Implementation and analysis of an on-farm surveillance system for enteric bacteria in Canadian dairy herds

Antimicrobial resistance (AMR) is an increasing concern for public and animal health as it diminishes the effectiveness of antimicrobials against resistant bacteria and make treatments more difficult and expensive. The research documented in this thesis aimed to describe the development and implementation of CaDNetASR, an on-farm surveillance system focused on collecting data on antimicrobial use (AMU) and AMR in enteric bacteria (E. coli, Campylobacter spp., and non-typhoidal Salmonella serovars) from Canadian dairy farms. The research also included the use of the data collected through CaDNetASR surveillance to describe the phenotypic resistance patterns of E. coli, Campylobacter spp., and Salmonella, and explore the association between AMU and AMR in Canadian dairy herds. The surveillance was implemented in the fall of 2019, and the data were collected yearly from a convenience sample of 144 dairy herds from five different provinces in Canada. Fecal samples from pre-weaned calves, post-weaned heifers, lactating cows, and manure storage were collected. Additionally, herd health, herd management and AMU information were gathered. Fecal samples were cultured for E. coli, Campylobacter spp., and Salmonella. Susceptibility testing on the stored isolates was done using the broth microdilution system method. The proportion of farms positive for Campylobacter spp. was 95.7%, suggesting that these bacteria are widespread among Canadian dairy herds. For Salmonella, the proportion of positive farms was lower ranging from 12% to 17% from 2019 to 2021. No Salmonella Dublin was identified. A higher proportion of resistance to tetracycline than other antimicrobials was observed for all three bacteria. For E. coli a low proportion of resistance was observed to highly important antimicrobials; however, for Campylobacter spp., 19.9% of the isolates were resistant to ciprofloxacin. No resistance was observed to highly important antimicrobials on Salmonella isolates, except for one isolate resistant to amoxicillin/clavulanic acid. The AMU was quantified in Defined Course Dose (DCD - the dose for a standardized complete treatment course on a standard size animal) and converted to a rate indicator - DCD/100 animal-years. The total AMU was split into systemic and intramammary routes of administration to explore the possible differences according to the administration route. Overall, the AMU varied substantially among the dairy farms. Regression models were built to explore the association of AMU and AMR in E. coli and Campylobacter spp. isolates. For Campylobacter spp., only the total AMU was associated with increased resistance to tetracycline. In E. coli, the systemic AMU was associated with increased resistance to nine antimicrobials; however, the intramammary AMU was not significantly associated with resistance. Overall, resistance in dairy farms was low compared to other food-producing animals such as poultry or swine. The findings documented in this thesis provided information that can be used in the future to develop interventions aiming to reduce the use of antimicrobials in dairy farms and promoting more sustainable and responsible husbandry practices.