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At least 19 recordsLinked to original sources

PubMed1977

Analysis of plasmid deoxyribonucleic acid in a cariogenic strain of Streptococcus faecalis: an approach to identifying genetic determinants on cryptic plasmids.

Streptococcus faecalis strains ND539 and OG1 have been previously shown to be cariogenic in gnotobiotic animals. Deoxyribonucleic acid analyses have revealed the presence of a single 26-megadalton plasmid designated pAM539 in the former strain, whereas the latter strain was found to be plasmid-free. By gene transfer experiments, it was possible to construct isogenic pairs of strains that differed only with regard to the presence or absence of pAM539. Comparative studies of isogenic pairs showed that the presence of pAM539 conferred bacterial sensitivity to a bacteriocin produced by S. faecalis strain 5952.

Animals↗

PubMed2026

Emergence of Acinetobacter soli harboring three carbapenemase-encoding genes (blaNDM-1, blaIMP-14, and blaOXA-58) on a single plasmid in an ICU patient.

Acinetobacter soli is an environmentally adaptable species increasingly recognized as an emerging pathogen in hospital settings, particularly in intensive care units (ICUs). In this study, we report the first A. soli isolate from an ICU patient that co-harbors three carbapenemase-encoding genes (blaNDM-1, blaIMP-14, and blaOXA-58) on a single plasmid. Whole-genome sequencing revealed that multidrug resistance in this strain is mediated by a 294,790 bp plasmid, pSLAB-A, carrying 16 antimicrobial resistance genes, including all three carbapenemases. Comparative plasmid analysis showed a highly conserved backbone but identified a unique ~40 kb multidrug-resistance region containing blaNDM-1, blaIMP-14, and eight additional resistance genes. Genetic context analysis indicated that insertion sequences (ISAba125 and ISAba3) and class 1 integrons contribute to the mobilization and accumulation of carbapenemase-encoding genes. Plasmid stability assays demonstrated that pSLAB-A remained stably maintained for more than 90 generations without antibiotic selection. A global survey of the NCBI database identified 15 A. soli strains carrying carbapenemase-encoding genes, most of which were isolated from China, with clinical specimens representing the predominant source. Seven carbapenemase-encoding genes were detected, with blaNDM-1 being the most prevalent. Among eight isolates with complete genomes, all carried carbapenemase-encoding genes on plasmids. Phylogenetic analysis revealed regional dissemination of a clonal lineage across hospitals in Zhejiang Province and sustained nosocomial transmission within a hospital in Taiwan. These findings suggest that the spread of carbapenem resistance in A. soli is largely driven by multidrug-resistance plasmids, facilitating clonal expansion in hospital environments and posing a growing challenge for antimicrobial therapy and infection control in ICUs.IMPORTANCECarbapenem-resistant A. soli is an emerging clinical concern, capable of causing severe invasive infections, including bacteremia, in intensive care unit settings, and its emergence poses substantial challenges to antimicrobial therapy. In this study, we demonstrate that carbapenem resistance in A. soli is predominantly mediated by the acquisition of multidrug-resistance plasmids carrying carbapenemase-encoding genes. Owing to its strong environmental persistence, A. soli can readily undergo nosocomial clonal dissemination once carbapenem resistance is acquired. Moreover, the spread of multidrug plasmids co-harboring multiple carbapenemase-encoding genes may accelerate the evolutionary trajectory of resistance in A. soli, further exacerbating the threat to clinical management. Given its demonstrated capacity to cause hospital-associated infections and to rapidly acquire multidrug resistance, A. soli warrants heightened vigilance from both clinical and public health perspectives.

beta-Lactamases↗

PubMed2026

Coexistence of carbapenemase and hypervirulence-associated genes among Klebsiella pneumoniae high-risk clones in Hungary.

