New Delhi Metallo-β-Lactamase-Producing Enterobacterales Bacteria, Switzerland, 2019-2020

Abstract

Carbapenemase-producing Enterobacterales (CPE) bacteria are a critical global health concern; New Delhi metallo-β-lactamase (NDM) enzymes account for >25% of all CPE found in Switzerland. We characterized NDM-positive CPE submitted to the Swiss National Reference Center for Emerging Antibiotic Resistance during a 2-year period (January 2019-December 2020) phenotypically and by using whole-genome sequencing. Most isolates were either Klebsiella pneumoniae (59/141) or Escherichia coli (52/141), and >50% were obtained from screening swabs. Among the 108 sequenced isolates, NDM-1 was the most prevalent variant, occurring in 56 isolates, mostly K. pneumoniae (34/56); the next most prevalent was NDM-5, which occurred in 49 isolates, mostly E. coli (40/49). Fourteen isolates coproduced a second carbapenemase, predominantly an OXA-48-like enzyme, and almost one third of isolates produced a 16S rRNA methylase conferring panresistance to aminoglycosides. We identified successful plasmids and global lineages as major factors contributing to the increasing prevalence of NDMs in Switzerland.

Keywords: Enterobacterales; Escherichia coli; Klebsiella pneumoniae; NDM; New Delhi metallo-β-lactamase; Switzerland; antimicrobial resistance; bacteria; carbapenemase; metallo-β-lactamase.

Figure 1

Regions of Switzerland from which Enterobacterale isolates positive for New Delhi metallo-β-lactamase were obtained, January 2019–December 2020.

Figure 2

Clustering and gene content of 46 Escherichia coli isolates collected in Switzerland, January 2019–December 2020. A) Phylogenetic tree showing clustering and the respective ST, NDM variant, and region of Switzerland from which each isolate was obtained. B) Gene matrix showing β-lactamase and RMTase gene content of the isolates. NDM, New Delhi metallo-β-lactamase; ST, sequence type.

Figure 3

Clustering and gene content of 42 Klebsiella pneumoniae isolates collected in Switzerland, January 2019–December 2020. A) Phylogenetic tree showing clustering and the respective ST, NDM variant, and region of Switzerland from which each isolate was obtained. B) Gene matrix showing β-lactamase and RMTase gene content of the isolates. NDM, New Delhi metallo-β-lactamase; ST, sequence type.