Zoonotic potential of uropathogenic Escherichia coli lineages from companion animals

Abstract Escherichia coli is responsible for urinary tract infections (UTI) in humans and pets. This study aims to provide data on the virulome and resistome of E. coli strains isolated during bacteriuria in companion animals and to assess their zoonotic potential. 135 E. coli strains prospectively collected from urine samples of 44 cats and 91 dogs in three French veterinary teaching hospitals were analyzed via antibiotic susceptibility tests and whole genome sequencing. Phylogroup B2 was overrepresented and several sequence types (STs) associated with human extra-intestinal pathogenic E. coli (ExPEC) were found. These included ST12, ST127 and ST141 (8 strains each), which were characterized by genetic homogeneity, and ST73 (23 strains) which contained several serotype-delineated sublineages with distinct distributions in pets and humans. Single nucleotide polymorphism (SNP) analysis further revealed the existence of highly related human and companion animal clones among these STs, indicative of a zoonotic potential. By contrast, other major human ExPEC STs (e.g. ST131, ST10, ST69, ST95 and ST1193) were rarely found (2 strains each), suggesting they might be less adapted to cats and dogs. Of note, ST372 (21 strains) was predominant and exclusively found in dogs. Pet E. coli UTI strains carried virulence genes commonly found in human E. coli UTI isolates. 15.6% of strains were predicted as multi-drug resistant. The major canine and feline ExPEC lineages were not associated with extended spectrum beta lactamase and AmpC production. Only one strain (from ST131) carried the blaCTX-M-15 gene. Persistent clones of E. coli isolated from five cats and nine dogs with recurrent infection had genetic traits similar to strains from other animals. Approximately one-third of the E. coli UTI strains from pets exhibited genetic similarities to those responsible for UTI in humans, suggesting a potential for zoonotic transmission. This study underscores the continued need to monitor and control antimicrobial resistance in companion animals.