INTRODUCTION: Strains of Klebsiella pneumoniae carrying hypervirulence and carbapenemase genes represent a rapidly emerging global public health threat. Our study aimed to comprehensively characterise the genomics of hypervirulence-associated and carbapenemase genes carrying K. pneumoniae (hv(a)CpKp) isolates in Hungary. MATERIALS AND METHODS: Between January 2022 and April 2024, 89 aerobactin (iucA-D/iutA)-positive non-duplicate carbapenemase-producing K. pneumoniae isolates from 15 Hungarian healthcare institutes underwent short-read (Illumina, MiSeq, NextSeq) whole-genome sequencing, followed by detailed plasmid analysis using long-read sequencing (Nanopore, MinION) in a representative subset of 32 strains. RESULTS: Most isolates (79/89) belonged to the high-risk clone ST147. Hypervirulence-associated (hva) genes-including rmpA/rmpA2, peg344, shiF, iucA-D, and iutA-were universally present, and 59 isolates possessed chromosomally integrated yersiniabactin loci. Most isolates (87/89) carried the bla NDM-1 carbapenemase gene. Hypervirulence-associated genes were most frequently (29/32) associated with IncHI1B/IncFIB(Mar) plasmids. Notably, we identified plasmids carrying both hva and carbapenemase genes-designated as hybrid plasmids-in 13 of 32 strains. The bla NDM-1 was linked to the IS26 transposase and was present in conserved, identical cassettes on all bla NDM-1-carrying plasmids. DISCUSSION/CONCLUSION: Our study identified hv(a)CpKp strains, particularly the ST147 clone, circulating in Hungary. Our findings highlight the need for routine virulence gene monitoring and continuous genomic and plasmid-based surveillance to mitigate the clinical and epidemiological impact of emerging hv(a)CpKp lineages.

Klebsiella pneumoniae↗

PubMed2026

Genomic surveillance reveals escalating antimicrobial resistance and plasmid diversity in clinical Salmonella 1,4,[5],12:i:- ST34 isolates from Guizhou Province, China.

INTRODUCTION: Salmonella 1,4,[5],12:i:- ST34 has emerged as a significant public health issue due to its association with various antimicrobial resistance genes (ARGs) and transferable plasmids. However, its genomic characteristics and potential influence on public health in Guizhou have not been comprehensively assessed. METHODS: From 2019 to 2023, a 5-year surveillance was conducted in nine cities (prefectures) of Guizhou Province. We integrated phenotypic and genomic analyses of 281 clinical Salmonella 1,4,[5],12:i:- ST34 isolates to investigate the prevalence of ARGs and plasmids and to analyze the molecular epidemiology and evolution. RESULTS: The isolates exhibited resistance to first-line antibiotics, with 22.4% for ciprofloxacin, 11.4% for azithromycin, 18.5% for ceftazidime, and 39.1% for cefotaxime. ARGs showed substantial agreement with phenotypes for tetracycline, macrolides, third-generation cephalosporins (3GCs), carbapenems, and colistin (80.8-100.0% consistency; Kappa: 0.50-1.00). Plasmid analysis identified IncQ1 (84.3%) and IncHI2/IncHI2A (26.3%) as the main replicons, with the variety of plasmid replicons increasing from 7 to 21 over the 5 years. ARGs associated with resistance to critically important antibiotics (CIAs) were frequently predicted to be located on plasmid-associated contigs, with significant associations observed between IncHI2/IncHI2A plasmids and ARGs conferring resistance to fluoroquinolones, macrolides, and cephalosporins (P < 0.05). Molecular typing divided 281 isolates into 37 cgSTs, with cgST52428 being the most common. Molecular epidemiological analysis revealed that Guizhou isolates primarily clustered together, sharing close genetic ties with those from Sichuan and Guangdong, and exhibited the highest genetic similarity to pork-derived isolates. Phylogenetic analysis revealed clustering of CIA-resistant ARGs and plasmids in Clades 4 and 5, with a significant association between IncHI2/IncHI2A plasmids and CIA-resistant ARGs (χ2 = 112.12, P < 0.001). Additionally, class 1 integron was associated with higher ARG burdens, while virulence-associated genes were conserved and predominantly chromosome-associated. Gene-content analysis revealed that isolates in Clades 4 and 5 harbored the largest mean gene complements, and cgST52428 isolates also harbored the largest among dominant cgSTs. DISCUSSION: This study presents a comprehensive genomic profile of Salmonella 1,4,[5],12:i:- ST34 in Guizhou, providing essential data for exploring the resistance characteristics and investigating the molecular epidemiology of Salmonella 1,4,[5],12:i:-.

ST34↗

PubMed2026

Wildlife as a reservoir of OXA-48-like carbapenemase-producing Enterobacterales.

