Global dissemination of Klebsiella pneumoniae in surface waters: genomic insights into drug resistance, virulence, and clinical relevance

Drug Resistance Updates, Journal Year: 2025, Volume and Issue: 79, P. 101204 - 101204

Published: Jan. 21, 2025

Language: Английский

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Molecular epidemiology and emergence of sequence type 25 hypervirulent Klebsiella pneumoniae in pigs in the Netherlands (2013–2020): a global comparative analysis with human and pig isolates

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(4)

Published: April 23, 2025

Klebsiella pneumoniae (Kp), a ubiquitous pathogen found in diverse ecological niches, poses threat to human and animal health. Hypervirulent Kp (hvKp) is concerning for its acquisition of virulence antimicrobial resistance genes through plasmids. This study investigates hvKp as cause septicaemia piglets the Netherlands examines role plasmids host association. We collected 41 isolates cultured from necropsies submitted 15 different farms (2013–2020) sequenced them using long-read sequencing. identified sequence type (ST) 25 dominant (67%, 10/15 farms) associated with pigs Netherlands. ST25 displayed hypervirulent profile, including K2 hyper-capsule carried an iuc 3 plasmid. Further analysis revealed two clonal groups: CG25 CG3804, novel porcine clone. Multidrug was five pig farms. There one colistin-resistant isolate carrying mcr -1 on Comparative genomic performed by large dataset related publicly available genomes humans ( n =230) =12) all STs phylogenetic plasmid analysis. Pangenomic significantly higher prevalence global (98%, 40/41) compared (10%, 24/234) correlating their enhanced (scores 3–4 vs 0–1). The highlights causing first time. Aerobactin lineage infections responsible increased score.

Language: Английский

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amr.watch – monitoring antimicrobial resistance trends from global genomics data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

Abstract Background Whole genome sequencing (WGS) is increasingly supporting routine pathogen surveillance at local and national levels, providing comparable data that can inform on the emergence spread of antimicrobial resistance (AMR) globally. However, potential for shared WGS to guide interventions around AMR remains under-exploited, in part due challenges collating transforming growing volumes into timely insights. We present an interactive platform, amr.watch ( https://amr.watch ), enables interrogation trends from public ongoing basis support research policy. Methods The platform incorporates, analyses visualises high-quality WHO-defined priority bacterial pathogens. Analytics are performed using community-standard methods with bespoke species-specific curation mechanisms. Findings By 31 March 2025, included 620,700 genomes geotemporal information, highly variable representation different species geographic regions. integrating sampling users assess among genotypic variants (e.g. sequence types) mechanisms, implications including prescribing drug vaccine development. Interpretation information scientists policy-makers delivering situational awareness genomic data. As broad adoption continues, positioned monitor both populations our global efforts surveillance, guiding control strategies tailored each pathogen’s characteristics. Funding UK National Institute Health Research & Gates Foundation. context Evidence before this study approaches enable us track pathogens high resolution local, levels. To date, studies assessing dynamics have largely used retrospective collected specific agendas. publicly-shared data, generated provide improved power detect novel interventions. Efforts collate exist, such as AllTheBacteria, although these aimed community do not facilitate usage interpretation by non-genomics experts, particularly those health. knowledge, no platforms exist readily interrogating continuously updated across array WHO Of note, however, TyphiNet provides online dashboard examining exclusively Salmonella Typhi a periodically-updated set Pathogenwatch platform. These findings based searching PubMed without language restrictions Jan 1 2000 December 2024, terms related “genomic surveillance” “antimicrobial resistance”. Added value developed which, first analysis visualisation spectrum via accessible interface. Crucially, incorporates processed live always-on stream, enabling insights delayed only time deposition. reviewed available up until contemporary landscape sequencing. While number annually grew over five-fold globally between 2010 2018, we also revealed extent differences representation, 89.6% originating high-income countries 89 contributing Implications all evidence Rapid generation sharing more precisely define characteristics circulating resistant solution retrieving, curating translating relevant actionable diverse stakeholders. It thereby forms monitoring progress efforts, alerting population changes enhanced precision interventional Additionally, review highlights need additional increase sustain implementation globally, improve its associated metadata.

Language: Английский

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Integrated population clustering and genomic epidemiology with PopPIPE

Microbial Genomics, Journal Year: 2025, Volume and Issue: 11(4)

Published: April 28, 2025

Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due their variable gene content order, reference-free methods offer more sensitive detection genetic differences, especially among samples found in outbreaks. However, across longer distances, frequent recombination make calculation interpretation these differences challenging, requiring significant bioinformatic expertise manual intervention during the analysis process. Here, we present a Pop ulation PIPE line (PopPIPE) which combines rapid genome analyse genomes two scales, splitting whole subclusters plausible events within clusters. We use k-mer sketching split strains, followed by removal create alignments strains. first show that this approach creates high-quality on population-wide dataset Streptococcus pneumoniae . When applied nosocomial vancomycin-resistant Enterococcus faecium samples, PopPIPE finds clusters are epidemiologically than core or multilocus sequence typing (MLST) approaches. Our pipeline is reproducible, interactive visualizations easily reconfigured re-run new datasets. Therefore, provides user-friendly for analyses spanning species-wide clustering outbreak investigations.

Language: Английский

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A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Genome Medicine, Journal Year: 2025, Volume and Issue: 17(1)

Published: April 28, 2025

Language: Английский

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