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

Nat Commun. 2020 Jan 24;11(1):466. doi: 10.1038/s41467-019-14139-5.


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.

Publication types

  • Case Reports

MeSH terms

  • Bacterial Proteins / biosynthesis*
  • Bacterial Proteins / genetics*
  • Burns / microbiology
  • Carbapenem-Resistant Enterobacteriaceae / enzymology*
  • Carbapenem-Resistant Enterobacteriaceae / genetics*
  • Carbapenem-Resistant Enterobacteriaceae / pathogenicity
  • Cross Infection / epidemiology
  • Cross Infection / microbiology
  • Disease Outbreaks*
  • Drug Resistance, Multiple, Bacterial / genetics
  • Enterobacter / enzymology*
  • Enterobacter / genetics*
  • Enterobacter / isolation & purification
  • Enterobacteriaceae Infections / epidemiology*
  • Enterobacteriaceae Infections / microbiology
  • Genome, Bacterial
  • Humans
  • Queensland / epidemiology
  • R Factors / genetics
  • Sanitary Engineering
  • Tertiary Care Centers
  • Whole Genome Sequencing / methods
  • beta-Lactam Resistance / genetics
  • beta-Lactamases / biosynthesis*
  • beta-Lactamases / genetics*


  • Bacterial Proteins
  • beta-Lactamases
  • carbapenemase

Supplementary concepts

  • Enterobacter hormaechei