance genes by enhancing horizontal gene transfer (HGT) in the short term, and in the later stages, shaped microbial community composition and co-selected with SDZ, thereby influencing the distribution and dissemination of resistance genes.},
}

@article {pmid40907215,
year = {2025},
author = {Li, J and Zuo, J and Xu, H and Yang, J and Hu, Y and Han, Y and Tang, Y and Lei, C and Li, C and Wang, H},
title = {Sub-inhibitory gentamicin promotes extracellular vesicles biogenesis and blaNDM dissemination in carbapenem-resistant Escherichia coli via mrdA/mrdB pathway.},
journal = {Veterinary microbiology},
volume = {310},
number = {},
pages = {110704},
doi = {10.1016/j.vetmic.2025.110704},
pmid = {40907215},
issn = {1873-2542},
abstract = {The increasing prevalence of carbapenem-resistant Escherichia coli (CRE) in swine production poses a significant public health threat, largely driven by the misuse of antibiotics. Recent studies highlight extracellular vesicles (EVs) as emerging mediators of horizontal gene transfer and antibiotic resistance dissemination. In this study, we investigated the regulatory effects of sub-inhibitory concentrations of gentamicin (GEN), a commonly used antibiotic in pig farms, on EVs production and blaNDM gene transfer in CRE isolates. EVs purified from porcine CRE strains exhibited typical spherical morphology with average diameters around 100 nm and particle concentrations exceeding 2.0 × 10 [11] particles/mL. Treatment with 1/64 minimum inhibitory concentration (MIC) GEN significantly increased EV secretion and enhanced the protective effect of EVs against meropenem in both intra-species (E. coli ATCC 25922) and inter-species recipient strains (S. Typhimurium ATCC 14028, P. aeruginosa ATCC 15692, K. pneumoniae CMCC 46117, L. monocytogenes ATCC 19115, and O. burkholderi ATCC 25416), in a dose- and time-dependent manner. Moreover, GEN-induced EVs facilitated blaNDM-5 (New Delhi metallo-β-lactamase-5) transfer preferentially to E. coli strains. Transcriptomic analysis revealed that GEN treatment led to differential expression of multiple genes, among which mrdA and mrdB were identified as key regulators of EVs biogenesis. Targeted deletion of mrdA or mrdB markedly reduced EVs production and blaNDM transfer frequency. These findings suggest that the mrdA/mrdB pathway plays a crucial role in GEN-mediated EVs formation and resistance gene dissemination, providing novel insights into the molecular mechanisms by which sub-inhibitory antibiotic exposure promotes antimicrobial resistance propagation. Our work may inform future strategies for controlling resistance dissemination in livestock production.},
}

@article {pmid40905702,
year = {2025},
author = {Nucci, A and Le Bris, J and Diaz-Diaz, S and Torres-Elizalde, L and Rocha, EPC and Rendueles, O},
title = {Phenotypic heterogeneity of capsule production across opportunistic pathogens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0180725},
doi = {10.1128/mbio.01807-25},
pmid = {40905702},
issn = {2150-7511},
abstract = {Phenotypic heterogeneity allows bacteria to adapt fast to changing environments. Extracellular capsules are well-known virulence factors, but also increase the cell adaptability and prevalence under hostile conditions. To limit their cost, some species regulate capsule production by genetic phase variation. Here, we demonstrated that phenotypic heterogeneity is a major mechanism controlling capsule production in Klebsiella and Acinetobacter species. We designed a method to agnostically measure heterogeneity and show that 71% of Klebsiella pneumoniae strains can be heterogeneous. This is mostly associated with K. pneumoniae strains that do not encode rmp, a genetic determinant of hypervirulence. Capsule serotype exchanges across several genetic backgrounds revealed that heterogeneity depends on specific genome-capsule locus interactions. Importantly, we showed that heterogeneity provides a fitness advantage especially in conditions where the capsule is costly, as estimated by comparing non-heterogeneous and heterogeneous strains during competition with their non-capsulated variants. Finally, heterogeneity impacts phage adsorption patterns, and could thus alter the rate of horizontal gene transfer events. This unsuspected heterogeneity may help understand the transition from commensalism to pathogenesis and can have important implications in virulence, environmental survival and evolution of some ESKAPE pathogens.IMPORTANCEThe polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. It is also an important virulence factor and a major target for both phage therapy and the development of vaccines. Here, we reveal that in two major genera of ESKAPE pathogens, Klebsiella spp. and Acinetobacter spp., capsule production within clonal populations is heterogeneous, leading to mixed populations of hyper-, hypo-, and intermediate-capsulated cells. Such heterogeneity responds to different environmental cues, including changes in nutrient availability and spatial structure. We show that this plasticity, known to enable faster, more efficient adaptation to environmental changes, limits capsule costs and could explain Klebsiella and Acinetobacter resilience. Finally, capsule heterogeneity can play a major role in bacterial evolution, as a driver of horizontal gene transfer, and in treatment failure. Thus, it should be taken into account in the design of prophylactic strategies and antimicrobial therapy.},
}

@article {pmid40905677,
year = {2025},
author = {Bucknell, A and Wilson, HM and Gonçalves Dos Santos, KC and Simpfendorfer, S and Milgate, A and Germain, H and Solomon, PS and Bentham, A and McDonald, MC},
title = {Sanctuary: a Starship transposon facilitating the movement of the virulence factor ToxA in fungal wheat pathogens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0137125},
doi = {10.1128/mbio.01371-25},
pmid = {40905677},
issn = {2150-7511},
abstract = {There is increasing evidence that mobile genetic elements can drive the emergence of pathogenic fungal species by moving virulence genes horizontally. The 14 kbp ToxhAT transposon was shown to move the necrotrophic effector, ToxA, horizontally between wheat pathogens, namely Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana. All three species utilize the ToxA protein to infect wheat. Previous work found ToxhAT in distinct chromosomal positions in two B. sorokiniana isolates, indicating that the transposon remains active in this species. Here, we confirm the movement of ToxhAT using long-read sequencing of eight new and one previously published B. sorokiniana isolates. One event of independent transposition of ToxhAT was observed, and target site duplications of "TA" were identified, confirming that this is an active transposon in this species that likely falls into the Tc1/Mariner transposon family. We propose renaming this non-autonomous transposon to ToxTA. Whole genome analysis revealed that ToxTA is a passenger embedded in a much larger, conserved 170-196 kbp mobile genetic element. This element, termed Sanctuary, belongs to the newly described Starship transposon superfamily. This classification is based on the presence of direct repeats, empty insertion sites, a putative tyrosine recombinase gene, and other features of Starship transposons. We also show that ToxTA has been independently acquired by two different Starships, Sanctuary and Horizon, which share little to no sequence identity, outside of ToxTA. This classification makes Horizon and Sanctuary part of a growing number of Starships involved in the horizontal gene transfer of adaptive genetic material between fungal species.IMPORTANCEThe work presented here expands our understanding of a novel group of mobile genetic elements called Starships that facilitate the horizontal exchange of numerous genes between fungal pathogens. Our analysis shows that Sanctuary and ToxTA are both active transposons within the Bipolaris sorokiniana genome. We also show that the smaller ToxTA transposon has been independently acquired by two different Starships, namely Sanctuary in B. sorokiniana and Horizon in Pyrenophora tritici-repentis and Parastagonospora nodorum. Outside of ToxTA, these two Starships share no sequence identity. The acquisition of ToxTA by two different mobile elements in three different fungal wheat pathogens demonstrates how horizontal transposon transfer is driving the evolution of virulence in these important wheat pathogens.},
}

@article {pmid40904310,
year = {2025},
author = {Wang, C and Qin, JX and Li, M and Shen, Z},
title = {[Genomic characteristics and mechanisms of horizontal plasmid transfer in Klebsiella pneumoniae producing NDM-1 and IMP-4 carbapenemases].},
journal = {Zhonghua yi xue za zhi},
volume = {105},
number = {34},
pages = {3013-3016},
doi = {10.3760/cma.j.cn112137-20250710-01687},
pmid = {40904310},
issn = {0376-2491},
support = {82272374//National Natural Science Foundation of China/ ; },
mesh = {*Klebsiella pneumoniae/genetics/drug effects ; *beta-Lactamases/genetics ; Plasmids ; Microbial Sensitivity Tests ; *Gene Transfer, Horizontal ; Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {A retrospective analysis was conducted on a clinically isolated Klebsiella pneumoniae strain KP1050 that produces both New Delhi Metallo-β-lactamase (NDM)-1 and Imipenem-hydrolyzing β-lactamase (IMP)-4 carbapenemases. The minimum inhibitory concentrations of various antimicrobial agents were determined using the microbroth dilution method. Whole-genome sequencing was performed to identify the resistance genes and resistance plasmids carried by the strain. Conjugation assays and gene knockout techniques were employed to clarify the mechanisms of horizontal transfer of resistance plasmids. Klebsiella pneumoniae KP1050 was resistant to multiple antimicrobial agents, including carbapenems, and only susceptible to amikacin, tigecycline, and polymyxin. The strain belonged to ST1245, carrying the blaNDM-1 and blaIMP-4 carbapenemase resistance genes on the 59 730 bp IncN-type and 289 270 bp IncHI5-type plasmids, respectively. Both IncN and IncHI5-type plasmids harbored complete gene clusters encoding the type Ⅳ secretion system and could be conjugated to recipient bacteria; however, the conjugation efficiency of the IncN-type NDM-1 plasmid (1×10[-3]) was higher than that of the IncHI5-type IMP-4 plasmid (5×10[-6]). Knockout of key genes in the plasmid type Ⅳ secretion system revealed that the IncHI5-type IMP-4 plasmid was not an independently conjugative plasmid but could undergo horizontal transmission through conjugation with the assistance of the IncN-type NDM-1 plasmid. Interactions between plasmids can promote the spread of carbapenemase resistance genes.},
}

*Klebsiella pneumoniae/genetics/drug effects
*beta-Lactamases/genetics
Plasmids
Microbial Sensitivity Tests
*Gene Transfer, Horizontal
Bacterial Proteins/genetics
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid40895615,
year = {2025},
author = {Zhu, L and Chen, K and Xu, L and Wang, A and Gan, H and Sun, J and Wu, Y and Li, Y and Guo, Y and Yi, Y and Qiang, X and He, J and Zhou, H and Lin, Y},
title = {Genomic Investigation of a Bacillus subtilis Strain Sourced from Commercially Available Milk Powder in China Reveals Potential Risk Factors.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4311-4328},
pmid = {40895615},
issn = {1178-6973},
abstract = {BACKGROUND: Milk powder is a key food source, especially for infants and vulnerable groups. However, Bacillus contamination during production, storage, or handling can cause spoilage, quality issues, or health risks. This study identified and isolated Bacillus subtilis from commercially available Chinese milk powder.

METHODS: A pure colony of Bacillus subtilis was isolated from an LB agar plate supplemented with milk powder and identified using mass spectrometry. The genome of this strain was sequenced using third-generation sequencing technology. Following assembly, the genome was functionally annotated and subjected to comprehensive bioinformatic analysis.

RESULTS: Genomic analysis classified the strain as Bacillus subtilis via MALDI-TOF and ANI (98.82% with B. subtilis AMR1). Its genome features a 4.26 Mbp chromosome and 97.6 kbp plasmid encoding 4,539 genes, including virulence factors (209 genes), antibiotic resistance genes (19 genes), and carbohydrate-active enzymes (253 genes). Key virulence mechanisms include immune modulation, stress adaptation, toxin production, and biofilm formation. Antibiotic resistance involves efflux pumps (eg, qacJ, bmr), enzymatic inactivation (eg, FosBx1, aadK), and target modification (eg, vanG cluster, tet(45)). Phylogenetically (LIN78), the strain clusters with foodborne B. subtilis isolates (eg, from Korean gochujang and soybean), diverging from B. cereus and environmental Bacillus clades. Comparative genomics revealed 53 LIN78-specific genes, encompassing defense mechanisms and mobile elements, and synteny in all homologs except B. subtilis ATCC 11774. Genomic islands, CRISPR arrays, and recombination-associated repeats indicate adaptive evolution.

