Abstract: Background – Antimicrobial resistance (AMR) is a growing One Health problem. Judicious antimicrobial use is needed to combat AMR, including identification and selection of antimicrobials less likely to select for AMR in treated patients. Objective – Compare changes in antimicrobial resistance gene content of the gastrointestinal microbiome of cats treated with amoxicillin-clavulanic acid or cefovecin. Animals – 16 adult, client-owned or shelter cats treated with amoxicillin-clavulanic acid (duration <15 days) or cefovecin (one injection). All treatment decisions were at the discretion of the animal’s primary veterinarian. Methods – In this prospective cohort study, voided fecal samples from treated cats were collected at enrollment, and at weeks 1 through 4, 8, and 12. Commensal E. coli and enterococci isolated from all samples were tested for resistance to cefovecin and other antimicrobials. The baseline and week 2, 8, and 12 samples were tested for 813 AMR genes using deep amplicon next-generation sequencing. Results – Sequencing of samples from the first seven cats showed increased total AMR genes detected at week 12 compared to baseline. The most common AMR genes conferred resistance to tetracyclines, beta-lactams, macrolides, aminoglycosides, and phenicols. Cats treated with amoxicillin-clavulanic acid had more AMR genes than cefovecin-treated cats at all timepoints. Kirby-Bauer disk diffusion identified E. coli resistant to nalidixic acid, tetracycline, and TMS, and intermediate resistance to ampicillin and amoxicillin-clavulanic acid. Conclusions and clinical importance – Understanding the AMR effects of specific antimicrobials will help shape treatment recommendations and guide veterinarians to make the most responsible antimicrobial selections.
