Characterization of Escherichia marmotae, a novel pathogen causing urinary tract infection in a dog

Escherichia is one of the most studied bacterial genera and includes several clinically significant pathogenic species. Unique strategies have evolved in members of this genus to allow their survival within different niches. Although initially the Escherichia cryptic clades (CCs) I-VIII were identified as environmental bacteria, they have been found as commensals and opportunistic pathogens in animals and humans. Notably, members of the Escherichia CCs are commonly mistaken for E. coli when using standard microbiologic techniques for species identification. We used whole-genome sequencing to correctly identify E. marmotae-a member of the Escherichia CCs-that was initially misidentified as E. coli as the causative agent of a urinary tract infection (UTI) in a female dog. The isolate had phenotypic and genotypic resistance to cefalexin-an antibiotic used commonly for the treatment of uncomplicated UTIs-and carried a set of virulence factors also present in uropathogenic E. coli, which would explain the capacity of the organism to colonize the urinary tract. As a relatively new species that is phenotypically very similar to E. coli, it is quite possible that E. marmotae infections may be underreported or misidentified. We hope that our work alerts veterinarians to consider E. marmotae as a possible cause of UTIs in dogs, especially because this could affect treatment decisions. Additionally, our findings broaden the current understanding of the E. marmotae ecology and host range.