Genomic analysis of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae isolated from a dog with a severe episode of self-trauma and urinary tract infection

Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are emerging pathogens of major importance in veterinary medicine. This study describes the clinical, microbiological, and genomic characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolated from a dog with paraparesis and concurrent pyelonephritis, chronic cystitis, and a self-traumatized limb lesion. A 12-year-old mixed-breed female dog underwent repeated antimicrobial therapy during hospitalization. Urine obtained by cystocentesis and wound samples were cultured, and ESBL-producing strains were characterized by antimicrobial susceptibility testing and whole-genome sequence-based analysis. CTX-M-55-producing E. coli sequence type (ST) 457, phylogroup F, O11:H25, and fimH145, was recovered from urine and wound samples, while the wound sample also yielded a CTX-M-15- and SHV-2-producing K. pneumoniae ST39, KL149:OL2α.2. The two closely related E. coli strains differed by 96 single nucleotide polymorphisms, despite sharing the same ST, resistome, plasmid replicons, and virulence profile. ESBL-positive strains carried multiple virulence genes, with the E. coli strains classified as extraintestinal pathogenic E. coli strains. To the best of our knowledge, this is the first report of ESBL-producing K. pneumoniae ST39 in an animal in Brazil. The co-occurrence of ESBL-producing E. coli ST457 and K. pneumoniae ST39 in the same dog highlights the potential for companion animals to harbor clinically relevant multidrug-resistant lineages and reinforces the need for continuous antimicrobial resistance monitoring and antimicrobial stewardship in this sector.