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7 recordsLinked to original sources
PubMed2026

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.

BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored. RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes. CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.

Plasmids↗
PubMed2026

Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.

BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized. RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments. CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.

Plasmids↗
PubMed2026

Triple carbapenemase-producing Klebsiella pneumoniae ST6668 resistant to novel β-lactam/β-lactamase inhibitor combinations and cefiderocol, Northern Italy, 2025.

OBJECTIVE: Klebsiella pneumoniae ST6668 has recently emerged in Northern Italy, but data on its resistance architecture remain limited. METHODS: We identified a K. pneumoniae ST6668 (KNVO1) strain co-producing NDM-1, VIM-1, and OXA-48 carbapenemases via multiple megaplasmids from an elderly hospitalized patient who experienced clinical deterioration during a prolonged period of health care exposure. RESULTS: KNVO1 showed resistance to all tested β-lactams, including novel β-lactam/β-lactamase inhibitor combinations and cefiderocol, with susceptibility retained only to colistin, gentamycin and aztreonam/avibactam. Whole-genome sequencing confirmed the ST6668. The plasmidome included two megaplasmids (pKPC-CAV1321 and IncFIB:IncHI) carrying blaVIM-1 and blaNDM-1, respectively, and an IncL plasmid harbouring blaOXA-48. SNPs-based phylogeny demonstrated genomic distance to other ST6668 strains circulating locally, suggesting an independent introduction event. CONCLUSION: The convergence of three major carbapenemase families within ST6668 highlights the capacity of this clone to accumulate complex resistance determinants via megaplasmids, posing a serious threat to infection control and antimicrobial stewardship in health care settings.

Klebsiella pneumoniae↗
PubMed2026

Emergence of a Tn7-associated blaVIM-1 within IncC plasmids in ST46 Providencia stuartii from Northern Italy.

OBJECTIVES: To characterize the genomic features and resistance determinants of carbapenem-resistant Providencia stuartii isolates circulating in Northern Italy, with a focus on the genetic context of blaVIM-1. METHODS: Five P. stuartii isolates collected between 2022 and 2024 from interconnected healthcare facilities underwent molecular characterization. Antimicrobial susceptibility testing was performed according to EUCAST 2025 criteria. Whole-genome sequencing was conducted using Illumina technology, followed by resistome, plasmidome, and phylogenetic analyses. Comparative genomics was used to investigate the genetic environment of blaVIM-1. RESULTS: All isolates belonged to the emerging ST46 lineage and exhibited an extensively drug-resistant phenotype, remaining susceptible only to amikacin. The blaVIM-1 gene was located on a &#x223c;100 kb mobilizable IncC plasmid shared across all isolates. Notably, blaVIM-1 was embedded within a 13 kb Tn7 transposon carrying a complete set of transposition genes and inserted into a class 1 integron structure. Comparative analysis revealed no full homology with previously described IncC plasmids, suggesting a novel genetic arrangement. Phylogenetic analysis demonstrated close relatedness among Italian isolates (<33 SNPs), supporting local clonal circulation, while showing clear separation from previously described NDM-producing ST46 strains. CONCLUSIONS: This study describes the rare association of blaVIM-1 with a Tn7 transposon in P. stuartii, highlighting the genomic plasticity of IncC plasmids and their role in the emergence of new resistance platforms. The identification of this structure in a high-risk lineage underscores the potential for further dissemination of carbapenem resistance in healthcare settings.

IncC↗
PubMed2026

Genomic characterization of novel human-associated CTX-M-15-producing Serratia nevei ST625 lineage infecting a vulnerable loggerhead sea turtle.

