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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
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Journal Article
Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
2020
Overview
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
IMP-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
bla
IMP-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.
Antibiotic-resistant bacteria are an urgent threat to human health. Here, Roberts et al. characterise and monitor an ongoing hospital outbreak of carbapenemase-producing
Enterobacter hormaechei
by integrating several technologies for whole-genome sequencing and shotgun metagenomics.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ Bacterial Proteins - biosynthesis
/ Bacterial Proteins - genetics
/ beta-Lactam Resistance - genetics
/ beta-Lactamases - biosynthesis
/ Carbapenem-Resistant Enterobacteriaceae - enzymology
/ Carbapenem-Resistant Enterobacteriaceae - genetics
/ Carbapenem-Resistant Enterobacteriaceae - pathogenicity
/ Cross Infection - epidemiology
/ Cross Infection - microbiology
/ Drug Resistance, Multiple, Bacterial - genetics
/ Enterobacter - isolation & purification
/ Enterobacteriaceae Infections - epidemiology
/ Enterobacteriaceae Infections - microbiology
/ Genomes
/ Humanities and Social Sciences
/ Humans
/ Porosity
/ Science
