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

Authors: Leah W. Roberts; Patrick N. A. Harris; Brian M. Forde; Nouri L. Ben Zakour; Elizabeth Catchpoole; Mitchell Stanton-Cook; Minh-Duy Phan; +12 Authors

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

Abstract

Abstract Carbapenem-resistant Enterobacteriaceae (CRE) represent one of the most urgent threats to human health posed by antibiotic resistant bacteria. Enterobacter hormaechei and other members of the Enterobacter cloacae complex are the most commonly encountered Enterobacter spp. 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 bla IMP-4 carbapenemase-producing E. 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 isolates to a 2013 isolate from the same ward, confirming the hospital environment as the most likely original source of infection in the 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 bla IMP-4 gene, 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. hormaechei and 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 bla IMP-4 on a multidrug resistant IncHI2 plasmid that appears to be widely distributed in Australia.

Country
Australia
Keywords

Biomedical and clinical sciences, 1300 Biochemistry, Science, R Factors, Enterobacter, 610, General Physics and Astronomy, Genetics and Molecular Biology, General Biochemistry, Genetics and Molecular Biology, Article, beta-Lactam Resistance, beta-Lactamases, Disease Outbreaks, Tertiary Care Centers, Bacterial Proteins, 1300 Biochemistry, Genetics and Molecular Biology, Drug Resistance, Multiple, Bacterial, 616, Humans, 3100 Physics and Astronomy, Cross Infection, Whole Genome Sequencing, Q, Enterobacteriaceae Infections, General Chemistry, 1600 Chemistry, Carbapenem-Resistant Enterobacteriaceae, General Biochemistry, Queensland, Sanitary Engineering, Burns, Genome, Bacterial

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    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 10%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
54
Top 1%
Top 10%
Top 10%
Green
gold