WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome

Mette Pinholt, Sion C. Bayliss, Heidi Gumpert, Peder Worning, Veronika V.S. Jensen, Michael Pedersen, Edward J. Feil, Henrik Westh

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Abstract

Objectives: From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycinsusceptible E. faecium(VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized. Methods: WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected fromlaboratory information systems. Results: Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and ∼29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes. Conclusions: Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to preexisting VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.

Original languageEnglish
Pages (from-to)1776-1785
Number of pages10
JournalJournal of Antimicrobial Chemotherapy
Volume74
Issue number7
Early online date30 Mar 2019
DOIs
Publication statusPublished - 1 Jul 2019

Bibliographical note

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: [email protected].

Funding

This project has been approved by the Danish Data Protection Agency (2012-58-0004/AHH-2015-047) and the Danish Health and Medicines Authority (3-3013-1118/1). Data have been presented at the 25th European Congress of Clinical Microbiology and Infectious Diseases, Copenhagen, Denmark, 2015 (oral presentation O168) and at the 11th International Meeting on Microbial Epidemiological Markers, Estoril, Portugal, 2016 (oral presentation OP43). Sequence data from 2012 to 2014 were presented in JAC (2017; 72: 40–7). We thank Louise Christensen, Susanne Rhode, Marianne S. Studstrup, Casper Dam-Nielsen and Maria Kristin Bjornsdóttir for excellent technical assistance. We thank the Scandinavian Society for Antimicrobial Chemotherapy Foundation, The A. P. Møller foundation (Fonden til Laegevidenskabens Fremme) and the Danish Ministry of Health. This work was supported by the Scandinavian Society for Antimicrobial Chemotherapy Foundation, the Danish Ministry of Health, The A. P. Møller foundation (Fonden til Laegevidenskabens Fremme) and internal funding.

ASJC Scopus subject areas

  • Pharmacology
  • Microbiology (medical)
  • Pharmacology (medical)
  • Infectious Diseases

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