Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone

Xiaoliang Ba; Yingyi Guo; Robert A. Moran; Emma L. Doughty; Baomo Liu; Likang Yao; Jiahui Li; Nanhao He; Siquan Shen; Yang Li; Willem van Schaik; Alan Mcnally; Mark A. Holmes; Chao Zhuo

doi:10.1038/s41467-023-43854-3

Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone

Xiaoliang Ba, Yingyi Guo, Robert A. Moran, Emma L. Doughty, Baomo Liu, Likang Yao, Jiahui Li, Nanhao He, Siquan Shen, Yang Li, Willem van Schaik, Alan Mcnally, Mark A. Holmes^*, Chao Zhuo^*

^*Corresponding author for this work

Microbiology and Infection

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Abstract

Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the bla_OXA-181-bearing X3 plasmid, but carries a F-type plasmid containing bla_NDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.

Original language	English
Article number	494
Number of pages	15
Journal	Nature Communications
Volume	15
Issue number	1
Early online date	12 Jan 2024
DOIs	https://doi.org/10.1038/s41467-023-43854-3
Publication status	Published - 12 Jan 2024

Bibliographical note

Acknowledgements:
This work was undertaken as part of the DETECTIVE research project funded by the National Natural Science Foundation of China (8181101332) and the Medical Research Council (MR/S013660/1). W.v.S. was also supported by a Wolfson Research Merit Award (WM160092). We thank Dr. Andries J. van Tonder for guidance on the bioinformatics analysis.

Copyright:
© 2024. The Author(s).

Keywords

Child
Humans
Escherichia coli/genetics
Escherichia coli Infections/epidemiology
Carbapenem-Resistant Enterobacteriaceae/genetics
Clone Cells
Carbapenems/pharmacology
Anti-Bacterial Agents/pharmacology
beta-Lactamases/genetics
Microbial Sensitivity Tests

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10.1038/s41467-023-43854-3Licence: Creative Commons: Attribution (CC BY)

BaX2023GlobalFinal published version, 3.9 MBLicence: Creative Commons: Attribution (CC BY)

DETECTIVE: Dissemination and resistance mechanisms of carbapenem-resistant Gram-negative bacilli
van Schaik, W. & McNally, A.
Medical Research Council
14/02/19 → 31/03/23
Project: Research Councils
Acquisition of antimicrobial resistance by opportunistic pathogens.
van Schaik, W. & Henderson, I.
The Royal Society
1/05/17 → 30/04/22
Project: Research Councils

Cite this

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title = "Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone",

abstract = "Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence. ",

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author = "Xiaoliang Ba and Yingyi Guo and Moran, {Robert A.} and Doughty, {Emma L.} and Baomo Liu and Likang Yao and Jiahui Li and Nanhao He and Siquan Shen and Yang Li and {van Schaik}, Willem and Alan Mcnally and Holmes, {Mark A.} and Chao Zhuo",

note = "Acknowledgements: This work was undertaken as part of the DETECTIVE research project funded by the National Natural Science Foundation of China (8181101332) and the Medical Research Council (MR/S013660/1). W.v.S. was also supported by a Wolfson Research Merit Award (WM160092). We thank Dr. Andries J. van Tonder for guidance on the bioinformatics analysis. Copyright: {\textcopyright} 2024. The Author(s).",

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AU - Guo, Yingyi

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AU - Doughty, Emma L.

AU - Liu, Baomo

AU - Yao, Likang

AU - Li, Jiahui

AU - He, Nanhao

AU - Shen, Siquan

AU - Li, Yang

AU - van Schaik, Willem

AU - Mcnally, Alan

AU - Holmes, Mark A.

AU - Zhuo, Chao

N1 - Acknowledgements: This work was undertaken as part of the DETECTIVE research project funded by the National Natural Science Foundation of China (8181101332) and the Medical Research Council (MR/S013660/1). W.v.S. was also supported by a Wolfson Research Merit Award (WM160092). We thank Dr. Andries J. van Tonder for guidance on the bioinformatics analysis. Copyright: © 2024. The Author(s).

PY - 2024/1/12

Y1 - 2024/1/12

N2 - Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.

AB - Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.

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KW - Humans

KW - Escherichia coli/genetics

KW - Escherichia coli Infections/epidemiology

KW - Carbapenem-Resistant Enterobacteriaceae/genetics

KW - Clone Cells

KW - Carbapenems/pharmacology

KW - Anti-Bacterial Agents/pharmacology

KW - beta-Lactamases/genetics

KW - Microbial Sensitivity Tests

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SN - 2041-1723

VL - 15

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 494

ER -

Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone

Abstract

Bibliographical note

Keywords

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Projects

DETECTIVE: Dissemination and resistance mechanisms of carbapenem-resistant Gram-negative bacilli

Acquisition of antimicrobial resistance by opportunistic pathogens.

Cite this