Carbapenemase-producing Enterobacterales (CPEs) have globally emerged and spread beyond human compartments. However, data in wild animals, especially from low- and middle-income countries, such as Algeria, are still very scarce. Here, we investigated CPEs recovered from feces samples collected between October 2021 and June 2023 from wild terrestrial and aquatic mammals, wild migratory/nesters/sedentary birds, and zoo animals, including their environment (water, food, and fecal samples of animal care workers) distributed over six Algerian provinces. Carbapenem-resistant Enterobacterales were characterized using MALDI-TOF-MS, Carba NP, immunochromatographic assay NG-Test CARBA 5, antimicrobial susceptibility testing, and whole-genome sequencing. Thirty CPEs were identified out of the 1,899 samples collected (1.6%). The carriage rate was higher in captive animals (3.2%) than in wild animals (1.2%). Twenty-six produced OXA-48, three OXA-244, and one OXA-181, along with CTX-M-15 ESBL. Clonal expansion of Enterobacter hormaechei hoffmannii ST145 and Klebsiella pneumoniae ST13 was evidenced. Plasmid analysis confirmed that 24/30 isolates harbored a transferable 62 kb IncL pOXA-48 plasmid. Five/six E. coli isolates belonged to high-risk clones with chromosome-mediated blaOXA-244 gene in three isolates, blaOXA-48 in two isolates, and blaOXA-181 gene encoded on an IncFII-ColKP3 hybrid plasmid in one isolate. This study showed widespread dissemination of OXA-48-like producing Enterobacterales in free and captive wild animals, largely driven by epidemic plasmids and clones. It underscores the role of wild animals as a reservoir of CPEs, particularly species living close to humans, such as gulls and pigeons, and occasionally food-producing animals, increasing the risk of bidirectional dissemination between animal, environmental, and human sectors.IMPORTANCEThe global rise of carbapenemase-producing Enterobacterales (CPEs) harboring blaOXA-48-like has been increasingly documented in clinical settings. However, their emergence and transmission in wild and captive animals are less documented. This study provides a high-resolution genomic characterization of CPEs isolated from the feces of wild animals, especially migratory birds, and from captive wild animals, to evaluate the potential risk of dissemination through these animals. Whole-genome sequencing data, genetic investigations, and antimicrobial susceptibility results highlighted the spread of multidrug-resistant CPEs in both animals and humans. The widespread detection of blaOXA-48 across multiple niches suggests sustained circulation beyond hospital settings in Algeria. Human-associated lineages, such as E. coli ST131, ST38, and ST540, were identified with a clear link with humans. This study demonstrates carriage of CPEs in multiple bird species living in areas commonly inhabited by humans and provides further evidence for an effective dissemination of resistance in wildlife, facilitated by feeding habits.

Animals↗

PubMed2026

Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces.

The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.

Animals↗

PubMed2024

Circulation of avian Chlamydia abortus in the Netherlands and community-acquired pneumonia: an outbreak investigation and retrospective cohort study.

BACKGROUND: In 2021, a novel group of Chlamydia strains in wild birds was classified as avian Chlamydia abortus, with unknown zoonotic potential. We report relevant features of avian C abortus infections from a Dutch family cluster and unrelated historical cases using clinical, epidemiological, and microbiological data. METHODS: An outbreak of avian C abortus started in the Netherlands in December, 2022. Source investigation was done using questionnaires to interview patients and environmental sampling. The outbreak strain of avian C abortus was cultured from three patients from whom sufficient material was available for culture and underwent whole-genome analysis. The outbreak strains and retrospective cohort study strains previously submitted to the National Human Psittacosis surveillance programme in the Netherlands between 2010 and 2022 were typed by partial ompA sequencing. Strains with the same aberrant ompA genotype were further analysed with XerC gene plasmid analysis and compared with closely related Chlamydia sequences available in GenBank. FINDINGS: An avian C abortus strain caused a cluster of respiratory illness in four family members. Three patients were hospitalised with community-acquired pneumonia, one of whom was admitted to the intensive care unit. The faeces of wild birds were considered a probable source for the index infection. For two family members, human-to-human transmission was a plausible route. Ten historical cases could be identified with avian C abortus with the same ompA genotype. All patients had been admitted to hospital, at least five developed pneumonia, and one died. INTERPRETATION: This cluster supports that avian C abortus strains can cause human infections and underlines that human-to-human transmission should be considered when tracing the source of such infections. FUNDING: National Institute for Public Health and the Environment and Dutch Ministry of Agriculture, Fisheries, Food Security and Nature. TRANSLATION: For the Dutch translation of the abstract see Supplementary Materials section.

Humans↗

PubMed2025

Exploring diagnostic m6A regulators in primary open-angle glaucoma: insight from gene signature and possible mechanisms by which key genes function.

