Hospital outbreak of carbapenem-resistant Enterobacterales associated with a blaOXA-48 plasmid carried mostly by Escherichia coli ST399

Alice Ledda, Martina Cummins, Liam P. Shaw, Elita Jauneikaite, Kevin Cole, Florent Lasalle, Deborah Barry, Jane Turton, Caryn Rosmarin, Sudy Anaraki, David Wareham, Nicole Stoesser, John Paul, Rohini Manuel, Benny P. Cherian, Xavier Didelot

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Abstract

A hospital outbreak of carbapenem-resistant Enterobacterales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous blaOXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacterales were involved in the outbreak. Escherichia coli ST399 accounted for 35 of all the 55 isolates. Comparative genomics analysis using publicly available E. coli ST399 genomes showed that the outbreak E. coli ST399 isolates formed a unique clade. We developed a mathematical model of pOXA-48-like plasmid transmission between host lineages and used it to estimate its conjugation rate, giving a lower bound of 0.23 conjugation events per lineage per year. Our analysis suggests that co-evolution between the pOXA-48-like plasmid and E. coli ST399 could have played a role in the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying blaOXA-48 as the main cause of a plasmid-borne outbreak within a hospital setting. Our findings suggest complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.

Original languageEnglish
Article number000675
JournalMicrobial Genomics
Volume8
Issue number4
DOIs
Publication statusPublished - 20 Apr 2022

Bibliographical note

Funding Information: A.L, X.D. and J.P. thank for funding the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Modelling Methodology at Imperial College London (grant HPRU-2012–10080). A.L. is funded by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford (NIHR200915) in partnership with Public Health England
(PHE).

X.D. thanks the NIHR HPRU in Genomics and Enabling Data at the University of Warwick (grant NIHR200892). E.J. is a Rosetrees/Stoneygrate 2017 Imperial College Research Fellow, funded by Rosetrees Trust and the Stoneygate Trust (M683) and acknowledges support from the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Infections in partnership with Public Health England (PHE), in collaboration with, Imperial Healthcare Partners, University of Cambridge and University of Warwick. L.P.S. is a Sir Henry Wellcome Postdoctoral Fellow funded by Wellcome (grant 220422/Z/20/Z). For the purpose of open access, a CC-BY public copyright licence applies to any author-accepted-manuscript version.

The authors declare that there are no conflicts of interest.

Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

Publisher Copyright: © 2022 Crown Copyright

Citation: Ledda, Alice, et al. "Hospital outbreak of carbapenem-resistant Enterobacterales associated with a blaOXA-48 plasmid carried mostly by Escherichia coli ST399." Microbial Genomics 8.4 (2022): 000675.

DOI: https://doi.org/10.1099/mgen.0.000675

Keywords

  • E. coli
  • OXA-48
  • carbapenem resistance
  • conjugation rate
  • enterobacterales
  • plasmid

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