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Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing.
Microb. Genomics 12:001644 (2026)
The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem resistance. We here evaluate the use of long-read nanopore sequencing to investigate carbapenem resistance dynamics and the role of plasmid transfers and environmental reservoirs in the hospital setting. Over 13 months, routine clinical diagnostics identified recurring isolates of carbapenem-resistant Citrobacter species carrying Klebsiella pneumoniae carbapenemases (KPCs) and/or OXA-48-like carbapenemases from patient screening and hospital drain samples. While routine diagnostic approaches provided limited insights into the carbapenem resistance dynamics, we show that near-complete de novo assembly of chromosomes and plasmids by long-read nanopore sequencing allowed for high-resolution strain identification, plasmid profiling, and antibiotic resistance gene detection. Notably, genomically nearly indistinguishable Citrobacter freundii of the high-risk sequence type ST91 genomes were recovered from screening samples collected in the same hospital room 1 year apart. We further provide evidence of a KPC-2-encoding IncN plasmid that is likely to have spread across bacterial species and between patient and drain isolates, which emphasizes the role of contaminated drains in the persistence and dissemination of antimicrobial resistance within the hospital environment. Overall, this study demonstrates the value of long-read nanopore sequencing for uncovering the complex dynamics of carbapenem resistance spread and persistence in the hospital setting and its potential implications for infection prevention and control.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Carbapenem Resistance Reservoirs ; Clinical Resistance Surveillance ; Long-read Nanopore Sequencing ; Strain And Plasmid Clustering; Tool
ISSN (print) / ISBN
2057-5858
e-ISSN
2057-5858
Journal
Microbial Genomics
Quellenangaben
Volume: 12,
Issue: 2,
Article Number: 001644
Publisher
Microbiology Society
Publishing Place
14-16 Meredith St, London, England
Reviewing status
Peer reviewed
Institute(s)
Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Helmholtz Pioneer Campus (HPC)
Helmholtz Pioneer Campus (HPC)
Grants
University of Zurich
Helmholtz Principal Investigator Grant
Helmholtz Principal Investigator Grant