WGS-based characterization of trans-sectoral OXA-48-producing Escherichia coli in Switzerland

The broad trans-sectoral (humans, animals, environment) dissemination potential of OXA-48 carbapenemase-producing Escherichia coli (OXA-48-Ec) and OXA-48-harboring plasmids represent a major One-Health concern. A whole-genome sequence analysis was conducted with 75 OXA-48-Ec isolated between 2018 and 2022 from dogs (n = 13) and cats (n = 4) hospitalized in a veterinary clinic, the environment of another veterinary clinic (n = 2), humans (n = 55), and river water (n = 1). Strain sequence types (ST), core-genome MLST-based complex type (CT), antimicrobial resistance genes, plasmid incompatibility (Inc) groups were determined by Illumina sequence analysis. Animal OXA-48-Ec and their respective plasmids as well as representative human strains harboring similar OXA-48 plasmids as those from animals were also sequenced using Oxford Nanopore Technologies for comparative analysis of complete plasmids. The 19 veterinary strains belonged to 13 STs, and the 55 human strains to 25 different STs. Only two animal strains shared the same ST as the human strains (ST58, ST405), but with different CTs. Strains carried blaOXA-48 mainly on IncL-type plasmids (n = 35), except some non-veterinary strains, where the gene was located on Col156-like plasmids (human, n = 14; water, n = 1), on the chromosome (n = 7) or onto yet-uncharacterized elements (n = 18) (humans). Two ST58 animal strains harbored blaOXA-48 onto a novel 76-kb IncL-type plasmid also harboring the sul1 and blaDHA-1 resistance genes. Our analysis showed a high genetic diversity between OXA-48-Ec deriving from the human and small animal clinical settings. However, diverse strains from all isolation sources harbored highly similar blaOXA-48-carrying IncL plasmids, underscoring the potential contribution of shared ecological niches in the spread of this hyperepidemic plasmid.