CONCLUSION: This study characterizes Bacillus subtilis LIN78, a genomically plastic strain isolated from Chinese milk powder. It exhibits adaptation to food environments via horizontal gene transfer, stress tolerance, and spoilage traits, while carrying antimicrobial resistance risks and potential biotechnological applications. The findings necessitate genomic monitoring to manage food safety, resistance spread, and leverage its dual role as both a spoilage organism and source of bioactive compounds..},
}

@article {pmid40755030,
year = {2025},
author = {Fang, Z and Li, Y and Huang, J and Chen, M and Chen, X and Mo, X and Zhong, Z and Li, X and Lu, G and Lin, G and Wang, Z and Zheng, H},
title = {Experimental insights into genome reconstruction driven by horizontal transfer of supernumerary chromosomes in Magnaporthe oryzae.},
journal = {The New phytologist},
volume = {248},
number = {1},
pages = {140-156},
doi = {10.1111/nph.70438},
pmid = {40755030},
issn = {1469-8137},
support = {2023YFD1400201//National Key Research and Development Program of China/ ; 32172365//National Natural Science Foundation of China/ ; 32272513//National Natural Science Foundation of China/ ; },
mesh = {*Gene Transfer, Horizontal/genetics ; *Chromosomes, Fungal/genetics ; *Genome, Fungal/genetics ; Oryza/microbiology ; Virulence/genetics ; *Ascomycota/genetics/pathogenicity ; *Magnaporthe/genetics/pathogenicity ; },
abstract = {Many pathogenic fungi display 'two-speed genome', with the fast-evolving genomic compartments enriched with repetitive sequences, particularly the transposons, which have been shown to drive the variation of pathogenicity-associated genes. Supernumerary chromosomes (SCs) are known to facilitate genomic variation in fungal pathogens, but their specific role in such processes remains understudied. In this study, we assessed the transferability of SCs between asexual Magnaporthe oryzae strains during co-culture and co-infection, and investigated their role in genome reconstruction through experimental evolution assays. We found that SCs could be horizontally transferred between M. oryzae strains and revealed frequent structural variations facilitated by SCs, including deletions, duplications, translocations, and SC-core chromosome recombinations during and after horizontal transfer. Remarkably, all observed intra- and inter-chromosome rearrangements were confined to core chromosome ends and SCs, indicating a robust role of SCs in facilitating genetic exchange within fast-evolving genomic compartments. Additionally, SC carrying the avirulence gene AvrPik[E] modulates M. oryzae virulence against Pikh rice through horizontal transfer, loss of whole SC, and segmental deletions. Our findings establish SCs as critical players in shaping the diversity and dynamics of the pathogenic fungal genomes, highlighting them as a cradle for the variation of pathogenicity-associated genes.},
}

*Gene Transfer, Horizontal/genetics
*Chromosomes, Fungal/genetics
*Genome, Fungal/genetics
Oryza/microbiology
Virulence/genetics
*Ascomycota/genetics/pathogenicity
*Magnaporthe/genetics/pathogenicity

@article {pmid40122738,
year = {2025},
author = {Rana, MS and Kim, S and Ko, SY and Kim, N and Kim, SY and Lee, DE and Kwon, KT and Kim, YK and Lee, JC},
title = {Co-carriage of blaNDM-1 and blaVIM-2 in different plasmids of Acinetobacter junii isolate and the transfer of blaNDM-1-carrying plasmids to Gram-negative bacteria.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {58},
number = {5},
pages = {613-616},
doi = {10.1016/j.jmii.2025.03.008},
pmid = {40122738},
issn = {1995-9133},
mesh = {*beta-Lactamases/genetics ; *Plasmids/genetics ; *Acinetobacter/genetics/drug effects/enzymology/isolation & purification ; Humans ; Carbapenems/pharmacology ; Anti-Bacterial Agents/pharmacology ; Acinetobacter Infections/microbiology ; *Gram-Negative Bacteria/genetics ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Gene Transfer, Horizontal ; },
abstract = {Carbapenem-resistant Acinetobacter junii isolate co-carried blaVIM-2 and blaNDM-1 in different plasmids. blaNDM-1- and blaVIM-2-carrying plasmids were characterized using the whole genome sequencing. The expression of blaNDM-1 was higher than that of blaVIM-2. blaNDM-1-carrying plasmid was conjugally transferred to various Gram-negative bacterial species. The transferability of blaNDM-1-carrying plasmid raises concerns about the potential spread of carbapenem resistance across diverse bacterial populations.},
}

*beta-Lactamases/genetics
*Plasmids/genetics
*Acinetobacter/genetics/drug effects/enzymology/isolation & purification
Humans
Carbapenems/pharmacology
Anti-Bacterial Agents/pharmacology
Acinetobacter Infections/microbiology
*Gram-Negative Bacteria/genetics
Microbial Sensitivity Tests
Whole Genome Sequencing
*Gene Transfer, Horizontal

@article {pmid40780870,
year = {2025},
author = {Muller, H and Savisaar, R and Peccoud, J and Charlat, S and Gilbert, C},
title = {Phylogenetic relatedness rather than aquatic habitat fosters horizontal transfer of transposable elements in animals.},
journal = {Genome research},
volume = {35},
number = {9},
pages = {2011-2022},
pmid = {40780870},
issn = {1549-5469},
mesh = {Animals ; *Phylogeny ; *Gene Transfer, Horizontal ; *DNA Transposable Elements/genetics ; *Ecosystem ; Evolution, Molecular ; Bayes Theorem ; Genome ; },
abstract = {Horizontal transfer of transposable elements (HTT) is an important driver of genome evolution, yet the factors conditioning this phenomenon remain poorly characterized. Here, we screen 247 animal genomes from four phyla (annelids, arthropods, mollusks, chordates), spanning 19 independent transitions between aquatic and terrestrial lifestyles, to evaluate the suspected positive effects of aquatic habitat and of phylogenetic relatedness on HTT. Among the 6043 independent HTT events recovered, the vast majority (>85%) involve DNA transposons, of which Mariner-like and hAT-like elements have the highest rates of horizontal transfer and of intragenomic amplification. Using a novel approach that circumvents putative biases linked to phylogenetic inertia and taxon sampling, we find that HTT rates positively correlate with similarity in habitat type but are not significantly higher in aquatic than in terrestrial animals. However, modeling the number of HTT events as a function of divergence time in a Bayesian framework reveals a clear positive effect of phylogenetic relatedness on HTT rates in most of the animal species studied (162 out of 247). The effect is very pronounced: A typical species is expected to show 10 times more transfers with a species it diverged from 250 million years (My) ago than with a species it diverged from 650 My ago. Overall, our study underscores the pervasiveness of HTT throughout animals and the impact of evolutionary relatedness on its dynamics.},
}

Animals
*Phylogeny
*Gene Transfer, Horizontal
*DNA Transposable Elements/genetics
*Ecosystem
Evolution, Molecular
Bayes Theorem
Genome

@article {pmid40895304,
year = {2025},
author = {Tanu, R and Chaudhary, AA and Prakash, G and Yasmeen, N and Ali, MAM and Raza, N and Sharma, PK and Kumar, A and Yadav, T and Kumar, V},
title = {Exploring the potential of photodynamic therapy in overcoming multidrug resistance: mechanisms, synergies, and clinical advancements in infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1624036},
doi = {10.3389/fcimb.2025.1624036},
pmid = {40895304},
issn = {2235-2988},
abstract = {Multidrug resistance (MDR) in bacterial and fungal pathogens poses a growing global health crisis, rendering many conventional antimicrobial therapies ineffective. The rise of MDR strains complicates treatment, prolongs illness, increases healthcare costs, and contributes to higher mortality rates. Mechanisms driving MDR include enzymatic drug inactivation, target modification, efflux pump activity, decreased permeability, and biofilm formation-often fueled by horizontal gene transfer and selective pressure from antimicrobial overuse. In response to the urgent need for novel therapeutic strategies, photodynamic therapy (PDT) has emerged as a promising, non-traditional approach. PDT utilizes a photosensitizing agent, light of a specific wavelength, and oxygen to generate reactive oxygen species (ROS) that inflict oxidative damage on microbial or cancer cells. This mechanism circumvents conventional resistance pathways, offering targeted, minimally invasive, and effective treatment for infections and malignancies. PDT is particularly adept at penetrating biofilms and resistant microbial populations, thus broadening its clinical applicability. In addition to direct microbial eradication, PDT may stimulate immune responses and demonstrates a favorable safety profile compared to traditional antibiotics or chemotherapy. Furthermore, advances in Antimicrobial Blue Light (aBL) and next-generation photosensitizers enhance PDT's effectiveness while minimizing resistance development. This review explores the biological mechanisms underlying MDR, the principles and evolution of PDT, and its synergistic potential in managing infectious diseases. By addressing critical gaps in antimicrobial therapy, PDT stands out as a transformative modality in the ongoing battle against drug-resistant pathogens.},
}

@article {pmid40895299,
year = {2025},
author = {Khan, MSI and Wu, J and Ji, S and Tan, D and Sui, B and Peng, S and Zhan, J and Yin, J},
title = {Expanding structural insights into DNA packaging apparatus and endolysin LysSA05 function of Epsilon15 bacteriophage.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1643576},
doi = {10.3389/fcimb.2025.1643576},
pmid = {40895299},
issn = {2235-2988},
abstract = {The rising prevalence of multidrug-resistant (MDR) foodborne pathogens, particularly Salmonella spp., necessitates alternative antimicrobial solutions. Phage therapy offers a promising solution against MDR Gram-negative infections; however, its clinical application is constrained by the presence of endotoxins, residual cellular debris, the risk of horizontal gene transfer by temperate phages, and an incomplete understanding of how phage structural integrity influences infectivity and enzyme function. In this study, we present a structural and functional analysis of temperate bacteriophage Epsilon15 (ϵ15), focusing on its DNA packaging and injection machinery, along with characterization of the dual-acting endolysin LysSA05. Iodixanol-purified virions suspended in phosphate-buffered saline (PBS), under conditions optimized to preserve virion stability, were analyzed using graphene oxide (GO)-supported cryo-electron microscopy. This approach resolved the full asymmetric architecture of ϵ15, revealing a detailed internal nucleic acid organization with at least eight concentric layers radially and approximately 28 axially compacted layers within the capsid. The DNA packaging machinery, comprising the core, portal, and hub, was resolved at high resolution, including a 42 nm-long and 18 nm-wide injection channel anchored by a dodecameric portal complex visualized at ~7 Å resolution. Concurrently, we characterized LysSA05, a dual-acting endolysin harboring a glycoside hydrolase 19 (GH19) catalytic domain accommodating peptidoglycan (PG) residues N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) through structural docking, indicating plausible binding interactions that promote hydrolysis support vector machine (SVM), random forest (RF), discriminant analysis (DA), artificial neural network (ANN) and physicochemical scanning identified an amphipathic helix (residues 59-112) with predicted antimicrobial peptide (AMP)-like properties. Biochemical validation confirmed that LysSA05 destabilizes lipopolysaccharides (LPS) and permeabilizes the outer membrane of Gram-negative bacteria independently of permeabilizers, with enhanced efficacy observed upon co-treatment with Ethylenediaminetetraacetic acid (EDTA) or citric acid. In summary, our findings elucidate key structural features of ϵ15 relevant to infection and genome delivery, while positioning LysSA05 as a promising enzybiotic candidate against MDR Gram-negative pathogens.},
}

@article {pmid40894724,
year = {2025},
author = {Charbonnier, M and Probst-Lotze, S and Racine, H and Radin, JN and Rios-Delgado, G and Laster, HM and Kohl, MP and Mazgaj, R and Blum, M and Marchand, V and Chicher, J and Marzi, S and Romby, P and Tree, JJ and Waldron, KJ and Boyd, JM and Dutheil, JY and Kehl-Fie, TE and Lalaouna, D},
title = {A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.23.671911},
pmid = {40894724},
issn = {2692-8205},
abstract = {Small regulatory RNAs (sRNAs) are key drivers of bacterial adaptation to environmental fluctuations, including iron and manganese restriction imposed by the host. This study explored the repertoire of sRNAs produced by the human pathogen Staphylococus aureus in response to metal limitation. Two sRNAs, S1077 and ZinS (RsaX20), regulated by zinc (Zn) availability, were identified. Further investigations revealed that, similar to the cnt operon from which it derives, S1077 synthesis is controlled by the transcription factors Zur and Fur. In contrast, zinS transcription is solely repressed by Zur. Amongst the ZinS targets are several Zn-dependent enzymes, such as the alcohol dehydrogenase Adh, whose synthesis is negatively regulated by ZinS. Loss of ZinS does not alter staphylococcal metal accumulation, suggesting a role in a Zn-sparing response. Remarkably, zinS also encodes a small peptide, ZinP. Genomic analysis suggests that the regulatory portion of ZinS emerged from the 3' untranslated region of zinP in S. aureus and closely related species after horizontal gene transfer from phylogenetically distant organisms. All our findings demonstrate that sRNAs also facilitate bacterial adaptation to Zn limitation, and that genetic exchange and subsequent neofunctionalization have enabled S. aureus to adapt to metal-restricted environments.},
}

@article {pmid40893973,
year = {2025},
author = {Forterre, P},
title = {Extensive lateral gene transfer between proto-eukaryotes and Heimdallarchaeia suggests their close association during eukaryogenesis.},
journal = {mLife},
volume = {4},
number = {4},
pages = {345-362},
doi = {10.1002/mlf2.70030},
pmid = {40893973},
issn = {2770-100X},
abstract = {It has been proposed by Ettema and colleagues, in the two-domain framework for the tree of life, that Eukarya emerged from Heimdallarchaeia, as sister group to Hodarchaeales. Looking at the individual trees of the protein markers used by these authors, I notice that Eukarya are only sister to Hodarchaeales or other Heimdallarchaeia in a minority of trees, whereas they are located far apart from these Asgard archaea in most other trees. Examination of single trees also reveals massive gene transfers from Crenarchaeota and/or Korachaeota to hyperthermophilic Njordarchaeales, explaining why their belonging to Asgard archaea is sometimes difficult to recover. Finally, I discuss several points raised by Ettema and colleagues, such as the phylogeny of Asgard archaea and the hyperthermophilic nature of their last common ancestor. The patchy localization of Eukarya in individual trees relative to Hodarchaeales and other Heimdallarchaeia, as well as the patchy distribution of eukaryotic signature proteins among Asgard archaea, is best explained by suggesting that multiple gene transfers take place between proto-eukaryotes and Asgard archaea in both directions. This suggests that the co-evolution of proto-eukaryotes and Asgard archaea has played a major role in eukaryogenesis but also in shaping the physiology and diversification of Asgard archaea.},
}