PURPOSE: The purpose of this study was to interrogate the potential role of N6-methyladenosine (m6A) regulators in the process of trabecular meshwork (TM) tissue damage in patients with primary open-angle glaucoma (POAG). METHODS: Firstly, the expression profile of m6A regulators in TM tissues of POAG patients was comprehensively analyzed by bioinformatics analysis; Plasmid transfection and siRNA gene interference were used to enhance or weaken the expression levels of YTHDC2 in human trabecular meshwork cells (HTMCs); Cell migration ability was detected by transwell chamber assay; Immunofluorescence staining assay was used to evaluate the expression of extracellular matrix (ECM) related proteins. RESULTS: Through the analysis of GSE27276 database, 5 m6A regulators with different expression in POAG were screened out. The results of random forest model showed that these 5 m6A regulators exhibited diagnostic potential and were characteristic genes of POAG. All POAG samples could be effectively divided into two groups based on the expression levels of these 5 hub m6A regulators. Immune cell infiltration analysis indicated that the levels of activated CD8+ T cells and regulatory T cells were different in the two subtypes. HTMC oxidative stress cell model and TGF-β2 stimulation cell model were further constructed to verify the expression of the aforementioned hub m6A regulators, and it was found that YTHDC2 mRNA showed the same expression trend in both models. The silencing of YTHDC2 enhanced the migration ability of HTMCs and increased the synthesis ability of ECM. However, when YTHDC2ΔYTH, which lacks the YTH domain, is overexpressed in HTMCs, there is no significant change in the ECM synthesis ability. CONCLUSIONS: The differentially expressed m6A regulators in TM tissues may serve as potential diagnostic biomarkers for POAG. And, in HTMCs, the expression level of YTHDC2 mRNA was changed under oxidative stress or TGF-β2 intervention, and then exerted its regulation on cell migration and ECM synthesis capability through m6A modification, which may be an important part of the disease process of POAG.

Humans↗

PubMed2026

Characterisation of Carbapenem-Resistant Raoultella planticola and Structural Analysis of NDM Composite Plasmids.

OBJECTIVE: This study aimed to investigate the molecular characteristics, resistant plasmid structures and phylogeny of a carbapenem-resistant Raoultella planticola (CRRP) strain from a patient with pneumonia to inform antimicrobial resistance control strategies. METHODS: We performed strain identification using MALDI-TOF MS, the BD Phoenix 100 system and whole-genome sequencing (WGS). We assessed antimicrobial susceptibility and resistance gene transfer using PCR, conjugation and stability assays, plasmid structure using a bioinformatics tool and phylogeny using a core-genome phylogenetic tree. RESULTS: WGS confirmed the isolate as R. planticola (average nucleotide identity (ANI) > 98.9% with reference type strains), co-harbouring blaKPC-2 and blaNDM-1. It was resistant to 19 antimicrobial agents and susceptible to only polymyxin, amikacin and chloramphenicol. Resistance genes were present on two conjugative plasmids: pzwx_KPC (IncFIA) and pzwx_NDM (a novel repFIB/repHI5B hybrid assembled via non-homologous end joining). Both plasmids demonstrated efficient transfer and stable inheritance over 12 passages. pzwx_KPC was highly homologous to plasmids from Klebsiella pneumoniae. Phylogenetic analysis revealed the closest relationship with German R. planticola strains. CONCLUSION: CRRP carries highly transmissible and stable resistance plasmids. Strengthened monitoring in immunocompromised patients and improved environmental disinfection are recommended. The risk of misidentification by automated systems underscores the importance of WGS for accurate pathogen identification.

Carbapenem resistance↗

PubMed2026

Spatiotemporal genomic analysis and risk assessment of the plasmids carrying blaOXA-48-like genes based on a large-scale international dataset.

