Whole-genome sequencing-based trans-sectoral characterization of carbapenemase-producing Enterobacterales

Carbapenemase-producing Enterobacterales (CPE) are a major health care concern as carbapenems are last resort β-lactams in human medicine. Recently, companion animals have been reported to carry CPE also developing infections. The presence of CPE in animals poses a risk for further dissemination to humans, other animals and the environment. Whole-genome sequencing (Illumina and Nanopore) and bioinformatic methods as well as antimicrobial susceptibility testing have been used to compare CPE strains from the different settings to determine their genetic relatedness. OXA-181-producing E. coli ST410 strains isolated from the veterinary setting were clonal (0-4 SNPs) but differed genetically from clinical human strains (>131 SNPs). However, strains from both settings shared identical IncX3 plasmids containing blaOXA-181. Additional multidrug resistance IncF plasmids were only detected in the human setting. Environmental screening of a public garden revealed the presence of a carbapenemase-producing Enterobacter asburiae ST657. It harbored a 163-kb conjugative plasmid containing blaIMI-6 and virulence factors, and was closely related to strains from a human patient in France and retail salad in Switzerland. These findings highlight the role of plasmids in the dissemination of carbapenamases in different clinical and non-clinical sectors further emphasizing the need for One Health surveillance.

2025

dissertation

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