@article {pmid40891883,
year = {2025},
author = {Wang, X and Fan, F and Dong, S and Zhang, Y},
title = {Emergence of carbapenem-resistant Serratia marcescens co-harboring blaNDM-1, blaKPC-2, and blaSRT-2 in bloodstream infection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0054525},
doi = {10.1128/spectrum.00545-25},
pmid = {40891883},
issn = {2165-0497},
abstract = {Serratia marcescens is an emerging opportunistic pathogen with high genetic diversity. The emergence and prevalence of carbapenem-resistant S. marcescens poses a major health threat due to its intrinsic resistance to multiple antibiotics, which severely restricts the selection and treatment of antibiotics for S. marcescens infection. This study presents the first documented case in China of a bloodstream infection caused by Staphylococcus epidermidis and S. marcescens strain (designated S96) co-producing blaNDM-1, blaKPC-2, and blaSRT-2. Strain S96 exhibited resistance to nearly all categories of β-lactam antimicrobials, β-lactam/inhibitor combinations, aminoglycosides, quinolones, and other clinical antibacterial agents, with the exception of tigecycline. Our main objective was to characterize the genetic mechanisms underlying its carbapenem resistance and plasmid transfer potential. Whole-genome sequencing revealed blaKPC-2 on a 44,047 bp "IncX6-like" plasmid and blaNDM-1 on a 100,081 bp IncFII(Yp)-type plasmid, alongside chromosomal blaSRT-2 and aac(6')-Ic. "IncX6-like" and IncFII(Yp)-type plasmids are widely distributed among carbapenem-resistant Enterobacteriaceae strains globally. Conjugation experiments demonstrated that the blaNDM-1-carrying plasmid could be successfully transferred to recipient Escherichia coli 600, with no significant fitness cost observed (P > 0.05). The experimental results demonstrate that carbapenem-resistant genes can disseminate among Enterobacteriaceae via plasmid-mediated horizontal transfer between bacterial cells. Comparative genomic analysis revealed plasmid structural homology with global counterparts, demonstrating IS-mediated recombination and horizontal gene transfer. The low adaptive cost of plasmid carriage and multidrug resistance phenotype pose significant challenges for clinical management. This study highlights the need for enhanced clinical surveillance and antibiotic stewardship to curb the spread of such multidrug-resistant pathogens.IMPORTANCECarbapenem resistance in Serratia marcescens is primarily mediated by Klebsiella pneumoniae carbapenemase (KPC), with New Delhi metallo-β-lactamase (NDM) being a relatively uncommon alternative resistance mechanism. KPC-2 and NDM-1 coexisting in S. marcescens is extremely rare clinically. This study reports the first clinical isolate of S. marcescens in China co-harboring blaNDM-1, blaKPC-2, and blaSRT-2. The isolate exhibits multidrug resistance to nearly all β-lactam antibiotics and β-lactam/inhibitor combinations, with low adaptive costs and high dissemination potential. The potential spread of resistance genes through mobile genetic elements poses a serious public health risk. The study underscores the need for enhanced surveillance, rational antibiotic use, and novel strategies to combat resistance. It also provides insights into the evolutionary mechanisms of bacterial resistance, emphasizing the urgent need for interventions to address the growing threat of antimicrobial resistance.},
}

@article {pmid40890562,
year = {2025},
author = {RoyChowdhury, D and Manna, A and Mandal, S and Mukherjee, P and Basu, A},
title = {Colistin resistance in the era of antimicrobial resistance: challenges and strategic countermeasures.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40890562},
issn = {1874-9356},
abstract = {Colistin resistance represents a mounting global health concern, particularly alarming in the face of multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacterial infections. As a polymyxin-class antibiotic, colistin has long served as a critical last-line defence against severe Gram-negative infections caused by pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. However, its increasing and, at times, indiscriminate use has driven the emergence of resistant strains, thereby compromising its clinical utility.Mechanistically, colistin resistance arises from diverse genetic adaptations that alter the bacterial outer membrane, diminishing the drug's binding affinity. Prominent among these are modifications to lipopolysaccharides (LPS), including the incorporation of cationic groups that neutralise the membrane's negative charge, effectively impeding colistin interaction. In addition to chromosomal mutations, resistance is often mediated through horizontal gene transfer-most notably via mobile colistin resistance (mcr) genes-which facilitates rapid dissemination among bacterial populations.To counter this growing threat, innovative therapeutic strategies are urgently needed. These include the development of novel antibiotics with distinct mechanisms of action, synergistic combination regimens (e.g., colistin paired with potentiating agents), and the exploration of alternative modalities such as bacteriophage therapy. Gene-editing technologies like CRISPR-Cas9 also offer a promising frontier for targeting resistance determinants directly at the genetic level.Equally important are robust antimicrobial stewardship programmes and comprehensive surveillance systems to monitor resistance trends and guide rational antibiotic use. Ultimately, overcoming colistin resistance demands a multifaceted and integrative approach-one that merges scientific innovation with global public health initiatives.},
}

@article {pmid40889866,
year = {2026},
author = {Wang, MG and Liu, KD and Jin, WJ and Li, RB and Liu, JQ and Fang, LX and Sun, J and Liao, XP},
title = {Mechanistic insight into curcumin-induced conjugative plasmid transfer acceleration: Role of intracellular arginine uptake.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104895},
doi = {10.1016/j.fm.2025.104895},
pmid = {40889866},
issn = {1095-9998},
mesh = {*Arginine/metabolism ; *Curcumin/pharmacology ; *Plasmids/genetics/metabolism ; *Gene Transfer, Horizontal/drug effects ; *Conjugation, Genetic/drug effects ; *Escherichia coli/genetics/drug effects/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/genetics/drug effects ; Biological Transport/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Curcumin exhibits a broad spectrum of applications spanning multiple domains, including its incorporation in dietary supplements, functional beverages, cosmetic formulations, and nutraceutical products. Nevertheless, its potential influence on the development of antibiotic resistance remains to be fully elucidated. Therefore, this study aims to investigate the effects of curcumin on the conjugative transfer of plasmids carrying antibiotic resistance genes (ARGs). Our findings indicate that curcumin significantly enhanced the transfer of RP4 plasmid, as well as clinically relevant plasmids carrying blaNDM, mcr-1 and tet(X4). Further mechanisms analysis revealed that curcumin facilitated plasmid conjugation transfer by increasing bacterial membrane permeability, inducing oxidative stress, and accelerating energy metabolism, while altering the expression levels of key genes involved in horizontal gene transfer (HGT). Notably, curcumin elevated intracellular arginine levels, and exogenous arginine supplementation further promoted plasmid transfer. Arginine uptake genes (artJ, artI and argT) were upregulated following curcumin exposure, and the absence of artJ significantly attenuated curcumin-induced arginine accumulation and plasmid transfer, demonstrating the crucial role of the artJ gene in facilitating curcumin-induced plasmid transfer through its promotion of arginine uptake. These findings provide new insights into an unrecognized risk of curcumin in potentially accelerating the spread of antibiotic resistance, highlight the unintended consequences of curcumin use in the food industry.},
}

*Arginine/metabolism
*Curcumin/pharmacology
*Plasmids/genetics/metabolism
*Gene Transfer, Horizontal/drug effects
*Conjugation, Genetic/drug effects
*Escherichia coli/genetics/drug effects/metabolism
Anti-Bacterial Agents/pharmacology
Bacterial Proteins/genetics/metabolism
Drug Resistance, Bacterial/genetics/drug effects
Biological Transport/drug effects
Oxidative Stress/drug effects

@article {pmid40888030,
year = {2025},
author = {Yang, H and Wang, Y},
title = {From Fragmentation to Resolution: High-Fidelity Genome Assembly of Zancudomyces culisetae through Comparative Insights from PacBio, Nanopore, and Illumina Sequencing.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf204},
pmid = {40888030},
issn = {2160-1836},
abstract = {Zancudomyces culisetae is an obligate symbiotic fungus inhabiting the digestive tracts of aquatic insect larvae, including black flies, midges, and mosquitoes. With a global distribution and high prevalence in disease-transmitting insects, Z. culisetae serves as a model for studying insect gut fungi. A previous draft genome assembly using Illumina short reads provided insights into its genome composition, such as a low GC ratio and evidence of horizontal gene transfer. However, its fragmented nature has limited deeper exploration of the evolutionary mechanisms shaping these gut symbionts. To address this gap, we generated a wealth of genomic resources for Z. culisetae using multiple sequencing platforms, including Illumina, Oxford Nanopore, PacBio-CLR (Complete Long Reads), and PacBio-HiFi (High Fidelity). This also provides an opportunity to compare these popular sequencing methods to suggest the optimal approach for fungal genome assembly. Our results suggest that PacBio-HiFi produced the most complete assembly, yielding a 27.8 Mb genome size with 26 contigs, representing the highest-quality genome of insect gut fungi to date. Additionally, we generated transcriptomic data to support genome annotation, identifying 8,484 protein-coding genes. Despite the improved genome quality, Z. culisetae lacks approximately 20% of Benchmarking Universal Single-Copy Orthologue (BUSCO) commonly found in fungi, reflecting adaptations to its obligate symbiotic lifestyle. This study not only provides valuable genomic resources for insect gut fungal research but also evaluates the strengths and limitations of current genome sequencing and assembly approaches, offering best practices for fungal genome analysis and genetic research.},
}

@article {pmid40884907,
year = {2025},
author = {Sanati, S and Bakhti, A and Mohammadipanah, F},
title = {Long-term toxic effects of nanoparticles on human microbiota.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {91},
number = {},
pages = {127723},
doi = {10.1016/j.jtemb.2025.127723},
pmid = {40884907},
issn = {1878-3252},
abstract = {Synthetic nanomaterials can penetrate various organs, such as the skin, lungs, and gastrointestinal tract, enter systemic circulation, and ultimately reach tissues and human cells. Nanomaterials used in medicine, food, cosmetics, and agricultural processes can accumulate in our intestines and cause dysbiosis. The direct and indirect detrimental impacts of nanomaterials on humans by altering our cells and microbiota are discussed in this paper. These adverse effects of nanomaterials can be slightly reduced by changing their physicochemical characteristics. Some of the gut microbiota can reduce or mitigate the toxicity of nanomaterials through various strategies providing approaches for pro- or postbiotics with detoxifying function. Moreover, nanomaterials influence the rate of horizontal gene transfer. The use of nanomaterials in food, water, and medicines needs to be legitimized based on the duration, dose, type, and level of toxicity. The negative implications of nanomaterials in human cells and their microbiota are surveyed in this paper.},
}

@article {pmid40883654,
year = {2025},
author = {Khosravi, H},
title = {Environmental risks of biofertilizers and their impact on soil microbial diversity: a mini review.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40883654},
issn = {1874-9356},
abstract = {Chemical fertilizers have substantially increased crop yields but have also contributed to significant environmental challenges, including soil and water contamination and the emergence of human health issues. As a more sustainable alternative, biofertilizers-comprising beneficial microorganisms such as bacteria-have been promoted as eco-friendly solutions. However, their use may pose risks to soil microbial communities and biodiversity under certain conditions. For instance, horizontal gene transfer among bacteria can convert non-pathogenic strains into pathogenic ones. Additionally, the introduction of microbial inoculants may outcompete native microbial species, potentially disrupting soil microbial balance and impairing ecosystem functioning. The long-term effects of biofertilizers on nutrient cycling and soil biodiversity remain insufficiently studied. To mitigate these risks, it is crucial to establish rigorous production standards, prioritize native microbial strains, continuously monitor soil microbial dynamics, and implement comprehensive regulatory frameworks. Therefore, the adoption of biofertilizers in agricultural practices should be approached cautiously and guided by evidence-based regulations.},
}

@article {pmid40882459,
year = {2025},
author = {Pennings, PS},
title = {Explaining the stable coexistence of drug-resistant and -susceptible pathogens: the resistance acquisition purifying selection model.},
journal = {Epidemics},
volume = {52},
number = {},
pages = {100848},
doi = {10.1016/j.epidem.2025.100848},
pmid = {40882459},
issn = {1878-0067},
abstract = {Drug resistance is a problem in many pathogens. While overall, levels of resistance have risen in recent decades, there are many examples where after an initial rise, levels of resistance have stabilized. The stable coexistence of resistance and susceptibility has proven hard to explain - in most evolutionary models, either resistance or susceptibility ultimately "wins" and takes over the population. Here, we show that a simple model, mathematically akin to mutation-selection balance theory, can explain several key observations about drug resistance: (1) the stable coexistence of resistant and susceptible strains (2) at levels that depend on population-level drug usage and (3) with resistance often due to many different strains (resistance is present on many different genetic backgrounds). The model is applicable to resistance due to both mutations and horizontal gene transfer (HGT). It predicts that new resistant strains should continuously appear (through mutation or HGT and positive selection within treated hosts) and disappear (due to a fitness cost of resistance). The result is that while resistance is stable, which strains carry resistance is constantly changing. We used data from a longitudinal genomic study on E. coli in Norway to test this prediction for resistance to five different drugs and found that, consistent with the model, most resistant strains indeed disappear quickly after they appear in the dataset. Having a model that explains the dynamics of drug resistance will allow us to plan science-backed interventions to reduce the burden of drug resistance.},
}

