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

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ID: 87055
2020
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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 bla 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 bla 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.
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roberts2020integratingnature Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Roberts, Leah W;Harris, Patrick N A;Forde, Brian M;Ben Zakour, Nouri L;Catchpoole, Elizabeth;Stanton-Cook, Mitchell;Phan, Minh-Duy;Sidjabat, Hanna E;Bergh, Haakon;Heney, Claire;Gawthorne, Jayde A;Lipman, Jeffrey;Allworth, Anthony;Chan, Kok-Gan;Chong, Teik Min;Yin, Wai-Fong;Schembri, Mark A;Paterson, David L;Beatson, Scott A;
Journal Nature communications
Year 2020
DOI
10.1038/s41467-019-14139-5
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