BACKGROUND: The spread of OXA-48-like carbapenemases represents a major public health challenge. Although previous studies have investigated OXA-48-like carbapenemases risk factors, nosocomial dissemination, and plasmid dynamics, an integrated plasmid-centered framework combining complete plasmid mining, transmission-unit analysis, phylogenetic reconstruction, and machine learning-based risk assessment remains limited. METHODS: We systematically collected 747 complete plasmid sequences carrying blaOXA-48-like genes from the NCBI database, establishing the largest collections of complete plasmid sequences to date. Using an integrative framework of population genomics, phylogenetic dating, and machine learning, this study aimed to characterize the dissemination patterns, plasmid replicon diversity, transmission units, mobile genetic elements, co-resistance profiles, and risk classification of these plasmid. RESULTS: Plasmids carrying blaOXA-48-like genes were detected across 50 countries on six continents, with blaOXA-48 predominating in Europe, blaOXA-181 in South Asia, and blaOXA-232 largely in Asia. IncL and ColKP3/IncX3 replicons, together with Tn1999.2 and other MGEs, were central drivers of plasmid maintenance and spread. Sixteen transmission units were defined, with AA068_Cluster3 estimated to have originated in the Netherlands around 2005 before expanding to Europe, the Middle East, Asia, and North America. Co-resistance analyses revealed frequent modules involving aminoglycoside and quinolone resistance, with qnrS1 and aph(3'')-Ib most prevalent. Notably, high-risk transposon structures were often identified in non-clinical environments, underscoring their cross-ecological transmission potential. Machine learning-based classification models showed good internal performance for predefined composite-risk categories, with plasmid mobility, clinical/non-clinical source composition, and host background contributing to the classification results. CONCLUSIONS: This study provides a large-scale plasmid-centered genomic analysis of publicly available complete plasmid sequences carrying blaOXA-48-like genes, integrating transmission-unit inference, phylogeographic reconstruction, mobile genetic element and co-resistance profiling, and composite genomic risk stratification. This gene-centered framework may support future One Health-oriented antimicrobial resistance surveillance and prioritization of plasmids with higher dissemination and resistance potential.

Plasmids↗

PubMed2026

Genomic characterization of KPC-2 and NDM coproducing carbapenem-resistant Klebsiella pneumoniae in a hospital: discovery of ST1869 clone and a novel hybrid plasmid.

UNLABELLED: To characterize the plasmid architecture and molecular background of KPC-NDM coproducing carbapenem-resistant Klebsiella pneumoniae (KN-CRKP) in a South China hospital. Five KN-CRKP isolates were collected, including three from one patient. All underwent Illumina sequencing; two (ST11 and ST1869) additionally had Nanopore sequencing. Antimicrobial susceptibility testing strain sequence types, conjugation assays, resistance gene profiling, plasmid typing, genetic structure comparison, core-genome single nucleotide polymorphisms (SNPs) analysis, and plasmid clustering were performed. All isolates exhibited an imipenem minimum inhibitory concentration (MIC) of ≥128 µg/mL and harbored multiple resistance genes. One isolate (1/5) belonged to ST1869 and co-harbored blaKPC-2 and blaNDM-5. The blaNDM-5-carrying plasmid was a novel IncI1/X3 fusion plasmid that also carried blaCMY-42. Unlike several IncX3 plasmids carrying blaNDM in publicly available KN-CRKP genomes from South China, this IncI1/X3 hybrid lacked a complete conjugative transfer system. ST11 was the predominant clone (4/5), co-harboring blaKPC-2 and blaNDM-1. A rare genetic structure, ΔISKpn6-blaKPC-2-ISKpn28, was identified on IncFII plasmids carrying blaKPC-2. Plasmid clustering analysis of 126 comparative KN-CRKP genomes showed diverse sequence types and plasmid backgrounds associated with the KPC/NDM co-production pattern. The observed plasmid diversity and structural variation in KN-CRKP support continued genomic surveillance, with particular attention to the ST1869 clone, the novel IncI1/X3 hybrid plasmid harboring blaNDM-5 and blaCMY-42, and the rare "ΔISKpn6-blaKPC-2-ISKpn28" genetic structure. Expanded genomic data on KN-CRKP are needed to further elucidate its resistance mechanisms and plasmid evolutionary trajectories. IMPORTANCE: The co-production of KPC and NDM carbapenemases in Klebsiella pneumoniae poses a formidable threat to clinical antimicrobial therapy, as these enzymes confer resistance to virtually all β-lactam agents, including carbapenems. Here, we report novel genomic features of KN-CRKP in South China, including the emergence of the ST1869 clone, a unique IncI1/X3 hybrid plasmid harboring blaNDM-5 and blaCMY-42, and the rare ΔISKpn6-blaKPC-2-ISKpn28 genetic structure. These findings substantially expand current understanding of plasmid evolution and resistance gene dissemination in this region. The identification of diverse resistance mechanisms and clonal backgrounds supports enhanced genomic surveillance and infection-control awareness for pan-resistant Enterobacterales.

