Comprehensive genomic analysis and antibiotic resistance profiles of Clostridioides difficile from cats and dogs in...

This study aimed to isolate Clostridioides difficile (C. difficile) from healthy and diarrhoeic cats and dogs, perform comprehensive genomic characterization of the isolates obtained, and investigate their antibiotic susceptibility profiles and antigenic features. For this purpose, a total of 200 rectal swabs from 100 cats and 100 dogs (50 healthy and 50 diarrhoeic in each group) were used. Isolation was performed using culture methods, and isolates were identified through species-specific PCR. Multi-Locus Sequence Typing (MLST) was used for genotyping. Antibacterial susceptibilities of isolates were determined by the E-test. Whole genome sequencing (WGS) was carried out using the Oxford-Nanopore platform as long reads. A total of 18 (9 %) swab samples, 12 (12 %) from dogs and 6 (6 %) from cats tested positive for C. difficile. The antibiotic to which the isolates showed the most resistance was clindamycin at 33.3 % (6/18), while all isolates were susceptible to vancomycin. The nimB gene associated with metronidazole resistance was detected in 83.3 % of the isolates. slpA and toxin genes were present in 77.8 % and 45 % of the isolates, respectively. Comprehensive phylogenetic analyses were conducted to determine the genetic relatedness of our isolates to C. difficile strains originating from diverse geographical regions and host species. The isolates obtained in this study belonged to six distinct sequence types (STs), several of which have been previously associated with human infection outbreaks. Taken together, the phylogenetic relationships, elevated antimicrobial resistance, and toxigenic profiles observed indicate that companion animals may serve as a reservoir for this pathogen, potentially contributing to public health risks.