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...
Saved in:
Main Authors: | , , , , , , , , , , , , , , , , , , |
---|---|
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 |