@article {pmid40882012,
year = {2025},
author = {Hong, W and Yang, Z and Wu, G and Liu, C and Wang, Y and Liao, N},
title = {Integrating serotyping, MLST, and phenotypic data: decoding the evolutionary drivers of Salmonella pathogenicity and drug resistance.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0151125},
doi = {10.1128/aem.01511-25},
pmid = {40882012},
issn = {1098-5336},
abstract = {Global surveillance of Salmonella enterica reveals dynamic evolutionary forces shaping pathogenicity and antimicrobial resistance (AMR), yet the integration of serotyping, multilocus sequence typing (MLST), and phenotypic landscapes remains unexplored. Here, we dissect 935 Salmonella isolates, collected from both clinical and food chain sources, through integrated genomics and phenomics to resolve population structure, spatiotemporal dynamics, and evolutionary drivers. Salmonella Typhimurium (18.7%) and Salmonella Enteritidis (17.1%) dominate the serotype landscape, while MLST uncovers ST34 (20.7%) as the pivotal sequence type bridging multiple serotypes. Temporal tracking (2018-2022) exposes alarming AMR trajectories: ciprofloxacin resistance doubled (15.3% to 30.4%) by 2020, and tetracycline resistance peaked at 77.3%. The serotype-specific epidemiology reveals that S. Typhimurium declined and then stabilized, S. Enteritidis fluctuated due to vaccination, and S. Derby emerged persistently (+69%). Network analysis reveals two evolutionary clusters: one anchored by S. Typhimurium/S. Enteritidis-ST34/ST11 and another harboring diverse STs associated with S. Derby. Notably, ST34 acts as a genetic backbone for serotype switching. Notably, S. Typhimurium exhibits the highest AMR gene burden (median: 4.2 genes/isolate) and virulence arsenal (spvB: 85.1%; pefA: 75.4%), which correlates with invasive disease. Geographic heterogeneity results in distinct serotype distributions: S. Enteritidis dominates in Xinyu (28.4%), S. Typhimurium prevails in Shangrao (31.5%), and Ganzhou exhibits balanced diversity. Our findings establish that clonal expansion, horizontal gene transfer, and regional ecologies are key factors jointly driving Salmonella evolution. This necessitates genotype-phenotype-integrated surveillance to preempt the emergence and widespread dissemination of resistance and virulence.IMPORTANCESalmonella enterica is a globally significant foodborne pathogen, whose pathogenicity and antimicrobial resistance (AMR) evolution are driven by complex mechanisms. This study provides a comprehensive analysis of 935 Salmonella isolates from clinical and food chain sources, integrating genomic and phenotypic data to elucidate population structure, spatiotemporal dynamics, and key evolutionary drivers. We reveal critical resistance trends, including a concerning doubling of ciprofloxacin resistance by 2020 and sustained high tetracycline resistance. Our comparative analysis of serotypes (e.g., S. Typhimurium and S. Enteritidis) highlights associations between AMR gene burden and virulence factors and identifies ST34 as a pivotal genetic element facilitating serotype switching. These findings underscore the imperative for integrated genotypic-phenotypic surveillance to predict resistance evolution and inform "One Health"-based interventions. By disrupting AMR dissemination across the animal food chain, this research offers novel strategies for global Salmonella control and improved public health outcomes.},
}

@article {pmid40881221,
year = {2025},
author = {Li, XL and Megdadi, M and Quadri, HS},
title = {Interaction between gut virome and microbiota on inflammatory bowel disease.},
journal = {World journal of methodology},
volume = {15},
number = {3},
pages = {100332},
doi = {10.5662/wjm.v15.i3.100332},
pmid = {40881221},
issn = {2222-0682},
abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, is a chronic condition marked by recurring gastrointestinal inflammation. While immune, genetic, and environmental factors are well-studied, the gut virome has received less attention. This editorial highlights the work which investigates the gut virome's role in IBD and its interactions with the bacterial microbiome and host immune system. The gut virome consists of bacteriophages, eukaryotic viruses, and endogenous retroviruses. Among these, Caudovirales bacteriophages are predominant and influence bacterial communities via lysogenic and lytic cycles. Eukaryotic viruses infect host cells directly, while endogenous retroviruses impact gene regulation and immune responses. In IBD, the virome shows distinct alterations, including an increased abundance of Caudovirales phages and reduced Microviridae diversity, suggesting a pro-inflammatory viral environment. Dysbiosis, chronic inflammation, and aberrant immune responses contribute to these changes by disrupting microbial communities and modifying virome composition. Phages affect bacterial dynamics through lysis, lysogeny, and horizontal gene transfer, shaping microbial adaptability and resilience. Understanding these interactions is crucial for identifying novel therapeutic targets and restoring microbial balance in IBD.},
}

@article {pmid40881179,
year = {2025},
author = {Osunla, CA and Akinbobola, A and Elshafea, A and Yeboah, EEA and Bakare, OS and Fayanju, A and Fatoba, DO and Boamah, B and Amoako, DG},
title = {Genomic and Bioinformatic Insights Into Enterococcus faecalis From Retail Meats in Nigeria.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {7325430},
doi = {10.1155/ijm/7325430},
pmid = {40881179},
issn = {1687-918X},
abstract = {Enterococcus faecalis is a commensal and opportunistic pathogen increasingly recognized for its antimicrobial resistance (AMR) and zoonotic potential. This study employs whole-genome sequencing (WGS) to characterize E. faecalis isolates from retail meat samples, focusing on antimicrobial resistance genes (ARGs), virulence determinants, mobile genetic elements, and phylogenomic relationships. Fifty raw meat samples, including chicken (n = 18), beef (n = 17), and turkey (n = 15), were collected from retail markets in Akungba-Akoko, Nigeria. Confirmed isolates underwent antimicrobial susceptibility testing and WGS-based genomic analysis. Ten E. faecalis isolates were recovered, predominantly from chicken. All exhibited resistance to clindamycin, erythromycin, and tetracycline. Dominant AMR genes included aac(6⁣')-aph(2⁣[″]), ant(6)-Ia, lsa(A), erm(B), tet(M), and tet(L). Plasmid replicons rep9c and repUS43 were associated with sequence types ST477 and ST16, respectively. MGEs such as IS3, IS6, IS256, and IS1380 colocalized with resistance and virulence genes. Phylogenomic analysis revealed two major lineages (ST477 and ST16) and indicated geographic clustering across African isolates. The co-occurrence of multidrug resistance, virulence factors, and MGEs in foodborne E. faecalis poses a public health concern due to the risk of horizontal gene transfer and zoonotic spread. These findings support the need for strengthened genomic surveillance and AMR control strategies in food systems, particularly within low- and middle-income countries.},
}

@article {pmid40880124,
year = {2025},
author = {Torosian, N and Covington, JK and Cook, AM and Nou, NO and Palmer, M and Mewalal, R and Harmon-Smith, M and Blaby, IK and Cheng, JF and Hess, M and Hedlund, BP},
title = {Characterization of the thermophilic xylanase Fsa02490Xyn from the hyperthermophile Fervidibacter sacchari belonging to glycoside hydrolase family 10.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70072},
pmid = {40880124},
issn = {2211-5463},
support = {DBI REU 1757316//National Science Foundation & Directorate for Biological Sciences/ ; HRD-1712523//National Science Foundation & Directorate for Biological Sciences/ ; 80NSSC17K0548/NASA/NASA/United States ; 80NSSC20M0043/NASA/NASA/United States ; 80NSSC21M0157/NASA/NASA/United States ; DE-AC02-05CH11231//U.S. Department of Energy & Office of Science/ ; },
abstract = {Fervidibacter sacchari is an aerobic hyperthermophile belonging to the phylum Armatimonadota that degrades a variety of polysaccharides. Its genome encodes 117 enzymes with one or more annotated glycoside hydrolase (GH) domain, but the roles of these putative GHs in polysaccharide catabolism are poorly defined. Here, we describe one F. sacchari enzyme encoding a GH10 domain, Fsa02490Xyn, that was previously shown to be active on Miscanthus, oat β-glucan, and beech-wood xylan, with optimal activity at 90-100 °C. We show that Fsa02490Xyn is also active on birch-wood xylan and gellan gum. The pH range on beech-wood xylan was 4.5 to 9.5 (pHopt 7.0-8.0). Fsa024940Xyn had a Km of 2.375 mm, Vmax of 1250 μm·min[-1], and kcat/Km of 1.259 × 10[4] s[-1]·m[-1] when using a para-nitrophenyl-𝛽-xylobioside assay. A phylogenetic analysis of GH10 family enzymes revealed a large clade of enzymes from diverse members of the class Fervidibacteria, including Fsa02490Xyn and a second enzyme from F. sacchari, with apparent horizontal gene transfer within Fervidibacteria and between Fervidibacteria and thermophilic Bacillota. This study establishes Fsa02490Xyn as a hyperthermophilic GH10 enzyme with endo-β-1,4-xylanase activity and identifies a large clade of homologous GH10 enzymes within the class Fervidibacteria. Impact statement The depolymerization of xylan at high temperatures is important because this process limits the degradation of polysaccharides in nature and the synthesis of biofuels from plant wastes. Our study is also important because F. sacchari is one of only a few cultivated members of the Armatimonadota, which are polysaccharide-degradation specialists.},
}

@article {pmid40879164,
year = {2025},
author = {Takano, S and Takenawa, S and Divya, N and Yan, K and Wen, X and Maehara, T and Nomura, N and Obana, N and Toyofuku, M and Usui, M and Ariyoshi, W and Okamoto, A},
title = {Enrichment of Horizontally Transferred Gene Clusters in Bacterial Extracellular Vesicles via Non-Lytic Mechanisms.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf193},
pmid = {40879164},
issn = {1751-7370},
abstract = {Bacterial extracellular vesicles are emerging as key mediators of horizontal gene transfer, enhancing microbial adaptability. A critical factor determining the effectiveness of horizontal gene transfer is the fraction of vesicles containing specific functional genes. However, the proportion of containing specific DNA fragments has not been adequately determined, which hinders the understanding of the conditions and mechanisms that facilitate the incorporation of specific genes into the vesicles and possible evolutionary roles of vesicle-derived DNA. Here, we demonstrate that enrichment of horizontally transferred genes into bacterial extracellular vesicles is driven by cellular processes by profiling the DNA content of hundreds of individual vesicles using a microdroplet-based sequencing technique. This approach revealed unique DNA profiles in vesicles from the oral pathogen Porphyromonas gingivalis, pinpointing genomic regions related to DNA reorganization such as CRISPR-Cas clusters. Comparative genomic and phylogenetic analyses of Porphyromonas genomes revealed traces of horizontal gene transfer in vesicle-enriched genes. Modulating vesicle-biogenesis routes, quantitative real-time PCR revealed that this selective enrichment was driven by blebbing-driven DNA packaging mechanisms rather than stress-induced lysis. Applied to dental plaque-derived bacterial extracellular vesicles, the droplet-based approach reveled O-antigen biosynthetic genes, key for host-bacterial interactions, were prevalent in the vesicles from Alcaligenes faecalis, suggesting the vesicles from this bacterium can modulate pathogenicity in oral biofilms through targeted DNA packaging. These findings suggest the prevalence of functionally relevant gene clusters in bacterial extracellular vesicles in oral microbiota and their evolutionary roles as DNA cargoes for modulating phage-bacterial and host-bacterial interactions via horizontal gene transfer.},
}

@article {pmid40877975,
year = {2025},
author = {Xu, L and Jiao, JY and Ling, C and Du, RB and Wu, Q and Xu, Y and Li, WJ},
title = {Mobilome-mediated transcriptional activation of biosynthetic gene clusters and its impact on strain competitiveness in food fermentation microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {191},
pmid = {40877975},
issn = {2049-2618},
support = {32172175//National Natural Science Foundation of China/ ; No. 111-2-06//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {Fermentation ; *Microbiota/genetics ; *Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism ; *Transcriptional Activation ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Food Microbiology ; Firmicutes/genetics ; *Fermented Foods/microbiology ; Microbial Interactions/genetics ; },
abstract = {BACKGROUND: Microbial interactions are critical for maintaining the stability of food fermentation microbiomes, and mobile genetic elements (MGEs) significantly influence these interactions by horizontal gene transfer events. Although MGEs are known to facilitate horizontal gene transfer, their distribution among microorganisms and specific effects on microbial interactions remain poorly understood.

RESULTS: We analyzed 590 metagenomic and 42 metatranscriptomic samples from food fermentations, recovering 1133 metagenome-assembled genomes (MAGs). Our analysis revealed that MGEs were widely distributed in food fermentation microbiomes, with higher occurrence rates in Firmicutes (Bacillota: 0.71 ~ 11.85%) and Proteobacteria (Pseudomonadota: 0.47 ~ 11.05%). MGEs tended to be located adjacent to functional genes, particularly biosynthetic gene clusters (BGCs), with co-occurrence rates ranging from 9.41 to 23.99%. Furthermore, the transcriptional activity of BGCs was significantly correlated with the number of MGEs that were co-located with BGCs, which might enhance the competitiveness of strains. Variability in the diversity of MGEs that were co-located with BGCs was also evident at the strain level. Using Lactiplantibacillus plantarum as a case, we revealed that the strain-level differences in MGEs that were co-located with BGCs are positively correlated with the transcription of BGCs and competitiveness of strains within the species.