Plasmids↗

PubMed2025

Global emergence and transmission dynamics of carbapenemase-producing Citrobacter freundii sequence type 22 high-risk international clone: a retrospective, genomic, epidemiological study.

BACKGROUND: Carbapenemase-producing Citrobacter (CPC) species have recently been recognised as emerging pathogens associated with nosocomial infections in humans. The increased rate of Citrobacter freundii infections is a public health concern and there is a paucity of genomic data regarding its global transmission dynamics. We aimed to characterise the genetic features of CPC species, and their associated carbapenemase-encoding plasmids, obtained from hospitalised patients in China and from publicly available global data, with a particular focus on high-risk clones. METHODS: This was a retrospective, genomic epidemiological study of CPC species obtained from a tertiary hospital in Zhejiang Province, China, from March 5, 2013, to March 5, 2023. We used antimicrobial susceptibility testing, short-read and long-read whole-genome sequencing, phylogenomic analysis, and plasmid structure analysis. A global dataset of complete plasmid sequences encoding blaKPC, blaNDM, and blaIMP was constructed from the National Center for Biotechnology Information (NCBI) RefSeq database to provide insights into their diversity and distribution. All carbapenemase-producing Citrobacter freundii genomes from the NCBI GenBank database were incorporated in the comparative genomic analyses. Bayesian phylogeographical analysis and growth rate assays were carried out to characterise the high-risk C freundii sequence type (ST) 22 clone. FINDINGS: 1724 Citrobacter species isolates were collected from diverse clinical specimens, with 48 identified as CPC species. Citrobacter koseri (22 [46%] of 48) and C freundii (20 [42%]) were the predominant CPC species. Comparative analysis found C freundii carried significantly higher median numbers of plasmid replicons (5·0 [IQR 3·3-6·0] vs 2·0 [2·0-3·0]; p<0·0001) and acquired antimicrobial resistance genes (12·0 [7·3-15·8] vs 3·0 [3·0-5·3]; p<0·0001) than did C koseri. Molecular characterisation identified Inc-type plasmids, In823::Kl.pn.I3/In1589-like/In837-like integrons, Tn6296/Tn125/Tn5060 transposons, and insertion sequences (eg, IS26, IS3000, IS5, ISAba125, ISCR1), collectively facilitating the dissemination of carbapenemase genes. Global analysis of 3126 carbapenemase-encoding plasmids found epidemic plasmids with broad host ranges and global diversity. Phylogenetic investigation of predominant carbapenemase-encoding plasmids showed their persistence across geographical regions, temporal spans, and Enterobacterales species, exhibiting high genetic similarity to our clinical plasmids. A phylogenetic tree of 726 global carbapenemase-producing C freundii genomes showed that ST22 (227 [31·3%]) represents the predominant multidrug-resistant clone across community, health-care, and environmental niches. Transmission across continents contributes to the global predominance of the ST22 clone, which carries a high load of resistance genes (median 15·0 [IQR 11·0-17·0] vs 12·0 [3·0-16·0]; p<0·0001) and enhanced plasmid maintenance capacity (median replicons 5·0 [IQR 4·0-7·0] vs 4·0 [3·0-6·0]; p<0·0001) relative to non-ST22 clones. INTERPRETATION: Our study provides evidence to suggest that Citrobacter species are emerging carriers of carbapenem-resistance genes. These findings provide insight into the population structure of CPC species and highlight C freundii ST22 as a prominent high-risk international clone. FUNDING: National Natural Science Foundation of China, National Health Commission Scientific Research Fund-Zhejiang Provincial Major Health Science and Technology Plan Project, Zhejiang Province Natural Science Foundation Project, Outstanding Youth Foundation of Jiangsu Province of China, the Priority Academic Program Development of Jiangsu Higher Education Institutions, and Postgraduate Research and Practice Innovation Program of Jiangsu Province.

Citrobacter freundii↗

PubMed2025

Comprehensive genomic analysis of antibiotic resistance plasmids in animal-associated Staphylococcus aureus in France.

