Genomic characterization of ESBL/AmpC-producing and high-risk clonal lineages of Escherichia coli and Klebsiella pneumoniae in imported dogs with shelter and stray background

ABSTRACT: Objectives: Extended spectrum β-lactamase (ESBL)- and ampicillinase C (AmpC)-carrying Enterobacteriaceae have been widely reported among companion animals. According to previous studies, dogs with a shelter or stray background might be at risk of carrying such bacteria. The aim of this study was to explore, with whole-genome sequencing (WGS), the genomic characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolated from imported dogs with a stray or shelter background. Methods: E. coli (n = 58) and K. pneumoniae (n = 2) isolates from imported dogs originating from seven countries were included. Phenotypic resistance was investigated by selective isolation and antibiotic susceptibility testing. Whole-genome sequencing was used to study the genomic characteristics and the presence of antimicrobial resistance genes (ARGs) and virulence determinants of the ESBL/AmpC-producing E. coli and K. pneumoniae isolates. Results: A high diversity of different ARGs (n = 56) and sequence types (STs) (n = 32), including high-risk clonal lineages ST410 (n = 3) and ST307 (n = 1), was identified in E. coli and K. pneumoniae isolates, respectively. Genes encoding resistance to β-lactams accounted for the majority, with the most frequent being blaCTX-M-15. Moreover, 17 (29%) E. coli isolates qualified as presumptive extraintestinal pathogenic and/or uropathogenic E. coli. Conclusions: Our results highlight the multiplicity of genetic backgrounds disseminating ESBL/AmpC-genes in the studied dogs, calling for further investigation of possible drivers responsible for the dissemination of ARGs in animal shelters and amongst stray dogs. From a public health perspective, enhanced genomic surveillance of ESBL/AmpC-producing Enterobacteriaceae in dogs is needed in Finland.