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Volume 10, Issue 9

pQEB1: a hospital outbreak plasmid lineage carrying Open Access

Abstract

While conducting genomic surveillance of carbapenemase-producing (CPE) from patient colonisation and clinical infections at Birmingham’s Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene . The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of , two STs of , and three species of . Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an isolated from a blood sample at the QE in 2016 and a isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , carbapenemase and plasmid
Funding
This study was supported by the:
  • Birmingham Biomedical Research Centre (Award NIHR203326)
    • Principle Award Recipient: AlanMcNally
© 2024 The Authors
  • 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.
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2024-09-19
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References

  1. UK Health Security Agency AMR local indicators - produced by the UKHSA - Data - OHID. https://fingertips.phe.org.uk/profile/amr-local-indicators/data#page/1/gid/1938133070/ati/118/iid/93868/age/1/sex/4/cat/-1/ctp/-1/yrr/1/cid/4/tbm/1
  2. Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 2018; 31:31 [View Article] [PubMed]
     [Google Scholar]
  3. Moran RA, Hall RM. Evolution of regions containing antibiotic resistance genes in FII-2-FIB-1 ColV-Colla virulence plasmids. Microb Drug Resist 2018; 24:411–421 [View Article] [PubMed]
     [Google Scholar]
  4. Hua X, Zhang L, Moran RA, Xu Q, Sun L et al. Cointegration as a mechanism for the evolution of a KPC-producing multidrug resistance plasmid in Proteus mirabilis. Emerg Microbes Infect 2020; 9:1206–1218 [View Article] [PubMed]
     [Google Scholar]
  5. Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40–55 [View Article] [PubMed]
     [Google Scholar]
  6. Sanderson ND, Hopkins KMV, Colpus M, Parker M, Lipworth S et al. Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing. Microb Genom 2024; 10:001246 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  9. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [View Article] [PubMed]
     [Google Scholar]
  10. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  11. Villa L, Feudi C, Fortini D, Brisse S, Passet V et al. Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone. Microb Genom 2017; 3:e000110 [View Article] [PubMed]
     [Google Scholar]
  12. Harmer CJ, Moran RA, Hall RM. Movement of IS26-associated antibiotic resistance genes occurs via a translocatable unit that includes a single IS26 and preferentially inserts adjacent to another IS26. mBio 2014; 5:e01801-14 [View Article] [PubMed]
     [Google Scholar]
  13. Yao Y, Falgenhauer L, Rezazadeh Y, Falgenhauer J. IncN Study Group et al. Predominant transmission of KPC-2 carbapenemase in Germany by a unique IncN plasmid variant harboring a novel non-transposable element (NTE KPC -Y). Microbiol Spectr 2024; 12:e0256423 [View Article] [PubMed]
     [Google Scholar]
  14. Turton JF, Turton JA. Long read sequencing provides an insight into plasmids found among carbapenemase producing enterobacterales from hospitals in the united kingdom during 2021 to 2023. bioRxiv 2024
     [Google Scholar]
  15. Blackwell GA, Holt KE, Bentley SD, Hsu LY, Hall RM. Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. J Antimicrob Chemother 2017; 72:1031–1039 [View Article] [PubMed]
     [Google Scholar]
  16. Rada AM, Cadena EDL, Agudelo C, Capataz C, Orozco N et al. Dynamics of blakpc-2 dissemination from non-CG258 Klebsiella pneumoniae to other enterobacterales via incn plasmids in an area of high endemicity. Antimicrob Agents Chemother 2020; 64:
     [Google Scholar]
  17. Harmer CJ, Hall RM. IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024e0011922
     [Google Scholar]
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pQEB1: a hospital outbreak plasmid lineage carrying blaKPC-2
M Gen 10, 001291 (2024); https://doi.org/10.1099/mgen.0.001291
/content/journal/mgen/10.1099/mgen.0.001291
/content/journal/mgen/10.1099/mgen.0.001291
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