CONCLUSIONS: This study highlighted the role of MGEs in enhancing transcription of BGCs and facilitating strain competitiveness, providing new insights into how MGEs enhance the adaptability of microbial communities. Video Abstract.},
}

Fermentation
*Microbiota/genetics
*Multigene Family
Metagenome
*Bacteria/genetics/classification/metabolism
*Transcriptional Activation
Gene Transfer, Horizontal
Metagenomics/methods
*Interspersed Repetitive Sequences
*Food Microbiology
Firmicutes/genetics
*Fermented Foods/microbiology
Microbial Interactions/genetics

@article {pmid40872695,
year = {2025},
author = {Skarlatoudi, T and Anagnostou, GM and Theodorakis, V and Bosnea, L and Mataragas, M},
title = {Escherichia coli Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS).},
journal = {Veterinary sciences},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/vetsci12080744},
pmid = {40872695},
issn = {2306-7381},
support = {M16SYN2-00164//European Regional Development Fund, Ministry of Rural Development and Food, ESPA 2014-2020, RDP 2014-2022/ ; },
abstract = {The objective of this work was to deliver a comprehensive genetic characterization of a collection of E. coli strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Shigella spp. and Salmonella spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the E. coli strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic E. coli strains is particularly alarming for cheese production in artisan dairies.},
}

@article {pmid40871370,
year = {2025},
author = {El Samak, M and Lotfy, H and Sedeek, AM and Mohamed, YS and Solyman, SM},
title = {Genomic Characterization of Marine Staphylococcus shinii Strain SC-M1C: Potential Genetic Adaptations and Ecological Role.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081866},
pmid = {40871370},
issn = {2076-2607},
support = {number (2024-IRG-MED-1)//Deanship of Research and Graduate Studies, Ajman University project awarded AY 2024/ 2025 REF./ ; },
abstract = {Staphylococcus shinii (S. shinii) is a coagulase-negative species primarily associated with the degradation of organic matter, contributing to nutrient cycling in natural environments. This species has been mainly studied in clinical and terrestrial contexts, with no previous reports of its presence in marine environments. In this study, we report the first isolation of S. shinii from a marine habitat. The strain SC-M1C was isolated from the Red Sea sponge Negombata magnifica. Whole-genome sequencing confirmed its taxonomic identity as S. shinii. The genome uncovers potential adaptive characteristics that facilitate survival in marine ecosystems, comprising genes associated with osmoregulation, nutrient acquisition, stress response, and resistance to heavy metals. Moreover, multiple genomic islands and plasmids were identified, suggesting a potential role in horizontal gene transfer and environmental adaptability. The presence of biosynthetic gene clusters linked to non-ribosomal peptides, siderophores, and terpene production indicates potential for biochemical versatility beyond traditional metabolic expectations. This study presents the first genomic insights into S. shinii in a marine context, highlighting its ecological significance and adaptive mechanisms in a high-salinity environment. These findings expand our understanding of staphylococcal ecology beyond terrestrial and clinical origins and provide a foundation for exploring the role of S. shinii in marine microbial interactions and environmental resilience.},
}

@article {pmid40871307,
year = {2025},
author = {Watanabe, Y and Ishiga, Y and Sakata, N},
title = {The Role of Genomic Islands in the Pathogenicity and Evolution of Plant-Pathogenic Gammaproteobacteria.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081803},
pmid = {40871307},
issn = {2076-2607},
abstract = {Genomic islands (GIs) including integrative and conjugative elements (ICEs), prophages, and integrative plasmids are central drivers of horizontal gene transfer in bacterial plant pathogens. These elements often carry cargo genes encoding virulence factors, antibiotic and metal resistance determinants, and metabolic functions that enhance environmental adaptability. In plant-pathogenic species such as Pseudomonas syringae, GIs contribute to host specificity, immune evasion, and the emergence of novel pathogenic variants. ICEclc and its homologs represent integrative and mobilizable elements whose tightly regulated excision and transfer are driven by a specialized transcriptional cascade, while ICEs in P. syringae highlight the ecological impact of cargo genes on pathogen virulence and fitness. Pathogenicity islands further modulate virulence gene expression in response to in planta stimuli. Beyond P. syringae, GIs in genera such as Erwinia, Pectobacterium, and Ralstonia underpin critical traits like toxin biosynthesis, secretion system acquisition, and topoisomerase-mediated stability. Leveraging high-throughput genomics and structural biology will be essential to dissect GI regulation and develop targeted interventions to curb disease spread. This review synthesizes the current understanding of GIs in plant-pathogenic gammaproteobacteria and outlines future research priorities for translating mechanistic insights into sustainable disease control strategies.},
}

@article {pmid40871306,
year = {2025},
author = {Yang, Y and Liu, Y and Wang, J and Li, C and Wu, R and Xin, J and Yang, X and Zheng, H and Zhong, Z and Fu, H and Zhou, Z and Liu, H and Peng, G},
title = {Proteus mirabilis from Captive Giant Pandas and Red Pandas Carries Diverse Antimicrobial Resistance Genes and Virulence Genes Associated with Mobile Genetic Elements.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081802},
pmid = {40871306},
issn = {2076-2607},
support = {ZDK202401//Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo/ ; 2024YFD1800200//The "14th Five-Year National Key R&D Project/ ; },
abstract = {Proteus mirabilis is a zoonotic pathogen that poses a growing threat to both animal and human health due to rising antimicrobial resistance (AMR). It is widely found in animals, including China's nationally protected captive giant and red pandas. This study isolated Proteus mirabilis from panda feces to assess AMR and virulence traits, and used whole-genome sequencing (WGS) to evaluate the spread of resistance genes (ARGs) and virulence genes (VAGs). In this study, 37 isolates were obtained, 20 from red pandas and 17 from giant pandas. Multidrug-resistant (MDR) strains were present in both hosts. Giant panda isolates showed the highest resistance to ampicillin and cefazolin (58.8%), while red panda isolates were most resistant to trimethoprim/sulfamethoxazole (65%) and imipenem (55%). Giant panda-derived strains also exhibited stronger biofilm formation and swarming motility. WGS identified 31 ARGs and 73 VAGs, many linked to mobile genetic elements (MGEs) such as plasmids, integrons, and ICEs. In addition, we found frequent co-localization of drug resistance genes/VAGs with MGEs, indicating a high possibility of horizontal gene transfer (HGT). This study provides crucial insights into AMR and virulence risks in P. mirabilis from captive pandas, supporting targeted surveillance and control strategies.},
}

@article {pmid40871267,
year = {2025},
author = {Wu, Z and Shao, X and Wang, Q},
title = {Antibiotics and Antibiotic Resistance Genes in the Environment: Dissemination, Ecological Risks, and Remediation Approaches.},
journal = {Microorganisms},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/microorganisms13081763},
pmid = {40871267},
issn = {2076-2607},
support = {LQN25E090002//Natural Science Foundation of Zhejiang Province/ ; EREH202404//the Key Laboratory of Environment Remediation and Ecological Health (Zhejiang University), Ministry of Education/ ; SKR-2022070//the Major Science and Technology Projects of the Ministry of Water Resources/ ; },
abstract = {Global antibiotic use saturates ecosystems with selective pressure, driving mobile genetic element (MGE)-mediated antibiotic resistance gene (ARG) dissemination that destabilizes ecological integrity and breaches public health defenses. This review synthesizes the sources, environmental distribution, and ecological risks of antibiotics and ARGs, emphasizing the mechanisms of horizontal gene transfer (HGT) driven by MGEs such as plasmids, transposons, and integrons. We further conduct a comparative critical analysis of the effectiveness and limitations of antibiotics and ARGs remediation strategies for adsorption (biochar, activated carbon, carbon nanotubes), chemical degradation (advanced oxidation processes, Fenton-based systems), and biological treatment (microbial degradation, constructed wetlands). To effectively curb the spread of antimicrobial resistance and safeguard the sustainability of ecosystems, we propose an integrated "One Health" framework encompassing enhanced global surveillance (antibiotic residues and ARGs dissemination) as well as public education.},
}

@article {pmid40870001,
year = {2025},
author = {Yang, C and Liang, W and Qin, Y and Li, Y and Wei, S and Huang, Q and El-Sappah, AH and Tan, G and Wei, Y and Gui, L and Wan, L},
title = {Mitochondrial Genome and RNA Editing Tissue Specificity of Centella asiatica.},
journal = {Genes},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/genes16080953},
pmid = {40870001},
issn = {2073-4425},
support = {(2023GXNSFAA026330); (Guike AD22035026); (GZKJ2305); (GZSY23-02); (ZJC2020003)//Natural Science Foundation of Guangxi Province (2023GXNSFAA026330), Gaungxi Bagui Brilliance Visiting Scholar Program (Lingyun Wan), Guangxi Science and Technology Base and Special Talents (Guike AD22035026), Innovative Team for Traditional Chinese Medici/ ; },
mesh = {*RNA Editing/genetics ; *Centella/genetics/classification ; *Genome, Mitochondrial/genetics ; Phylogeny ; Organ Specificity ; Gene Transfer, Horizontal ; Evolution, Molecular ; RNA, Transfer/genetics ; RNA, Long Noncoding/genetics ; },
abstract = {BACKGROUND: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms.

METHODS: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites.

RESULTS: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems.

CONCLUSIONS: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species.},
}

*RNA Editing/genetics
*Centella/genetics/classification
*Genome, Mitochondrial/genetics
Phylogeny
Organ Specificity
Gene Transfer, Horizontal
Evolution, Molecular
RNA, Transfer/genetics
RNA, Long Noncoding/genetics

@article {pmid40869916,
year = {2025},
author = {Li, R and Bi, C},
title = {Comparative Genomic Analysis of Lactiplantibacillus plantarum: Insights into Its Genetic Diversity, Metabolic Function, and Antibiotic Resistance.},
journal = {Genes},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/genes16080869},
pmid = {40869916},
issn = {2073-4425},
support = {2024ZXDXB58//Heilongjiang Provincial Science and Technology Department/ ; },
mesh = {*Lactobacillus plantarum/genetics/metabolism/drug effects ; Phylogeny ; *Genetic Variation ; *Genome, Bacterial ; Genomics/methods ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Background/Objectives: Lactiplantibacillus plantarum is widely utilized in the fermentation industry and offers potential health benefits. However, large-scale comparative genomic analyses aimed at exploring its metabolic functions and conducting safety assessments are still lacking. Methods: In this study, we performed a comparative genomic analysis of 324 L. plantarum strains sourced from various origins and geographical locations. Results: The results revealed that L. plantarum possesses a total of 2403 core genes, of which 12.3% have an unknown function. The phylogenetic analysis revealed a mixed distribution from various origins, suggesting complex transmission pathways. The metabolic analysis demonstrated that L. plantarum strains can produce several beneficial metabolites, including lysine, acetate, and riboflavin. Furthermore, L. plantarum is highly capable of degrading various carbohydrates and proteins, increasing its adaptability. Further, we profiled the antimicrobial peptides (AMPs) in the genomes of L. plantarum. We identified a widely distributed AMP and its variants, presenting in a total of 280 genomes. In our biosafety assessment of L. plantarum, we identified several antibiotic resistance genes, such as Tet(M), ANT(6)-Ia, and mdeA, which may have potential for horizontal gene transfer within the Lactobacillaceae family. Conclusions: This study provides genomic insights into the genetic diversity, metabolic functions, antimicrobial properties, and biosafety of L. plantarum, underscoring its potential applications in biotechnology and environmental adaptation.},
}

*Lactobacillus plantarum/genetics/metabolism/drug effects
Phylogeny
*Genetic Variation
*Genome, Bacterial
Genomics/methods
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40869035,
year = {2025},
author = {Horodyska, I and Kasperska, P and Michalski, K and Bubak, J and Herman, I and Miszczak, M},
title = {Natural Microbiota of Dogs and Cats as a Source and Vector of Resistance Genes-Clinical Significance.},
journal = {International journal of molecular sciences},
volume = {26},
number = {16},
pages = {},
doi = {10.3390/ijms26167717},
pmid = {40869035},
issn = {1422-0067},
mesh = {Animals ; Dogs/microbiology ; Cats/microbiology ; *Microbiota/genetics ; Gene Transfer, Horizontal ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Clinical Relevance ; },
abstract = {Antimicrobial resistance (AMR) presents a growing global threat, driven by widespread antibiotic misuse across human and veterinary medicine. Companion animals, particularly dogs and cats, harbor complex natural microbiota-including skin, mucosal, and gastrointestinal communities-that are essential to their health yet also serve as reservoirs of antibiotic resistance genes (ARGs). These ARGs can spread through horizontal gene transfer (HGT), especially during bacterial imbalances such as endogenous infections or surgical interventions, increasing the risk of difficult-to-treat infections. Documented zoonotic and anthroponotic transmissions of resistant strains such as MRSA, MRSP, and ESBL-producing E. coli highlight the bidirectional nature of ARG flow between animals and humans. This underscores the critical importance of the One Health approach, which promotes interdisciplinary collaboration to monitor, understand, and combat AMR across the human-animal-environment interface. Key mechanisms of ARG dissemination, the role of companion animal microbiota, and real-world examples of resistance transfer between species illustrate the complexity and urgency of addressing AMR. Targeted surveillance, rational antibiotic use, and public awareness are essential to preserving antimicrobial efficacy and safeguarding both human and animal populations.},
}

Animals
Dogs/microbiology
Cats/microbiology
*Microbiota/genetics
Gene Transfer, Horizontal
Humans
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology/therapeutic use
Clinical Relevance

@article {pmid40868013,
year = {2025},
author = {Sartori, L and Furlan, JPR and Sellera, FP and Barbosa, FB and Chikhani, YCDSA and Gandolfi, G and Knöbl, T},
title = {Clonal Diversity of Extraintestinal Pathogenic Escherichia coli Strains Isolated from Canine Urinary Tract Infections in Brazil.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/antibiotics14080819},
pmid = {40868013},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: Extraintestinal pathogenic Escherichia coli (ExPEC) strains, particularly those belonging to phylogenetic group B2, are clinically significant due to their frequent involvement in urinary tract infections (UTIs) and display antimicrobial resistance profiles. While the association of phylogroup B2 E. coli with human urinary tract infections is well established, the growing number of reports of ExPEC strains in canine UTIs highlights their clinical relevance in small animal medicine and raises concerns about their potential role in zoonotic transmission. This study investigated the microbiological and genomic features of E. coli strains isolated from dogs with UTIs in São Paulo, Brazil.

