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

Leah W. Roberts, Patrick N. A. Harris (), Brian M. Forde, Nouri L. Ben Zakour, Elizabeth Catchpoole, Mitchell Stanton-Cook, Minh-Duy Phan, Hanna E. Sidjabat, Haakon Bergh, Claire Heney, Jayde A. Gawthorne, Jeffrey Lipman, Anthony Allworth, Kok-Gan Chan, Teik Min Chong, Wai-Fong Yin, Mark A. Schembri, David L. Paterson and Scott A. Beatson ()
Additional contact information
Leah W. Roberts: The University of Queensland
Patrick N. A. Harris: The University of Queensland
Brian M. Forde: The University of Queensland
Nouri L. Ben Zakour: The University of Queensland
Elizabeth Catchpoole: Pathology Queensland, Central Microbiology
Mitchell Stanton-Cook: The University of Queensland
Minh-Duy Phan: The University of Queensland
Hanna E. Sidjabat: The University of Queensland
Haakon Bergh: Pathology Queensland, Central Microbiology
Claire Heney: Pathology Queensland, Central Microbiology
Jayde A. Gawthorne: The University of Queensland
Jeffrey Lipman: The University of Queensland
Anthony Allworth: Royal Brisbane & Women’s Hospital
Kok-Gan Chan: University of Malaya
Teik Min Chong: University of Malaya
Wai-Fong Yin: University of Malaya
Mark A. Schembri: The University of Queensland
David L. Paterson: The University of Queensland
Scott A. Beatson: The University of Queensland

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-019-14139-5

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