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Abstract

Here, we describe a putatively hypervirulent, carbapenem-resistant (hv-CRKP) outbreak. Nanopore sequencing guided the infection prevention and control (IPC) responses during the outbreak. Twelve patients were identified as either being colonized and/or having clinical infections with the putative hv-CRKP, with an all-cause mortality within 6 months of 36%. Multiple IPC responses were put in place, with enhanced cleaning of the environment being the key intervention to halt the outbreak. All isolates were ST395 and contained at least one carbapenemase gene, along with a variable array of other antimicrobial resistance and virulence genes, due to a rapidly evolving set of plasmids.

Funding
This study was supported by the:
  • Medical Research Council (Award MR/Y015037/1)
    • Principal Award Recipient: AlanMcNally
  • Birmingham Biomedical Research Centre (Award NIHR203326)
    • Principal Award Recipient: AlanMcNally
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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/content/journal/mgen/10.1099/mgen.0.001571
2025-11-20
2025-12-16

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References

  1. Shon AS, Russo TA. Hypervirulent Klebsiella pneumoniae: the next superbug?. Future Microbiol 2012; 7:669–671 [View Article] [PubMed]
    [Google Scholar]
  2. Lan P, Jiang Y, Zhou J, Yu Y. A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae. J Glob Antimicrob Resist 2021; 25:26–34 [View Article] [PubMed]
    [Google Scholar]
  3. Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ et al. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies. Microb Genom 2024; 10:001244 [View Article] [PubMed]
    [Google Scholar]
  4. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188 [View Article] [PubMed]
    [Google Scholar]
  5. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–6 [View Article] [PubMed]
    [Google Scholar]
  6. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015; 43:e15 [View Article] [PubMed]
    [Google Scholar]
  7. Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 2020; 21:180 [View Article] [PubMed]
    [Google Scholar]
  8. Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom 2021; 7:11 [View Article] [PubMed]
    [Google Scholar]
  9. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019; 35:4453–4455 [View Article] [PubMed]
    [Google Scholar]
  10. Didelot X, Wilson DJ. n.d. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 11:e1004041 [View Article]
    [Google Scholar]
  11. Wahl A, Fischer MA, Klaper K, Müller A, Borgmann S et al. Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany. Int J Med Microbiol 2024; 314:151601 [View Article] [PubMed]
    [Google Scholar]
  12. Ljungquist O, Magda M, Giske CG, Tellapragada C, Nazarchuk O et al. Pandrug-resistant Klebsiella pneumoniae isolated from Ukrainian war victims are hypervirulent. J Infect 2024; 89:106312 [View Article] [PubMed]
    [Google Scholar]
  13. Garvey MI, Winfield J, Wiley C, Reid M, Cooper M. Reduction in methicillin-resistant Staphylococcus aureus colonisation: impact of a screening and decolonisation programme. J Infect Prev 2016; 17:294–297 [View Article] [PubMed]
    [Google Scholar]
  14. Harmer CJ, Hall RM. IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024e0011922 [View Article] [PubMed]
    [Google Scholar]
  15. Moran RA, Behruznia M, Holden E, Garvey MI, McNally A. pQEB1: a hospital outbreak plasmid lineage carrying bla KPC-2. Microb Genom 2024; 10:001291 [View Article]
    [Google Scholar]
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