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

Publication

Date: 24th January 2020 | Source: Nature Communications

Authors: 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, Scott A. Beatson.

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.

Read the full text Identifying an MDR E. hormaechei outbreak

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