Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan

Yoko Nukui; Alafate Ayibieke; Makoto Taniguchi; Yoshibumi Aiso; Yuka Shibuya; Kazunari Sonobe; Jun Nakajima; Saki Kanehira; Yoshiro Hadano; Shuji Tohda; Ryuji Koike; Ryoichi Saito

doi:10.1016/j.jgar.2019.07.001

Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan

J Glob Antimicrob Resist. 2019 Sep:18:148-150. doi: 10.1016/j.jgar.2019.07.001. Epub 2019 Jul 8.

Authors

Yoko Nukui¹, Alafate Ayibieke², Makoto Taniguchi³, Yoshibumi Aiso⁴, Yuka Shibuya⁴, Kazunari Sonobe⁵, Jun Nakajima⁵, Saki Kanehira⁵, Yoshiro Hadano⁴, Shuji Tohda⁶, Ryuji Koike⁴, Ryoichi Saito⁷

Affiliations

¹ Department of Infection Control and Prevention, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan. Electronic address: nucku-tky@umin.ac.jp.
² Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan.
³ Oral Microbiome Center, Kagawa, Japan.
⁴ Department of Infection Control and Prevention, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan.
⁵ Department of Infection Control and Prevention, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan; Department of Clinical Laboratory, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan.
⁶ Department of Clinical Laboratory, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan.
⁷ Department of Infection Control and Prevention, Medical Hospital, Tokyo Medical and Dental University, Tokyo, Japan; Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan.

PMID: 31295582
DOI: 10.1016/j.jgar.2019.07.001

Abstract

Objectives: The emergence and spread of carbapenemase-producing Enterobacteriaceae is a worldwide concern. This study reports the whole genome sequence of an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli sequence type 167 (ST167) multidrug-resistant clinical strain (EC129) isolated from a sputum sample of a hospitalised patient diagnosed with pneumonia.

Methods: The genome of E. coli EC129 was subjected to next-generation sequencing and reads were assembled. The draft genome was annotated using DDBJ Read Annotation Pipeline DFAST server, followed by subsequent in silico analysis.

Results: The genome of E. coli ST167 strain EC129 is 5319159 bp in length and contains 5022 protein-coding sequences. The bla_NDM-5, bla_CTX-M-14, bla_OXA-10 and mcr-1 genes were detected along with other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulfonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed that the isolate was resistant to all antimicrobial agents except colistin.

Conclusion: To our knowledge, this study is the first to report anE. coli ST167 strain co-producing NDM-5, CTX-M-14, OXA-10 and MCR-1 isolated from a sputum sample of an individual with pneumonia in Japan, thus elucidating the molecular characteristics and resistance gene diversity of this strain.

Keywords: Escherichia coli; NDM-5; Whole-genome sequencing; mcr-1.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Carbapenem-Resistant Enterobacteriaceae
Drug Resistance, Multiple, Bacterial / drug effects
Drug Resistance, Multiple, Bacterial / genetics*
Escherichia coli / drug effects
Escherichia coli / genetics*
Escherichia coli / isolation & purification
Escherichia coli / metabolism*
Escherichia coli Proteins / genetics
Genes, Bacterial / genetics*
Genome, Bacterial
Japan
Microbial Sensitivity Tests
Whole Genome Sequencing*
beta-Lactamases / genetics*
beta-Lactamases / metabolism*

Substances

Anti-Bacterial Agents
Escherichia coli Proteins
MCR-1 protein, E coli
beta-lactamase CTX-M-14, E coli
beta-lactamase OXA-10
beta lactamase NDM-5, E coli
beta-Lactamases