METHODS: Between March and May 2023, a total of 60 E. coli strains from canine UTIs were screened for antimicrobial susceptibility and phylotyping. Accordingly, four strains (6.6%) were identified as multidrug-resistant (MDR) or belonging to phylogroup B2 and, therefore, were submitted for characterization by whole-genome sequencing.

RESULTS: The four E. coli strains exhibited diverse antimicrobial resistance profiles, including resistance to third- and fourth-generation cephalosporins and fluoroquinolones. Phylogenetic groups B1, B2, and G, and sequence types (ST) 73, ST224, ST1193, and ST12960 were identified. The resistome included clinically important β-lactam resistance genes, such as blaCTX-M-55 and blaCMY-2, as well as mutations in the quinolone-resistance-determining region. Virulence factors associated with ExPEC pathogenesis, including adhesion, iron acquisition, immune evasion, and toxin, were detected. Plasmid sequences were identified as carrying antimicrobial resistance and virulence genes, highlighting the potential for horizontal gene transfer.

CONCLUSIONS: Our findings underscore the importance of genomic surveillance in companion animals to better understand the epidemiology of ExPEC strains and monitor the spread of MDR strains.},
}

@article {pmid40867959,
year = {2025},
author = {Sassi, A and Basher, NS and Kirat, H and Meradji, S and Ibrahim, NA and Idres, T and Touati, A},
title = {The Role of the Environment (Water, Air, Soil) in the Emergence and Dissemination of Antimicrobial Resistance: A One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/antibiotics14080764},
pmid = {40867959},
issn = {2079-6382},
support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a planetary health emergency, driven not only by the clinical misuse of antibiotics but also by diverse environmental dissemination pathways. This review critically examines the role of environmental compartments-water, soil, and air-as dynamic reservoirs and transmission routes for antibiotic-resistant bacteria (ARB) and resistance genes (ARGs). Recent metagenomic, epidemiological, and mechanistic evidence demonstrates that anthropogenic pressures-including pharmaceutical effluents, agricultural runoff, untreated sewage, and airborne emissions-amplify resistance evolution and interspecies gene transfer via horizontal gene transfer mechanisms, biofilms, and mobile genetic elements. Importantly, it is not only highly polluted rivers such as the Ganges that contribute to the spread of AMR; even low concentrations of antibiotics and their metabolites, formed during or after treatment, can significantly promote the selection and dissemination of resistance. Environmental hotspots such as European agricultural soils and airborne particulate zones near wastewater treatment plants further illustrate the complexity and global scope of pollution-driven AMR. The synergistic roles of co-selective agents, including heavy metals, disinfectants, and microplastics, are highlighted for their impact in exacerbating resistance gene propagation across ecological and geographical boundaries. The efficacy and limitations of current mitigation strategies, including advanced wastewater treatments, thermophilic composting, biosensor-based surveillance, and emerging regulatory frameworks, are evaluated. By integrating a One Health perspective, this review underscores the imperative of including environmental considerations in global AMR containment policies and proposes a multidisciplinary roadmap to mitigate resistance spread across interconnected human, animal, and environmental domains.},
}

@article {pmid40867958,
year = {2025},
author = {Meradji, S and Basher, NS and Sassi, A and Ibrahim, NA and Idres, T and Touati, A},
title = {The Role of Water as a Reservoir for Antibiotic-Resistant Bacteria.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/antibiotics14080763},
pmid = {40867958},
issn = {2079-6382},
support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Water systems serve as multifaceted environmental pools for antibiotic-resistant bacteria (ARB) and resistance genes (ARGs), influencing human, animal, and ecosystem health. This review synthesizes current understanding of how antibiotics, ARB, and ARGs enter surface, ground, and drinking waters via wastewater discharge, agricultural runoff, hospital effluents, and urban stormwater. We highlight key mechanisms of biofilm formation, horizontal gene transfer, and co-selection by chemical stressors that facilitate persistence and spread. Case studies illustrate widespread detection of clinically meaningful ARB (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and mobile ARGs (e.g., sul1/2, tet, bla variants) in treated effluents, recycled water, and irrigation return flows. The interplay between treatment inefficiencies and environmental processes underscores the need for advanced treatment technologies, integrated monitoring, and policy interventions. Addressing these challenges is critical to curbing the environmental dissemination of resistance and protecting human and ecosystem health.},
}

@article {pmid40867941,
year = {2025},
author = {Yinsai, O and Yuantrakul, S and Srisithan, P and Zhou, W and Chittaprapan, S and Intajak, N and Kruayoo, T and Khamnoi, P and Tongjai, S and Daungsonk, K},
title = {Genomic Insights into Emerging Multidrug-Resistant Chryseobacterium indologenes Strains: First Report from Thailand.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/antibiotics14080746},
pmid = {40867941},
issn = {2079-6382},
support = {HSRI 64-145 and HSRI 66-147//Health Systems Research Institute (HSRI), Thailand/ ; },
abstract = {Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83-5.00 Mb and GC content of 37.15-37.35%. Genomic characterization identified conserved resistance genes (blaIND-2, blaCIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch. Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94-100 kb) carrying significant resistance genes (blaOXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen.},
}

@article {pmid40864264,
year = {2025},
author = {Pozzi, CM and Gaiti, A and Spada, A},
title = {Climate change and plant genomic plasticity.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {138},
number = {9},
pages = {231},
pmid = {40864264},
issn = {1432-2242},
mesh = {*Climate Change ; *Genome, Plant ; *Plants/genetics ; Quantitative Trait Loci ; DNA Transposable Elements ; *Adaptation, Physiological/genetics ; Genetic Variation ; Genomic Instability ; Evolution, Molecular ; },
abstract = {Genome adaptation, driven by mutations, transposable elements, and structural variations, relies on plasticity and instability. This allows populations to evolve, enhance fitness, and adapt to challenges like climate change. Genomes adapt via mutations, transposable elements, DNA structural changes, and epigenetics. Genome plasticity enhances fitness by providing the genetic variation necessary for organisms to adapt their traits and survive, which is especially critical during rapid climate shifts. This plasticity often stems from genome instability, which facilitates significant genomic alterations like duplications or deletions. While potentially harmful initially, these changes increase genetic diversity, aiding adaptation. Major genome reorganizations arise from polyploidization and horizontal gene transfer, both linked to instability. Plasticity and restructuring can modify Quantitative Trait Loci (QTLs), contributing to adaptation. Tools like landscape genomics identify climate-selected regions, resurrection ecology reveals past adaptive responses, and pangenome analysis examines a species' complete gene set. Signatures of past selection include reduced diversity and allele frequency shifts. Gene expression plasticity allows environmental adaptation without genetic change through mechanisms like alternative splicing, tailoring protein function. Co-opted transposable elements also generate genetic and regulatory diversity, contributing to genome evolution. This review consolidates these findings, repositioning genome instability not as a mere source of random error but as a fundamental evolutionary engine that provides the rapid adaptive potential required for plant survival in the face of accelerating climate change.},
}

*Climate Change
*Genome, Plant
*Plants/genetics
Quantitative Trait Loci
DNA Transposable Elements
*Adaptation, Physiological/genetics
Genetic Variation
Genomic Instability
Evolution, Molecular

@article {pmid40863943,
year = {2025},
author = {Zhao, E and Li, Y and Zhang, J and Geng, B},
title = {A Review on the Degradation of Antibiotic Resistance Genes During Composting of Livestock Manure.},
journal = {Toxics},
volume = {13},
number = {8},
pages = {},
pmid = {40863943},
issn = {2305-6304},
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) have been recognized as originating from diverse sources. Among these, the use of livestock feed and veterinary drugs was identified as the primary source of ARGs in livestock manure. ARGs were found to be widely distributed in global environments, particularly in agriculture-related soils, water bodies, and the atmosphere, posing potential threats to ecological environments and human health. This paper reviewed the degradation mechanisms of ARGs during aerobic composting of livestock manure and the safety evaluation of compost products. Aerobic composting was demonstrated to be an effective method for degrading ARGs, primarily through mechanisms such as high-temperature elimination of ARG-carrying microorganisms, reduction in host bacterial abundance, and inhibition of horizontal gene transfer. Factors including the physicochemical properties of the composting substrate, the use of additives, and the presence of antibiotic and heavy metal residues were shown to influence the degradation efficiency of ARGs, with compost temperature being the core factor. The safety of organic fertilizers encompassed multiple aspects, including heavy metal content, seed germination index, and risk assessments based on ARG residues. The analysis indicated that deficiencies existed in areas such as the persistence of thermotolerant bacteria carrying ARGs, the dissemination of extracellular antibiotic resistance genes (eARGs), and virus-mediated gene transfer. Future research should focus on (1) the removal of thermotolerant bacteria harboring ARGs; (2) the decomposition of eARGs or the blocking of their transmission pathways; (3) the optimization of ultra-high temperature composting parameters; and (4) the analysis of interactions between viruses and resistant hosts. This study reviews the mechanisms, influencing factors, and safety assessment of aerobic composting for degrading ARGs in livestock manure. It not only deepens the understanding of this important environmental biotechnology process but also provides a crucial knowledge base and practical guidance for effectively controlling ARG pollution, ensuring agricultural environmental safety, and protecting public health. Additionally, it clearly outlines the key paths for future technological optimization, thus holding significant implications for the environment, agriculture, and public health.},
}

@article {pmid40863608,
year = {2025},
author = {Gopal, C and Al Tarify, H and Pirhadi, E and O'Brien, EG and Dagar, A and Yong, X and Schertzer, JW},
title = {Membrane Stress Enhances Specific PQS-Lipid Interactions That Drive Bacterial Outer Membrane Vesicle Biogenesis.},
journal = {Membranes},
volume = {15},
number = {8},
pages = {},
pmid = {40863608},
issn = {2077-0375},
support = {1R15GM135862-01//NIH (NIGMS)/ ; },
abstract = {Gram-negative bacteria use outer membrane vesicles (OMVs) for toxin trafficking, immune interference, horizontal gene transfer, antibiotic protection, and cell-cell communication. Despite their direct contribution to many pathogenesis-related behaviors, our understanding of how OMVs are produced remains surprisingly incomplete. The Bilayer Couple model describes the induction of OMV formation resulting from the preferential accumulation of small molecules in the outer leaflet of the membrane, resulting in leaflet expansion and membrane bending. Previous work has highlighted the importance of the structure of the Pseudomonas Quinolone Signal (PQS) in driving OMV formation, but the nature of interactions with membrane lipids remains unclear. Our recent in silico analysis suggested that a new interaction, between the PQS ring nitrogen and Lipid A, is critical for PQS function. Here, we used chemical analogs to interrogate the importance of specific PQS functional groups in its ability to stimulate OMV biogenesis. We demonstrated that OMV induction requires the presence of all PQS functional groups together. Further modeling uncovered that PQS prefers interaction with the outer leaflet of the membrane, consistent with its unique ability to drive OMV biogenesis. This was explained by much greater hydrogen bond formation between PQS and Lipid A. Interestingly, the preference of PQS for the outer leaflet coincided with that leaflet becoming crowded. Thus, the initial insertion of PQS into the outer leaflet would be expected to encourage local accumulation of more PQS to drive the induction of membrane curvature and subsequent OMV formation.},
}

@article {pmid40862159,
year = {2025},
author = {Wang, Y and Jiang, L and Zhou, F and Zhang, Y and Fine, RD and Li, M},
title = {The hidden dancers in water: the symbiotic mystery of Legionella pneumophila and free-living amoebae.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634806},
pmid = {40862159},
issn = {1664-302X},
abstract = {Legionella pneumophila, a Gram-negative bacillus, is the primary etiological agent of Legionnaires' disease, a severe respiratory infection. The symbiotic relationship between L. pneumophila and free-living amoebae (FLAs), particularly Acanthamoeba spp., represents a critical intersection of microbial ecology and human pathogenesis. This symbiosis provides Legionella with a protective intracellular niche, enhancing its resistance to biocides, increasing its pathogenicity, and facilitating horizontal gene transfer. These interactions not only boost the environmental persistence and dissemination of L. pneumophila but also elevate the risk of human exposure through contaminated drinking water systems. This review delves into the sophisticated survival strategies employed by L. pneumophila within host cells, including evasion of endocytic pathways, inhibition of phagosome maturation and acidification, and prevention of phagosome-lysosome fusion. By elucidating these mechanisms, we underscore the critical need for in-depth research into the Legionella-amoebae symbiosis and its broader implications for public health. Additionally, we address the challenges and strategies for mitigating environmental risks, emphasizing the importance of innovative approaches to ensure water system safety and prevent pathogen transmission.},
}