BACKGROUND: Serratia nevei is a newly classified and opportunistic bacterial species belonging to the Serratia marcescens complex (SMC). Genomic data from this species is highly relevant for public health and epidemiological tracking. OBJECTIVE: To report the first identification and genomic characterization of extended-spectrum &#x3b2;-lactamase (CTX-M-15)-producing S. nevei sequence type (ST) ST625 lineage infecting a vulnerable loggerhead sea turtle. METHODS: Strain BP02 was recovered from the coelomic cavity of a loggerhead sea turtle (Caretta caretta) admitted to a rehabilitation center in southeastern Brazil. MALDI-TOF MS was initially used for species identification and was further confirmed by whole-genome sequencing on the Illumina HiSeq platform, followed by ANI, dDDH, multilocus sequence typing, resistome, plasmidome, virulome, and SNP-based phylogenomic analyses. RESULTS: Strain BP02 exhibited a multidrug-resistant profile, including resistance to third- and fourth-generation cephalosporins. Genomic analyses identified BP02 as S. nevei ST625 carrying blaCTX-M-15 within the ISEcp1-blaCTX-M-15-wbuC-&#x394;Tn2 genetic environment, in addition to multiple AMR determinants and the IncC plasmid replicon. Phylogenomic analysis demonstrated close relatedness between BP02 and human clinical ST625 strains, previously reported in S&#xe3;o Paulo, Brazil, including a urine-derived strain isolated in 2019, differing by only 27 SNPs. Notably, all publicly available ST625 genomes were associated with human clinical sources and displayed multidrug resistance genotypes. CONCLUSION: This study expands the current knowledge regarding the ecology and genomic features of S. nevei, demonstrating the emergence of a human multidrug-resistant clone in marine wildlife. Our findings reinforce the importance of monitoring clinically relevant SMC members across distinct ecological niches within a One Health perspective.

ESBL↗
PubMed2025

Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems.

The genomes of 43 distinct lactococcal strains were reconstructed by a combination of long- and short-read sequencing, resolving the plasmid complement and methylome of these strains. The genomes comprised 43 chromosomes of approximately 2.5 Mb each and 269 plasmids ranging from 2 to&#xa0;211 kb (at an average occurrence of 6 per strain). A total of 953 antiphage genes representing 538 phage defence systems were identified in the 43 strains and were catalogued and cross-correlated with co-occurrent mobile elements, which indicated that almost 60% of these systems are predicted to be mobile. Detailed analysis established that restriction-modification (R-M) systems form a significant portion of this mobile phage defensome. As such, all detected Type&#xa0;I, II, and III-associated methylated motifs (46 of which were unique to this study) were matched to their corresponding methylating enzymes by homology detection or molecular cloning. The cumulative antiphage activity of selected systems and the ability of truncated R-M genes to contribute to methylation were demonstrated. This study reveals, for the first time, the dairy lactococcal plasmidome to be a rich reservoir of orphan HsdS-encoding genes, in a comprehensive survey of (mobile) phage defence systems in lactic acid bacteria.

Bacteriophages↗
PubMed2026

Genomic insights into the first blaKPC-2-carrying Klebsiella pneumoniae isolate reported in Chile: limited local dissemination of the globally distributed ST101 lineage.

OBJECTIVE: To genomically characterize Kpn-KPC-1, the first blaKPC-2-carrying Klebsiella pneumoniae isolate reported in Chile, and contextualize it within the global ST101 lineage. METHODS: Kpn-KPC-1 was analyzed by whole-genome sequencing. Its resistome, virulome, plasmid content, and blaKPC-2 genetic context were characterized, and 537 publicly available ST101 genomes were used for comparative phylogenomics. RESULTS: Kpn-KPC-1 belonged to ST101 and carried blaKPC-2 within the conventional Tn4401a transposon on a mosaic plasmid encoding multiple replication initiators and conjugation-associated genes. The isolate also harbored an OmpK36 porin alteration and accessory resistance- and virulence-associated determinants, including ICEKp3/ybt-9, K17, and O1&#x3b1;&#x3b2;,2&#x3b1;. Phylogenomic analysis placed Kpn-KPC-1 within a predominantly European clade, closest to Italian isolates recovered between 2012 and 2018. The absence of additional Chilean ST101 isolates related to Kpn-KPC-1 supports limited local dissemination of this lineage. Globally, ST101 was enriched in carbapenemase genes, particularly blaOXA-48-like and blaKPC variants. CONCLUSIONS: Kpn-KPC-1 represents a transient introduction of a carbapenemase-prone, high-risk ST101 lineage rather than the founder of a locally disseminated clone in Chile. Genome-level analysis resolved the blaKPC-2 context in this historical isolate, linking the carbapenemase gene to Tn4401a on a mosaic multidrug-resistance plasmid within an imported ST101 background. These findings underscore the value of retrospective genomics for reconstructing early antimicrobial-resistance introduction events.

Carbapenem-resistant enterobacterales↗