Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

Trinad Chakraborty; Mustafa Sadek; Yancheng Yao; Can Imirzalioglu; Roger Stephan; Laurent Poirel; Patrice Nordmann

doi:10.1128/JCM.02238-20

Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany

J Clin Microbiol. 2021 Feb 18;59(3):e02238-20. doi: 10.1128/JCM.02238-20. Print 2021 Feb 18.

Authors

Trinad Chakraborty^{1

2}, Mustafa Sadek³, Yancheng Yao^{1

2}, Can Imirzalioglu^{1

2}, Roger Stephan⁴, Laurent Poirel^{3

5

6}, Patrice Nordmann^{7

3

5

6}

Affiliations

¹ Institute of Medical Microbiology, Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.
² German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.
³ Medical and Molecular Microbiology, Section of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.
⁴ Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
⁵ INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland.
⁶ Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.
⁷ Institute for Microbiology, University Hospital Centre, Lausanne, Switzerland patrice.nordmann@unifr.ch.

Abstract

A series of clinical NDM-5-producing Escherichia coli isolates obtained from two surveillance networks for carbapenem-producing Enterobacterales from 2018 to 2019, namely, Switzerland (NARA) and Germany (SurvCARE), were analyzed. The 33 NDM-5-producing E. coli isolates were highly resistant to β-lactams, including novel β-lactam/β-lactamase inhibitor combinations (ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam), and remained susceptible to fosfomycin, colistin, and tigecycline. These isolates were assigned to different sequence types (STs) and indicated a predominance of isolates exhibiting ST167 in Switzerland and Germany (n = 10) (phylogenetic group C), followed by ST405 (n = 4) (phylogenetic group E), ST1284 (n = 4) (phylogenetic group C), and ST361 (n = 4) (phylogenetic group C). The bla_NDM-5 gene was predominantly present on an IncF-type plasmid (n = 29) and, to a lesser extent, on the narrow-host-range IncX3 plasmid (n = 4). Sequence analyses of eight NDM-5 plasmids indicated that NDM-5-encoding F-type plasmids varied in size between 86 and 132 kb. The two IncX3 plasmids pCH8NDM5 and pD12NDM5 were 46 and 45 kb in size, respectively. The highly conserved bla_NDM-5 genetic surrounding structures (ΔISAba125-bla_NDM-5-ble_MBL-trpT-dsbD-IS26) of both the F-type and IncX3 plasmids suggested a common genetic origin. The emergence of the NDM-5 carbapenemase was evidenced in particular for the E. coli ST167 clone, which is a successful epidemic clone known to be associated with both multiresistance and virulence traits and is therefore of high public health concern. The occurrence of clonally related NDM-5-producing E. coli isolates in Switzerland and Germany further indicates the international spread of this multidrug-resistant superbug at least throughout Europe.

Keywords: Escherichia coli; NDM; NDM-5; ST167; WGS; plasmid replicon; whole-genome sequencing.

Publication types

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

MeSH terms

Bacterial Proteins
Escherichia coli* / genetics
Europe
Germany
Humans
Microbial Sensitivity Tests
Phylogeny
Plasmids / genetics
Switzerland
beta-Lactamases* / genetics

Substances

Bacterial Proteins
beta-Lactamases
carbapenemase