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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Roberts LW 1 , Harris PNA 2 , Forde BM 1 , Ben Zakour NL 1 , Catchpoole E 3 , Stanton-Cook M 1 Show all authors , Phan MD 1 , Sidjabat HE 4 , Bergh H 3 , Heney C 3 , Gawthorne JA 1 , Lipman J 5 , Allworth A 6 , Chan KG 7 , Chong TM 7 , Yin WF 7 , Schembri MA 1 , Paterson DL 4 , Beatson SA 8

Affiliations 

  • 1 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
  • 2 UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia. p.harris@uq.edu.au
  • 3 Pathology Queensland, Central Microbiology, Brisbane, QLD, Australia
  • 4 Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
  • 5 UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
  • 6 Infectious Disease Unit, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia
  • 7 Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
  • 8 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia. s.beatson@uq.edu.au
Nat Commun, 2020 01 24;11(1):466.
PMID: 31980604 DOI: 10.1038/s41467-019-14139-5

Abstract

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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