Genomic analyses of Escherichia coli ST410 harbouring the blaOXA-181 carbapenemase gene from companion animals and humans in Switzerland.

Abstract

Aims: To determine the genomic relatedness of E. coli (Ec) sequence type (ST) 410 producing the carbapenemase OXA-181 (ST410-OXA-181) which caused an outbreak in a Swiss companion animal (CA) clinic in 2018 with those isolated from humans between 2017 and 2021 in Switzerland, and to characterize complete plasmids harbouring antimicrobial resistance genes (ARGs).

Methods and results: The complete genomes of 31 Ec ST410-OXA-181 (8 from CA, 23 from humans) were obtained by hybrid assembly of reads from Illumina and Nanopore sequencing technologies. The genomes were used for in silico phylogenetic analysis (cgMLST, SNP, ST410 clade analysis), ARG screening and for comparative analysis of complete plasmids. Antimicrobial susceptibility was determined by MIC measurement. All veterinary strains (CA, veterinarian) belonged to the phylogenetic clade ST410-B2 and the human strains to either ST410-B2 or B3. Strains recovered from the veterinary setting were clonal, differing by 0-4 SNPs. A higher genetic distance (>131 SNPs) was observed between the veterinary and the clinical human strains. All veterinary and 15 human strains shared an identical IncX3 plasmid harbouring blaOXA-181. Additional multidrug resistance plasmids were detected in human strains only.

Conclusions: The Ec ST410-B2-OXA-181 lineage was detected in both humans and animals. They share the same OXA-181 plasmids but differed by SNP-based genetic distances and ARG contents indicating broad dissemination potential and independent evolution of strains of this lineage.