The effects of antimicrobial therapy on faecal Escherichia coli and mucosal Staphylococci in dogs

Canine infections with antimicrobial resistant (AMR), particularly multi-drug resistant (MDR) bacteria are increasing, severely limiting therapeutic options, and representing an animal health issue. In addition, with potential transfer of AMR bacteria between dogs, their environment, humans and other animals, there may also be a public health risk. Commensal isolates can be a source of clinical infections and studies reporting the prevalence of AMR and risk factors for such isolates are important. Furthermore, one of the most significant impacts upon commensal bacterial populations is antimicrobial therapy that may select for pre-existing AMR organisms or transmission of resistance determinants. The aim of this work was to investigate AMR amongst canine commensal bacterial populations and the effects of five different antimicrobials, authorised to treat dogs in the UK, on these populations both during and after therapy. Three groups of dogs were enrolled: healthy non-antimicrobial treated, non-vet visiting dogs (n = 28), to investigate longitudinal carriage of faecal E. coli; healthy non-antimicrobial treated, non-vet visiting, dogs (n = 73) and antimicrobial treated, non-hospitalised dogs (n = 127) to investigate longitudinal carriage of mucosal staphylococci and faecal E. coli. Staphylococci and E. coli isolated from swabs (nose/perineum) and faecal samples respectively, were tested for phenotypic AMR and carriage of resistance genes by PCR assay. Staphylococci were assigned to species by PCR assay (nuc gene), MALDI-TOF-MS and sequencing (tuf gene). Healthy dog E. coli underwent phylo-typing, and a selection of longitudinal healthy dog E. coli isolates were genotyped. Questionnaire data were used to formulate independent variables. Statistical analysis included Pearson’s Chi-square, survival analysis and multivariable logistic regression; multilevel for clustered data. The prevalence of meticillin-resistant (MR; 42%) and MDR staphylococci (resistant to ≥ 3 antimicrobial classes; 34%) was high amongst healthy dogs, however MR-coagulase positive staphylococci were not detected. The most common species detected was S. epidermidis (52% of dogs), followed by S. pseudintermedius (44%). S. aureus was only detected in a small number of dogs (8%). Faecal E. coli with AMR to at least one tested drug (63%), MDR (30%) and AmpC-production (16%) were prevalent in healthy dogs, however ESBL-producers (1%) were rare. Healthy dogs carried a predominance of phylogenetic group B1; group B2 E. coli isolates were less likely to have AMR while group D isolates were more likely. Carriage of E. coli with AMR to at least one tested drug was common and persistent, whereas MDR, AmpC- and ESBL-types were intermittent or transient. Genotyping revealed high intra-dog diversity with frequent new genotypes and resistance phenotypes detected over time. AMR staphylococci and E. coli were detected in more dogs following antimicrobial treatment than baseline, but generally returned to pre-treatment levels within three months. Eating raw meat/animal stools, living with other dogs/in-contact humans or pets that had been hospitalised/in-contact humans working with farm animals were associated with the detection of AMR canine commensal bacteria. In particular, following treatment with beta-lactams or fluoroquinolones there was a significant increase in the detection of MDR and AmpC-producing E. coli or MR- and MDR staphylococci, respectively. However significant differences were not detected at one month after the end of treatment. Antimicrobial therapy is a risk factor for antimicrobial resistant commensal bacteria in dogs and recovery may take up to three months after the end of treatment. This highlights the importance of prudent antimicrobial use and prescribing guidelines. However other factors, such as diet, in-contacts, co-selection and bacterial fitness may be involved in the carriage of resistant bacteria and should be considered.