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

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 sequencin...

Full description

Saved in:
Bibliographic Details
Main 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.
Format: Article
Published: Nature Research 2020
Subjects:
Online Access:http://eprints.um.edu.my/25251/
https://doi.org/10.1038/s41467-019-14139-5
Tags: Add Tag
No Tags, Be the first to tag this record!
id my.um.eprints.25251
record_format eprints
spelling my.um.eprints.252512020-08-05T03:42:31Z http://eprints.um.edu.my/25251/ Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei 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. Q Science (General) QH Natural history 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). Nature Research 2020 Article PeerReviewed Roberts, Leah W. and Harris, Patrick N.A. and Forde, Brian M. and Ben Zakour, Nouri L. and Catchpoole, Elizabeth and Stanton-Cook, Mitchell and Phan, Minh-Duy and Sidjabat, Hanna E. and Bergh, Haakon and Heney, Claire and Gawthorne, Jayde A. and Lipman, Jeffrey and Allworth, Anthony and Chan, Kok Gan and Chong, Teik Min and Yin, Wai Fong and Schembri, Mark A. and Paterson, David L. and Beatson, Scott A. (2020) Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. Nature Communications, 11 (1). p. 466. ISSN 2041-1723 https://doi.org/10.1038/s41467-019-14139-5 doi:10.1038/s41467-019-14139-5
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic Q Science (General)
QH Natural history
spellingShingle Q Science (General)
QH Natural history
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.
Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
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).
format Article
author 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.
author_facet 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.
author_sort Roberts, Leah W.
title Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
title_short Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
title_full Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
title_fullStr Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
title_full_unstemmed Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei
title_sort integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing enterobacter hormaechei
publisher Nature Research
publishDate 2020
url http://eprints.um.edu.my/25251/
https://doi.org/10.1038/s41467-019-14139-5
_version_ 1680857013688467456
score 13.214268