@article {pmid40862153,
year = {2025},
author = {Pacheco-Acosta, S and Castro-Toro, G and Rojas-Villalobos, C and Valenzuela, C and Haristoy, JJ and Zapata-Araya, A and Moya-Beltrán, A and Sepúlveda-Rebolledo, P and Pérez-Rueda, E and Ulloa, R and Giaveno, A and Issotta, F and Díez, B and Beard, S and Quatrini, R},
title = {Exploring the eco-evolutionary role of plasmids and defense systems in 'Fervidacidithiobacillus caldus' extreme acidophile.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610279},
pmid = {40862153},
issn = {1664-302X},
abstract = {Plasmids are major drivers of microbial evolution, enabling horizontal gene transfer (HGT) and facilitating adaptation through the dissemination of relevant functional genes and traits. However, little is known about plasmid diversity and function in extremophiles. 'Fervidacidithiobacillus caldus', a meso-thermo-acidophilic sulfur oxidizer, is a key player in sulfur cycling in natural and industrially engineered acidic environments. Here, we present a bioinformatic analysis of the plasmidome, and associated anti-mobile genetic element (anti-MGE) defense systems (defensome), across genomes of this species and metagenomes from diverse natural and industrial settings harboring 'F. caldus'. We identified >30 distinct plasmids, representing five consistent replication-mobilization families. Plasmids ranged in size between 2.5-65 kb, with gene content and plasmid modularity scaling with element size and copy numbers inversely correlating with size. Plasmids carried variable numbers of hypothetical proteins and transposases, with annotated cargo genes reflecting functional differentiation by habitat. Defensome profiling revealed over 50 anti-MGE systems in sequenced 'F. caldus' isolates, including diverse restriction-modification systems, CRISPR-Cas types IV-A and V-F, and widespread abortive infection and composite defense systems such as Wadjet, Gabija, and Zorya. In environmental populations, an inverse relationship was observed between defensome complexity and plasmidome abundance and diversity, underscoring a pivotal role of the host defensome in modulating persistence, compatibility, and overall plasmid diversity across 'F. caldus' populations. Yet, other plasmids appeared decoupled from both host abundance and defensome complexity, suggesting potential host shifts, environmental persistence, or differential replication under suboptimal growth conditions for the host. Altogether, these findings point to a modular, functionally diverse adaptive plasmidome shaped by environmental pressures, by the interplay with the host's defensome, and likely also by other eco-evolutionary processes at play in natural environments. While these associations are compelling, causal relationships remain to be experimentally validated. These insights broaden our understanding of mobile genetic elements in extreme environments and provide a foundation for plasmid-based vector design and synthetic biology applications in acidophiles, with direct implications to biomining and environmental remediation.},
}

@article {pmid40860440,
year = {2025},
author = {She, T and Tan, D and Balcazar, JL and Friman, VP and Wang, D and Zhu, D and Ye, M and Sun, M and Yuan, S and Hu, F},
title = {Phage-mediated horizontal transfer of Salmonella enterica virulence genes with regulatory feedback from the host.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70042},
pmid = {40860440},
issn = {2770-596X},
abstract = {Phage-mediated horizontal transfer of virulence genes can enhance the transmission and pathogenicity of Salmonella enterica (S. enterica), a process potentially regulated by its regulatory mechanisms. In this study, we explored the global dynamics of phage-mediated horizontal transfer in S. enterica and investigated the role of its regulatory mechanisms in transduction. A total of 5178 viral sequences encoding 12 S. enterica virulence genes were retrieved from the Integrated Microbial Genomes and Virome (IMG/VR) database, alongside 466,136 S. enterica genomes from EnteroBase. Virulence genes, including iacP (acyl carrier protein), mgtB (P-type Mg[2+] transporter), misL (autotransporter porin), and fliC (flagellar filament protein), were widely distributed in phages and S. enterica across North America, Europe, and Asia. Phylogenetic analysis revealed close genetic affinity between phage- and bacterial-encoded virulence genes, suggesting shared ancestry and historical horizontal gene transfer events. The global regulator carbon storage regulator A (csrA) was highly conserved and ubiquitous in S. enterica. Overexpression of csrA inhibited prophage cyclization and release by upregulating the prophage cI repressor during horizontal gene transfer. Overall, these findings enhance our understanding of phage-mediated horizontal transfer of virulence genes, explore new areas of bacterial regulators that inhibit gene exchange and evolution by affecting phage life cycles, and offer a novel approach to controlling the transmission of phage-mediated S. enterica virulence genes.},
}

@article {pmid40858011,
year = {2025},
author = {Ji, Q and Zhu, J and Hou, G and Liang, G and Yan, P and Liu, X and Yu, Z and Xue, K and Wang, Z and Liu, R},
title = {Antibiotic stress alters lysogeny-lysis dynamics and drives phage-mediated transfer of antibiotic resistance genes in the activated sludge process.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139659},
doi = {10.1016/j.jhazmat.2025.139659},
pmid = {40858011},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) in wastewater treatment systems poses a significant public health concern, yet the role of bacteriophages (phages), particularly temperate phages, in mediating horizontal gene transfer (HGT) of ARGs under antibiotic stress remains poorly understood. This study investigated the effects of escalating ciprofloxacin (CIP; 0-200 μg/L)-selected as a representative antibiotic due to its frequent occurrence and persistence in wastewater-on phage lysogeny-lysis dynamics and phage-mediated ARG transfer in a laboratory-scale activated sludge reactor. Integrating metaviromic and metagenomic analysis revealed that the phage-mediated ARG-HGT events mainly occurred at the highest CIP concentration stage (200 μg/L), indicating that high-level antibiotic stress is essential for triggering significant ARG transfer. Notably, all these HGT events were associated with temperate phages. The HGT-associated ARGs may confer host resistance to antibiotics, as supported by the ARG expression and antibiotic resistance activity experiment. Although temperate dynamics generally shifted toward lysogeny under escalating stress, most of the temperate phages involved in ARG-HGT became more active at higher CIP concentration stages, which may facilitate host survival under stress conditions.},
}

@article {pmid40849092,
year = {2025},
author = {Kumar, M and Ballamoole, KK and Shetty, VA and Rao, RSP and Gollapalli, P},
title = {Perspective on integrated multi-omics approaches and constraint-based modeling to explore metabolic functionality on the evolution of bacterial antibiotic resistance.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107999},
doi = {10.1016/j.micpath.2025.107999},
pmid = {40849092},
issn = {1096-1208},
abstract = {Antimicrobial resistance (AMR) is one of the greatest threats to humanity globally as it has been escalated by the over-prescription and usage of antibiotics for both humans and animals. AMR occurs when the bacteria develop a way of resisting the antimicrobial compounds, thus leading to increased mortality rates, health expenses, and issues of handling infections. The development of AMR occurs through mutations of bacterial genes or through horizontal gene transfer that results in increased minimum inhibitory concentration and bacterial tolerance. Perspectives from evolutionary trade-offs and constraint-based modeling were used to analyze the relationship between mutational changes and antimicrobial resistance. The idea of "adaptive landscape" helps in explaining how microbial traits develop based on selective forces, and the "dimensionality of phenotypic states" looks at how resistance occurs in various biological systems. The omics approaches give multi-dimensional data to focus further on bacterial adaptation factors and explore future antimicrobial resistance trends. Information on condition-dependent resistance and the weakness of the resistant strains is obtained when involving constraint-based modeling and resequencing of the genome. It also involves bacterial metabolic plasticity under antibiotic pressure and provides fresh approaches to combat antimicrobial resistance. This perspective emphasizes the importance of new strategies highlighting the availability of multiple omics approaches to understand the bacterial resistance mechanisms and construct early therapeutic approaches.},
}

@article {pmid40505407,
year = {2025},
author = {Jiang, Q and Zhuang, W and Zhang, Z and Wu, Z and Liu, J and Shi, J and Deng, H},
title = {Reactive chlorine species inhibiting interspecies spread of antibiotic resistance via disrupting donor - Recipient cells and regulating plasmid conjugation genes.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138864},
doi = {10.1016/j.jhazmat.2025.138864},
pmid = {40505407},
issn = {1873-3336},
mesh = {*Escherichia coli/genetics/drug effects ; *Plasmids/genetics ; *Bacillus subtilis/drug effects/genetics ; *Chlorine/pharmacology/chemistry ; *Conjugation, Genetic/drug effects ; *Drug Resistance, Microbial/genetics/drug effects ; Ultraviolet Rays ; *Drug Resistance, Bacterial/drug effects/genetics ; Reactive Oxygen Species/metabolism ; Gene Transfer, Horizontal/drug effects ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Current drinking water treatment plant (DWTP) disinfection technologies face limitations, allowing plasmid-mediated antibiotic resistance genes (ARGs) transfer to occur among viable but nonculturable (VBNC) bacteria, heightening the risk of antibiotic-resistant infections. While UV/Chlorine has been adopted to curb ARGs abundance, its impacts on the interspecies transfer of ARG-carrying plasmids remain hardly explored. This study investigated how reactive chlorine species (RCS) in the UV/Chlorine system inhibited the transfer of antibiotic resistance from antibiotic-resistant Escherichia coli (AR E. coli) to Bacillus subtilis (B.S) by inactivating both donor and recipient strains and regulating plasmid conjugation genes. RCS reduced plasmid transfer frequencies by 2.1-log and 3.2-log compared to UV or chlorine alone. By impairing [•]OH scavenging ability, it led to ROS accumulation in AR E. coli, disrupting cellular energy metabolism and DNA repair, ultimately causing DNA degradation and membrane damage, resulting in AR E. coli inactivation rather than entering the VBNC state. Additionally, RCS induced structural and intracellular disruption in B.S, compromising its capacity for plasmid uptake and stable maintenance. Finally, RCS inhibited plasmid horizontal transfer while enhancing vertical transfer, with its damage to outer membrane proteins further restricting interspecies plasmid conjugation transfer. This study provides novel insights for DWTPs to better control ARGs interspecies transfer and improve drinking water safety.},
}

*Escherichia coli/genetics/drug effects
*Plasmids/genetics
*Bacillus subtilis/drug effects/genetics
*Chlorine/pharmacology/chemistry
*Conjugation, Genetic/drug effects
*Drug Resistance, Microbial/genetics/drug effects
Ultraviolet Rays
*Drug Resistance, Bacterial/drug effects/genetics
Reactive Oxygen Species/metabolism
Gene Transfer, Horizontal/drug effects
Anti-Bacterial Agents/pharmacology

@article {pmid40848936,
year = {2025},
author = {Zhaxybayeva, O and Nesbø, CL},
title = {Impact of Horizontal Gene Transfer on Adaptations to Extreme Environments.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169403},
doi = {10.1016/j.jmb.2025.169403},
pmid = {40848936},
issn = {1089-8638},
abstract = {Horizontal (or lateral) gene transfer - an acquisition of genetic material not associated with the organismal reproduction - is known to alter genomes of most, if not all, living organisms. There is mounting evidence for the importance of gene exchange in organismal adaptations to new or changing environmental conditions. In comparison to accumulation of de novo mutations, acquisition of a gene already beneficial in the environment is fast and less costly, and thus an advantageous, way to adjust to survival and growth in new conditions. Adaptation to extreme environments at the boundaries of habitat conditions beyond which cellular integrity, metabolism and growth are not possible, is not an exception. Here we review the impact of horizontal gene transfer on organismal adaptations to natural and human-made extreme environments. This includes thermophiles living at high temperatures, psychrophiles found at low temperatures, acidophiles inhabiting high acidity environments, alkaliphiles thriving at high pH, halophiles found in high salt environments, xerophiles that can tolerate extremely low water availability, oligotrophes thriving at low nutrient availability, piezophiles inhabiting high pressure environments, and organisms that can withstand high levels of ionizing radiation. We also discuss the challenges and future directions for deciphering genetic determinants and horizontal gene transfer events of extremophiles' adaptations.},
}

@article {pmid40846514,
year = {2025},
author = {Yoshimoto, S and Hattori, M and Inoue, S and Mori, S and Ohara, Y and Hori, K},
title = {Identification of toluene degradation genes in Acinetobacter sp. Tol 5.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.07.010},
pmid = {40846514},
issn = {1347-4421},
abstract = {Microbial degradation of aromatic compounds provides sustainable solutions for environmental remediation and bioconversion. Acinetobacter sp. Tol 5 is notable for its strong adhesiveness and potential as a biocatalyst for toluene degradation; however, its toluene metabolic pathway has not been fully elucidated. In this study, genomic analysis identified a cluster of genes in Tol 5 highly similar to the well-known tod operon of Pseudomonas putida, encoding enzymes responsible for toluene metabolism. Phylogenetic analyses indicated that these tod genes, unusual among Acinetobacter species, were likely acquired through horizontal gene transfer. Transcriptomic analyses revealed that todF and todC1 are co-transcribed, while the adjacent fadL2 gene, encoding a putative outer membrane transporter corresponding to P. putida todX, is independently transcribed. Growth experiments using gene-knockout mutants revealed that TodC1, the large subunit of dioxygenase, is essential for growth on toluene, whereas FadL2 is not essential. Growth curves on each carbon source further showed that the todC1 knockout mutant could metabolize benzoate, but not toluene or benzene, confirming that the TOD pathway is the primary route for toluene and benzene degradation in Tol 5. The identification of the functional TOD pathway, which is unique within Acinetobacter, provides genetic and biochemical insights for the development of Tol 5 as an efficient immobilized biocatalyst for the bioremediation and bioconversion of aromatic compounds.},
}

@article {pmid40838736,
year = {2025},
author = {Fang, J and Chen, Z and Yu, Z and Shan, S and Hou, Y and Liu, L and Huang, J and Li, B and Guo, J},
title = {Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf187},
pmid = {40838736},
issn = {1751-7370},
abstract = {The environmental dissemination of antibiotic resistance genes (ARGs), particularly in manure-amended soils, poses a growing threat to public health due to the potential transfer of ARGs to humans and animals. Effective strategies are urgently needed to mitigate ARG spread in agricultural settings. Biochar, an eco-friendly soil amendment, shows promise for pollution control, yet its role in suppressing ARG horizontal gene transfer remains unclear. Here, metagenomic analysis showed that manure application significantly increased the relative abundance of ARGs in soil microbiota, whereas biochar amendment reduced it. To determine whether biochar suppresses ARG dissemination by inhibiting horizontal transfer, we established a soil microcosm. Manure application increased the conjugative transfer ratio by 3-fold, whereas biochar effectively suppressed this transfer reducing it to levels observed in unamended soils. Cell sorting and 16S rRNA gene amplicon sequencing demonstrated that biochar treatment reduced the diversity of transconjugant pools at both phylum and genus level. Transconjugants were primarily affiliated with Pseudomonadota, Bacillota, and Actinomycetota, with Massilia, Delftia, and Ammoniphilus being the most abundant genera in biochar treatment soil. Mechanistic investigations revealed that biochar-mediated inhibition of ARG transfer was linked to reduced ATP energy supply, decreased reactive oxygen species production, and lower cell membrane permeability, and diminished bioavailability of heavy metals and antibiotics. Additionally, biochar altered soil enzyme activity and microbial community structure, further limiting ARG dissemination. The findings provide insights into biochar-induced mitigation of ARG spread in manure-amended soils and highlight its potential as an effective strategy for controlling environmental ARG transmission.},
}

