Antimicrobial resistance trends among canine Escherichia coli isolated at a New York veterinary diagnostic laboratory between 2007 and 2020

Abstract

Dogs are a potential source of drug-resistant Escherichia coli, but very few large-scale antimicrobial resistance surveillance studies have been conducted in the canine population. Here, we assess the antimicrobial susceptibility patterns, identify temporal resistance and minimum inhibitory concentration (MIC) trends, and describe associations between resistance phenotypes among canine clinical E. coli isolates in the northeastern United States. Through a retrospective study design, we collected MICs from 7709 E. coli isolates from canine infections at the Cornell University Animal Health Diagnostic Center between 2007 and 2020. The available clinical data were limited to body site. Isolates were classified as resistant or susceptible to six (urinary) and 22 (non-urinary) antimicrobials based on Clinical and Laboratory Standards Institute breakpoints. We used the Mann-Kendall test (MKT) and Sen's slope to identify the presence of a significant trend in the percent of resistant isolates over the study period. Multivariable logistic regression (MLR) models were built with ceftiofur, enrofloxacin, or trimethoprim-sulfamethoxazole resistance as the outcome and either body site and isolation date, or resistance to other antimicrobials as predictors. MIC trends were characterized with survival analysis models, controlling for body site and year of isolation. Overall, 16.4% of isolates were resistant to enrofloxacin, 14.3% to ceftiofur, and 14% to trimethoprim-sulfamethoxazole. The MKT and Sen's slope revealed a significant decreasing temporal trend for gentamicin and trimethoprim-sulfamethoxazole resistance among non-urinary isolates. No significant temporal resistance trends were detected by MKT for other antimicrobials. However, controlling for body-site in MLR models identified a decrease in resistance rates to enrofloxacin and trimethoprim-sulfamethoxazole after 2010. Similarly, survival analysis data confirmed these findings and showed a decrease in MIC values after 2010 for gentamicin and trimethoprim-sulfamethoxazole, but an increase in cephalosporin MICs. MLR showed that non-urinary isolates were significantly more likely than urinary isolates to demonstrate in vitro resistance to ceftiofur, enrofloxacin, and trimethoprim-sulfamethoxazole after controlling for year of isolation. We identified a higher level of ceftiofur resistance among enrofloxacin resistant isolates from urinary and non-urinary origins. Our findings confirmed that dogs are still a non-negligeable reservoir of drug-resistant E. coli in the northeastern United States. The increase in extended-spectrum cephalosporin MIC values in 2018–2020 compared to 2007–2010 constitutes a particularly worrying issue; the relationship between ceftiofur and enrofloxacin resistance suggests that the use of fluoroquinolones could contribute to this trend. Trimethoprim-sulfamethoxazole may be a good first-line choice for empiric treatment of E. coli infections; it is already recommended for canine urinary tract infections.