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Volume 6, Issue 4

Genomic surveillance of ST131 identifies local expansion and serial replacement of subclones Open Access

Abstract

sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (=69) with other Irish (=35) and global (=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short- and long-read genome sequencing, assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that Clade C was the most prevalent (686 out of 794 isolates, 86 %) of the three major ST131 clades circulating worldwide (A with , B with , C with ), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in . 1985 and subsequently acquired different ESBL gene variants ( vs ). An ISEcpmediated transposition of the gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of at the gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10), highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , Escherichia coli , genomics , long-term care facilities and ST131
Funding
This study was supported by the:
  • Department of Health (UK) (Award HICF-T5-342)
    • Principle Award Recipient: Sharon J. Peacock
  • ESPRC Vaccine Hub
    • Principle Award Recipient: Derek Pickard
  • Dublin City University
    • Principle Award Recipient: Arun Gonzales Decano
  • Wellcome Trust (Award WT098600)
    • Principle Award Recipient: Sharon J. Peacock
  • Wellcome Trust (Award 110243/Z/15/Z)
    • Principle Award Recipient: Catherine Ludden
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones
M Gen 6, e000352 (2020); https://doi.org/10.1099/mgen.0.000352
/content/journal/mgen/10.1099/mgen.0.000352
/content/journal/mgen/10.1099/mgen.0.000352
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