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

Roberts, Leah W. and Harris, Patrick N.A. and Forde, Brian M. and Ben Zakour, Nouri L. and Catchpoole, Elizabeth and Stanton-Cook, Mitchell and Phan, Minh-Duy and Sidjabat, Hanna E. and Bergh, Haakon and Heney, Claire and Gawthorne, Jayde A. and Lipman, Jeffrey and Allworth, Anthony and Chan, Kok Gan and Chong, Teik Min and Yin, Wai Fong and Schembri, Mark A. and Paterson, David L. and Beatson, Scott A. (2020) Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. Nature Communications, 11 (1). p. 466. ISSN 2041-1723

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Official URL: https://doi.org/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. © 2020, The Author(s).

Item Type: Article
Uncontrolled Keywords: Beta-Lactamases; Carbapenem-Resistant Enterobacteriaceae; Carbapenems
Subjects: Q Science > Q Science (General)
Q Science > QH Natural history
Divisions: Faculty of Science > Institute of Biological Sciences
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 05 Aug 2020 03:42
Last Modified: 05 Aug 2020 03:42
URI: http://eprints.um.edu.my/id/eprint/25251

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