Prevalence, antimicrobial susceptibility, and virulence profiles of fluoroquinolone-resistant Escherichia coli isolated from companion animals in Sapporo, Japan

Antimicrobial resistance in Escherichia coli is a growing concern in both human and veterinary medicine. Although fluoroquinolone-resistant (FQ-R) E. coli has been reported in companion animals, no integrated analysis incorporating antimicrobial susceptibility, clonality, resistance genes, and virulence factors (VFs) to assess human health risks has been conducted in Japan. This study aimed to characterize FQ-R E. coli isolates from companion animals in Sapporo, Japan by identifying antimicrobial susceptibility, clonality, resistance genes, and VFs. Among 106 animals sampled, 33.0% carried FQ-R E. coli. Among 104 FQ-R E. coli isolates, 58 isolates (55.8%) were identified as ST131. Whole-genome sequencing of 35 representative FQ-R E. coli isolates, including 20 ST131 isolates, showed that the ST131 isolates were distributed among five clades/sub-clades (C1-nM27, C1-M27, A, C2 and Unclassified), indicating increased clade diversity compared to previous years. ST1193, another international high-risk clone, was also detected. All isolates harbored mutations of quinolone resistance-determining regions in gyrA and parC, and 51.4% carried blaCTX-M genes, including blaCTX-M-27 and blaCTX-M-14. Most isolates remained susceptible to aminoglycosides and cefmetazole, although the latter is not approved for veterinary use in Japan. Additionally, 72 VFs were identified, and eight were shared by all isolates, suggesting potential risk to human health. Our findings indicate that companion animals share certain E. coli lineages including ST131 and ST1193 with humans. Prudent antimicrobial use and routine hygiene practices are essential to limit the transmission. Further studies incorporating human and environmental isolates are needed to better understand the transmission dynamics of FQ-R E. coli within communities.