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, Scott A. Beatson

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May 15, 2019

Received Date: 20th April 19

Carbapenem-resistant Enterobacteriaceae (CRE) represent one of the most urgent threats to human health posed by antibiotic resistant bacteria. Enterobacter hormaecheiand other members of the Enterobacter cloacaecomplex are the most commonly encountered Enterobacterspp. within clinical settings, responsible for numerous outbreaks and ultimately poorer patient outcomes. Here we applied three complementary whole genome sequencing (WGS) technologies to characterise a hospital cluster of blaIMP-4 carbapenemase-producingE. hormaechei.  

In response to a suspected CRE outbreak in 2015 within an Intensive Care Unit (ICU)/Burns Unit in a Brisbane tertiary referral hospital we used Illumina sequencing to determine that all outbreak isolates were sequence type (ST)90 and near-identical at the core genome level. Comparison to publicly available data unequivocally linked all 10 isolatesto a 2013 isolate from the same ward, confirming the hospital environment as the most likely originalsource of infection inthe 2015 cases.No clonal relationship was found to IMP-4-producing isolates identified from other local hospitals. However, using Pacific Biosciences long-read sequencing we were able to resolve the complete context of the blaIMP-4gene, which was found to be on a large IncHI2 plasmid carried by all IMP-4-producing isolates. Continued surveillance of the hospital environment was carried out using Oxford Nanopore long-read sequencing, which was able to rapidly resolve the true relationship of subsequent isolates to the initial outbreak. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaecheiand the IncHI2 plasmid within the hospital plumbing.

Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak, including the transmission dynamics of a carbapenemase-producing E. hormaechei cluster, identification of possible hospital reservoirs and the full context of blaIMP-4 on a multidrug resistant IncHI2 plasmid that appears to be widely distributed in Australia.

Read in full at bioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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Nature Communications

Nature Research, Springer Nature