UNLABELLED: In Staphylococcus aureus, an animal pathogen and zoonotic agent, plasmids play a pivotal role in the acquisition and spread of antibiotic resistance genes (ARGs). This study investigated the plasmid content of 329 S. aureus isolates from livestock and companion animals collected in France between 2010 and 2021. Plasmids (n = 211) were identified from 139 isolates. The major families identified-rep7a, rep20, and rep10-were associated with specific resistance genes (str, cat, blaZ, erm(C)) and exhibited widespread horizontal transfer across different S. aureus sequence types (STs) and animal hosts. In temporal analysis, the rep7a/str and rep7a/cat plasmids circulating in horses were progressively replaced by a rep7a plasmid carrying both str and cat genes. The study also highlighted the presence of mosaic plasmids, which combined elements from different bacterial species/genera, confirming the broad host range of S. aureus plasmids and their ability to acquire ARGs from diverse sources. Moreover, the occurrence of hybrid plasmids (carrying multiple rep genes) underscores the plasticity of these vectors of ARGs. This study emphasizes the need to investigate the mechanisms driving the spread and persistence of antibiotic-resistant plasmids in S. aureus, with a view to developing strategies aimed at combating antibiotic resistance. IMPORTANCE: The spread of antibiotic resistance in Staphylococcus aureus is a growing concern, particularly in animals that can serve as reservoirs for resistant strains. This study highlights the crucial role of plasmids in transmitting resistance genes among different animal hosts and S. aureus lineages. The characterization of 329 isolates collected over 10 years revealed how certain plasmid families are associated with specific resistance genes and how they evolve over time. The occurrence of mosaic and hybrid plasmids further underscores the ability of S. aureus to acquire resistance from diverse bacterial sources. These findings provide key insights into the mechanisms shaping antibiotic resistance in this pathogen and emphasize the fact that understanding plasmid-driven resistance is essential for developing effective interventions to limit the spread of multidrug-resistant S. aureus in both veterinary and human medicine.

Animals↗

PubMed2026

pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.

MOTIVATION: The increasing number of fully sequenced bacterial plasmids being annotated and catalogued has prompted the development of computational tools for comparing and classifying them. Existing approaches typically compare full-length DNA sequences (e.g. Mash, BLASTn, and ANI-based methods) or translated open reading frames (ORFs) (e.g. DIAMOND), with plasmid-level scores obtained by aggregating ORF-to-ORF similarities; however, they are either restricted to closely related plasmids or become computationally demanding in large-scale analyses. RESULTS: We describe pLAST (plasmid Language Analysis and Search Tool), a plasmid-search tool built using word2vec representations of protein-family content informed by local genomic context. Benchmarks indicate that pLAST outperforms nucleotide-based methods and performs comparably to DIAMOND in identifying functionally similar plasmids and compared with the widely used Mash, it achieves 26% and 24% improvements in detecting shared mating-pair formation system type and relaxase type, respectively. This performance scales to database searches across hundreds of thousands of sequences, as demonstrated using the precomputed PlasmidScope collection of ∼750 000 plasmids. Beyond global similarity, pLAST also returns per-ORF plasmid-plasmid alignments, enabling detection of shared functional modules. AVAILABILITY AND IMPLEMENTATION: pLAST is freely accessible as a web server at https://plast.lbs.cent.uw.edu.pl/ or https://plast.lbs.biol.uw.edu.pl/ and available as a Python module along with a precomputed database at https://github.com/labstructbioinf/pLAST for customized analysis.

Plasmids↗

PubMed2026

Transferable IncHI2-Associated blaLAP-2 and blaCTX-M-55 Resistance Platforms in Foodborne Salmonella.

Extended-spectrum β-lactamase genes in foodborne Salmonella enterica can disseminate through mobile multidrug-resistance platforms. IncHI2 plasmids are important resistance vehicles capable of carrying complex resistance regions and facilitating their horizontal transfer across diverse bacterial backgrounds, but the transfer and genomic organization of IncHI2 elements co-carrying blaLAP-2 and blaCTX-M-55 remain insufficiently characterized. This study investigated two multidrug-resistant foodborne isolates recovered in Shanghai in 2022: Salmonella Agona ST13 isolate Sal22C150 and Salmonella Havana ST1527 isolate Sal22P208. Antimicrobial susceptibility testing, whole-genome sequencing, conjugation, plasmid-retention analysis, comparative genomics, as well as strain- and plasmid-level phylogenetic analyses were performed. Both isolates exhibited broad antimicrobial resistance, including resistance to extended-spectrum cephalosporins. In both isolates, blaLAP-2 and blaCTX-M-55 co-transferred with the IncHI2 replicon to Escherichia coli J53 at frequencies of (4.95 ± 0.41) × 10-5 and (4.46 ± 0.42) × 10-6 transconjugants per donor cell, respectively. All tested plasmid markers remained detectable through 20 passages without antimicrobial selection. Complete assembly of Sal22P208 confirmed the location of the three β-lactamase genes on the 275,096 bp IncHI2 plasmid pSal22P208. The plasmid contained a conserved conjugative backbone and mosaic accessory regions carrying 15 antimicrobial-resistance determinants together with mercury- and tellurium-resistance loci. SNP-based analysis placed pSal22P208 within a closely related cluster containing six reference IncHI2 plasmids differing by fewer than 30 SNPs and recovered from Salmonella and E. coli of animal, food, and human origin, suggesting a broad distribution of this plasmid lineage across diverse bacterial and ecological backgrounds. Sal22P208 additionally contained a Tn3-associated chromosomal multidrug-resistance region between rpmJ and rpmE that shared extensive structural similarity with a region in Citrobacter braakii LBA3. These findings highlight the role of transferable IncHI2 resistance platforms in the horizontal dissemination and short-term post-transfer maintenance of linked resistance determinants, while chromosomally integrated resistance regions may provide an additional route for the accumulation and inheritance of multidrug resistance in foodborne Salmonella.

