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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
Nature Communications, Volume 11, No. 1, Article 466, Year 2020
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Description
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. © 2020, The Author(s).
Authors & Co-Authors
Roberts, Leah W.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Harris, Patrick N.A.
Australia, Brisbane
The University of Queensland
Forde, Brian M.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Ben Zakour, Nouri L.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Phan, Minh Duy
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Sidjabat, Hanna E.
Australia, Brisbane
Australian Infectious Diseases Research Centre
Australia, Brisbane
The University of Queensland
Heney, Claire
Unknown Affiliation
Gawthorne, Jayde A.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Lipman, Jeffrey
Australia, Brisbane
The University of Queensland
Chan, Kok Gan
Malaysia, Kuala Lumpur
Universiti Malaya
China, Zhenjiang
Jiangsu University
Chong, Teik Min
Malaysia, Kuala Lumpur
Universiti Malaya
Yin, Wai Fong
Malaysia, Kuala Lumpur
Universiti Malaya
Schembri, Mark A.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Paterson, David L.
Australia, Brisbane
Australian Infectious Diseases Research Centre
Australia, Brisbane
The University of Queensland
Beatson, Scott A.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Australian Infectious Diseases Research Centre
Statistics
Citations: 30
Authors: 15
Affiliations: 5
Identifiers
Doi:
10.1038/s41467-019-14139-5
ISSN:
20411723
Research Areas
Genetics And Genomics
Health System And Policy
Study Design
Case Study
Study Approach
Qualitative