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

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

Trinad Chakraborty  1   2 , Mustafa Sadek  3 , Yancheng Yao  1   2 , Can Imirzalioglu  1   2 , Roger Stephan  4 , Laurent Poirel  3   5   6 , Patrice Nordmann  7   3   5   6
Affiliations

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

Trinad Chakraborty et al. J Clin Microbiol. .

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 blaNDM-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 blaNDM-5 genetic surrounding structures (ΔISAba125-blaNDM-5-bleMBL-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.

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Figures

FIG 1
FIG 1
Plasmid characterization of blaNDM-5-bearing E. coli isolates. All the antibiotic resistance genes are shown. The blaNDM-5 genes were located on plasmids of four different IncF groups and the IncX3 group. The blaNDM-5-carrying IncF-type plasmids harbored commonly aadA2-aadA5, sul1, and dfrA12, and in addition, some of them contained more or fewer other genes.
FIG 2
FIG 2
Phylogenomic clustering of NDM-5-producing E. coli isolates with the respective STs and phylogenic groups indicated and plasmids harbored.
FIG 3
FIG 3
(A and B) Circular comparison between different F-type plasmids. The plasmids pD13NDM5 (A) and pECH3NDM5 (B) (inner circle) were used by BRIG software as reference plasmids. (C) Genome comparison of the IncX3 plasmids pCH8NDM5 and pD12NDM5. Gaps indicate regions that were missing in the respective plasmids compared to the reference plasmid. The outmost rings (black) show the functional genes, including the resistance and structural genes. The different colors indicate different plasmids and are listed in the color key.
FIG 4
FIG 4
Structures of the blaNDM-5 genetic context of the IncX3 and F-type plasmids. CS, conserved segment of integron.
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