IncHI2 plasmid↗

PubMed2025

Emergence of carbapenem-resistant Serratia marcescens co-harboring blaNDM-1, blaKPC-2, and blaSRT-2 in bloodstream infection.

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.

Humans↗

PubMed1979

Functional analysis of the replicator structure of lambdoid bacteriophage DNAs.

In our hybrid-plasmid reconstruction analysis of lambda (lambdoid) DNA signal structures involved in phage DNA replication, we have detected a dual system alternatingly able to initiate a first primer-RNA synthesis. Both of them--the major, primase-dependent ori system and the minor and usually suppressed, RNA-polymerase-dependent oop system--act in conjunction with a common signal structure for inception of DNA synthesis. It appears that in situations such as this, where one has to deal with the existence of regular as well as backup systems serving the same function, straightforward conclusions are no longer possible in their genetic analysis. For example, even though the oop-DNA segment can be deleted entirely from bacteriophage lambda DNA without disturbing its ability to replicate, it may not be valid to conclude that the oop system has no function in DNA replication. Dual systems of this type or organization in general have also been observed previously for some other replicons such as the R-factors R6-5 and R6K (Timmis et al. 1978; Crosa et al., this volume) or the F factor (Helinski et al., this volume), and they may be more common than presently expected.

Bacteriophage lambda↗

PubMed2026

Whole-genome characterization of seven multidrug-resistant Neisseria gonorrhoeae isolates from a single tertiary center in Beijing.

BACKGROUND: To characterize the whole-genome features of Neisseria gonorrhoeae clinical isolates collected from a tertiary medical institution in Beijing, with a focus on the genomic basis of ceftriaxone non-susceptibility and multidrug resistance. METHODS: Clinical isolates were collected from April 2023 to November 2024. Of 14 collected isolates, seven were successfully subcultured after revival and included in subsequent analyses. Minimum inhibitory concentrations (MICs) were determined by the Etest method. Whole-genome data were obtained using a combination of second- and third-generation sequencing technologies. The isolates were combined with global and Chinese reference datasets to construct a core-genome single-nucleotide polymorphism (core-SNP) phylogenetic tree. Chromosomal resistance-associated mutations and plasmid characteristics were subsequently analyzed. RESULTS: The seven isolates displayed genomic diversity at the whole-genome level. Four isolates (8087, 8423, 8461, and 8801) carried penA 60.001 and belonged to distinct sequence types, including ST7365, ST8123, and ST7367. One additional isolate (8726) carried penA 273.001; both alleles encode PBP2 proteins sharing the core substitutions A311V, I312M, V316T, and T483S. All five isolates were non-susceptible to ceftriaxone (MIC 0.25-0.5 mg/L). Ceftriaxone non-susceptibility was associated with the co-occurrence of mutations at core penA positions and additional mutations in porB and ponA, with an mtrR mutation present in one isolate. Plasmid collinearity analysis revealed that several multidrug-resistant isolates simultaneously harbored an intact conjugative plasmid and an African-type resistance plasmid carrying bla TEM-1. CONCLUSION: The multidrug-resistant phenotype of Neisseria gonorrhoeae results from the co-existence of chromosomal multi-locus mutations and resistance plasmids. The penA 60.001 isolates in this study did not originate from a single source. This allele appeared in multiple local clonal lineages. This pattern is consistent with horizontal gene transfer of this resistance determinant into multiple endemic lineages.

Neisseria gonorrhoeae↗