@article {pmid40837691,
year = {2025},
author = {Zhai, ZQ and Yang, LK and Zhu, LB and Zhao, FJ and Xie, WY and Wang, P},
title = {Early Life Exposure to Manure-Fertilized Soil Shapes the Gut Antibiotic Resistome.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {8},
pages = {931-941},
pmid = {40837691},
issn = {2833-8278},
abstract = {The global rise of antimicrobial resistance (AMR) presents a pressing public health challenge with agricultural practices such as the use of manure fertilization, excessive antibiotic use in livestock, and the irrigation of crops with contaminated water contributing to the spread of antibiotic resistance genes (ARGs). Despite growing concerns, the pathways through which ARGs migrate from environmental reservoirs to animal microbiomes are poorly understood. In this study, we raised mice from birth in pig manure-fertilized red (Ultisols) and black (Mollisols) soils or unfertilized controls, sampling their gut microbiomes at 8 weeks, to show that early life exposure to manure-fertilized soil profoundly shapes the gut antibiotic resistome in mice. Application of organic manure significantly enriched tetracycline-resistant ARGs in both red and black soils. Mice living in these environments harbored markedly higher abundances of ARGs, particularly the tet-(Q) gene, compared to those in nonfertilized environments. Notably, Muribaculaceae and Bacteroidaceae were identified as key hosts of tet-(Q), with evidence suggesting a horizontal gene transfer between these families. These findings indicate that manure fertilization not only increases ARG abundance in soils but also facilitates its transfer to animal microbiomes, thereby amplifying the risk of AMR dissemination. This research underscores the importance of improved agricultural management practices to mitigate the environmental transmission of AMR.},
}

@article {pmid40837528,
year = {2025},
author = {Trejo-Meléndez, VJ and Contreras-Garduño, J},
title = {Master of Puppets: How Microbiota Drive the Nematoda Ecology and Evolution?.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71549},
pmid = {40837528},
issn = {2045-7758},
abstract = {In recent decades, the microbiota has emerged as a key driver of biological functions in metazoans, and nematodes are no exception. Advances in genomic technologies have enabled detailed exploration of nematode-microbiota interactions, revealing compelling insights. However, much of our current understanding is derived from studies on the model organism Caenorhabditis elegans, where the microbiota's role in shaping host phenotypes and genotypes has been extensively characterized. These studies have uncovered the selective pressures influencing the function, structure, and assembly of the microbiota, highlighting the dynamic interplay between nematodes and their associated microbial communities. Despite these findings, the ecological and evolutionary implications of the microbiota in nematodes remain underappreciated. Emerging evidence indicates that the microbiota can modulate nematode life-history traits and mediate trade-offs among fitness components. Moreover, mechanisms such as horizontal gene transfer from bacteria have been shown to alter nematode phenotypes and genotypes, facilitating adaptation to novel or challenging environments. In this review, we integrate life-history theory into the nematodes-microbiota interactions, offering a framework to identify the mechanisms driving phenotypic variation in nematodes. Understanding these processes is essential for uncovering the evolutionary and ecological bases of metazoan diversification, with the microbiota acting as a crucial source of phenotypic and genetic variability.},
}

@article {pmid40835192,
year = {2025},
author = {Bui-Nguyen, TA and Huynh, TB and Tran-Van, H},
title = {Molecular Epidemiology of Acute Hepatopancreatic Necrosis Disease: A Review.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105444},
doi = {10.1016/j.dci.2025.105444},
pmid = {40835192},
issn = {1879-0089},
abstract = {Acute hepatopancreatic necrosis disease (AHPND) is one of the major shrimp diseases worldwide which affects global economy up to 44 billion USD from 2010 to 2016. The causative agent of AHPND is the binary toxin PirAB, a toxin that causes sloughing effect on shrimp hepatopancreatic cells. This toxin is encoded by pirAB[vp] gene located within a 5.5-kb composite transposon Tn6264, on a ∼70-kb plasmid pVA carried by Vibrio parahaemolyticus. Up to date, the pathogenesis and epidemiological links between AHPND-causing strains are still unclear. Therefore, this review aims to collect achieved results about the distribution, origin, transmission, and antibiotic resistance status of AHPND-causing strains, the molecular mechanism of PirAB toxin, and the mobile genetic elements that promote the spread of AHPND to provide valuable insights for future studies. Phylogenetic studies on AHPND reveal its evolutionary history, transmission routes, and genetic variations, with findings suggesting diverse origins of AHPND strains across different regions, facilitated by horizontal gene transfer and adaptation mechanisms in V. parahaemolyticus populations. Antimicrobial resistance profiles of AHPND-causing strains are also diverse and prevalent, particularly in Vietnam, South Korea, and Thailand, encompassing antibiotics like ampicillin, amoxicillin, sulfadiazine sodium, streptomycin, colistin, cefalexin, erythromycin, ceftazidime, and neomycin, raising concerns regarding multidrug resistance. PirAB toxin might function through the pore-forming activity of PirB[vp] and the receptor-binding activity of PirA[vp], as predicted by Cry toxin model, while its expression is regulated by the quorum sensing system in V. parahaemolyticus. The pVA plasmid and the composite transposon Tn6264 both facilitates the dissemination of AHPND-causing strains, while the evolutionary mechanisms of these elements have not been widely understood. Transcriptomic and metabolomic studies also identify numerous differentially expressed genes in shrimp infected by AHPND-causing V. parahaemolyticus, and its immunity is also dependent on developmental stage and gut microbiota.},
}

@article {pmid40834228,
year = {2025},
author = {Mariault, L and Puginier, C and Keller, J and El Baidouri, M and Delaux, PM},
title = {Mechanisms, Detection, and Impact of Horizontal Gene Transfer in Plant Functional Evolution.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf195},
pmid = {40834228},
issn = {1532-298X},
abstract = {Horizontal gene transfers (HGT) have been observed across the tree of life. While their adaptive importance in bacteria is conspicuous, the occurrence of HGT and their evolutionary significance in Eukaryotes has only recently started to be considered. In this review, we explore the extent of HGT in the plant kingdom, indicating the widespread occurrence of microbe - plant HGT and Plant - Plant HGT. We propose mechanisms that mediate these transfers, and detail the methods available to identify and test the robustness of putative HGT using both sequence-based and phylogenomic approaches. Exploring recently sequenced plant genomes across the green lineage has revealed hundreds of such HGT. We discuss the impact of these transfers on plant adaptation and functional diversification. In the future, expanding the phylogenomic scrutinization of the plant kingdom should reveal the full extent of HGT. In situ sequencing and combinations of synthetic biology and experimental evolution may allow catching ongoing HGT and testing the functional relevance of such events.},
}

@article {pmid40831643,
year = {2025},
author = {Meza, C and Sepulveda, B and Flores-Castañón, N and Valenzuela, F and Ormeño, C and Castillo, A and Echeverría-Vega, A and Jasem Mohammed Breig, S and Alardhi, SM and Gonzalez, A and Mora-Lagos, B and Banerjee, A},
title = {Genomic basis and functional characterization of the exopolysaccharide production by a thermotolerant Bacillus isolated from Tolhuaca hot spring.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1622325},
pmid = {40831643},
issn = {1664-302X},
abstract = {Bacillus licheniformis Tol1, a thermotolerant bacterial strain isolated from the Tolhuaca hot spring in Chile, was investigated for its genomic features and the functional properties of its exopolysaccharide (EPS). The whole-genome sequencing revealed ∼4.25 Mbp genome with a GC content of 45.9% and a rich repertoire of genes associated with environmental stress adaptation, antibiotic resistance, sporulation, biofilm formation, and EPS biosynthesis, including the presence of epsD and epsC. The strain also harbored intact prophage elements and a Type I-A CRISPR-Cas system, indicating potential horizontal gene transfer and genome plasticity. Confocal microscopy revealed robust biofilm formation at 45-55°C under neutral to slightly alkaline pH, with strong EPS matrix development. EPS production was optimized using OFAT and Response Surface Methodology (RSM), achieving a yield of 2.11 g L[-1] under optimized conditions, which was further validated using an Artificial Neural Network (ANN) model (R [2] = 0.9909). The EPS exhibited promising antioxidant activity and significant emulsification potential across various vegetable oils, which were comparable or superior to commercial bacterial EPS xanthan gum. Notably, the EPS also showed cytotoxic effects against AGS gastric adenocarcinoma cells, reducing viability by 38.38 and 37% at 50-100 μg μL[-1] concentrations, respectively, suggesting potential anticancer activity. Altogether, the study highlights B. licheniformis Tol1 as a multifunctional thermophile with valuable biotechnological potential, particularly for applications in food, pharmaceutical, and biomedical industries.},
}

@article {pmid40831357,
year = {2025},
author = {Cerda-Herrera, JD and Zhang, H and Wafula, EK and Adhikari, S and Park, SY and Carey, SB and Harkess, A and Ralph, PE and Westwood, JH and Axtell, MJ and dePamphilis, CW},
title = {Chromosome level assembly and annotation of Cuscuta campestris Yunck. ("field dodder"), a model parasitic plant.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf193},
pmid = {40831357},
issn = {2160-1836},
abstract = {We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, interspecies RNA movement, and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. C. campestris is a recent tetraploid with a high retention of duplicated genes and chromosomes, and less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of C. campestris with the RUBY marker system allows visualization of transformed Cuscuta-derived fluorescent mobile molecules that have entered the host stem. This genome will be of value for scientists performing fundamental research in a wide range of molecular, developmental, population and evolutionary biology, as well as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and for the development of highly specific herbicides.},
}

@article {pmid40830872,
year = {2025},
author = {Saffari Natanzi, A and Poudineh, M and Karimi, E and Khaledi, A and Haddad Kashani, H},
title = {Innovative approaches to combat antibiotic resistance: integrating CRISPR/Cas9 and nanoparticles against biofilm-driven infections.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {486},
pmid = {40830872},
issn = {1741-7015},
mesh = {*Biofilms/drug effects ; *CRISPR-Cas Systems ; Humans ; *Nanoparticles ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Gene Editing/methods ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/drug therapy ; Pseudomonas aeruginosa/drug effects ; },
abstract = {The increasing prevalence of antibiotic-resistant bacterial infections is a major global health concern, with biofilms playing a key role in bacterial persistence and resistance. Biofilms provide a protective matrix that limits antibiotic penetration, enhances horizontal gene transfer, and enables bacterial survival in hostile environments. Conventional antimicrobial therapies are often ineffective against biofilm-associated infections, necessitating the development of novel therapeutic strategies. The CRISPR/Cas9 gene-editing system has emerged as a revolutionary tool for precision genome modification, offering targeted disruption of antibiotic resistance genes, quorum sensing pathways, and biofilm-regulating factors. However, the clinical application of CRISPR-based antibacterials faces significant challenges, particularly in efficient delivery and stability within bacterial populations. Nanoparticles (NPs) present an innovative solution, serving as effective carriers for CRISPR/Cas9 components while exhibiting intrinsic antibacterial properties. Nanoparticles can enhance CRISPR delivery by improving cellular uptake, increasing target specificity, and ensuring controlled release within biofilm environments. Recent advances have demonstrated that liposomal CRISPR-Cas9 formulations can reduce Pseudomonas aeruginosa biofilm biomass by over 90% in vitro, while gold nanoparticle carriers enhance editing efficiency up to 3.5-fold compared to non-carrier systems. These hybrid platforms also enable co-delivery with antibiotics, producing synergistic antibacterial effects and superior biofilm disruption. Additionally, they can facilitate co-delivery of antibiotics or antimicrobial peptides, further enhancing therapeutic efficacy. This review explores the synergistic integration of CRISPR/Cas9 and nanoparticles in combating biofilm-associated antibiotic resistance. We discuss the mechanisms of action, recent advancements, and current challenges in translating this approach into clinical practice. While CRISPR-nanoparticle hybrid systems hold immense potential for next-generation precision antimicrobial therapies, further research is required to optimize delivery platforms, minimize off-target effects, and assess long-term safety. Understanding and overcoming these challenges will be critical for developing effective biofilm-targeted antibacterial strategies.},
}

*Biofilms/drug effects
*CRISPR-Cas Systems
Humans
*Nanoparticles
*Anti-Bacterial Agents/administration & dosage/pharmacology
Gene Editing/methods
*Drug Resistance, Bacterial/genetics
*Bacterial Infections/drug therapy
Pseudomonas aeruginosa/drug effects

@article {pmid40829589,
year = {2025},
author = {Sibbald, SJ and Lawton, M and Maclean, C and Roger, AJ and Archibald, JM},
title = {Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.07.055},
pmid = {40829589},
issn = {1879-0445},
abstract = {In prokaryotes, lateral gene transfer (LGT) is a key mechanism leading to intraspecies variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens-a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Ac. anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase pairs [Mbp]), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain-level genetic variation in Ac. anophagefferens, with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. A total of 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5%-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.},
}