Herd-level Risk Factors Associated with Antimicrobial Susceptibility Patterns and Distributions in Fecal Bacteria of Porcine Origin.

The purpose of this dissertation is threefold: to determine the differences in apparent prevalence and the antimicrobial susceptibility of Campylobacter spp. between antimicrobial-free and conventional swine farms; secondly, to introduce an appropriate statistical model to compare the minimum inhibitory concentration distributions of Escherichia coli and Campylobacter spp. isolated from both farm types; and thirdly, to examine the potential herd level risk factors that may be associated with antimicrobial resistance of Campylobacter spp. and E. coli isolates from finishers on antimicrobial-free and conventional farming systems. In addition, a critical review of studies that have compared the levels and patterns of antimicrobial resistance among animals from antimicrobial-free and conventional farming practices was performed.

Fecal samples from 15 pigs were collected from each of 35 antimicrobial-free and 60 conventional farms in the Midwestern U.S. Campylobacter spp. was isolated from 464 of 1,422 fecal samples, and each isolate was tested for susceptibility to 6 antimicrobials. The apparent prevalence of Campylobacter spp. isolates was approximately 33 percent on both conventional and antimicrobial-free farms. The proportion of antimicrobial resistance among Campylobacter was higher for three antimicrobials within conventional compared to antimicrobial-free farms.

The susceptibilities of populations of bacteria to antimicrobial drugs were summarized as minimum inhibitory concentration (MIC) frequency distributions. The use of MIC values removed the subjectivity associated with the choice of breakpoints which define an isolate as susceptible or resistant. A discrete-time survival analysis model was introduced as the recommended statistical model when MICs are the outcome.

A questionnaire was completed by each farm manager on biosecurity, preventive medication, vaccines, disease history, and production management. Multivariable population-averaged statistical models were used to determine the relationships among antimicrobial susceptibility patterns and potential herd-level risk factors. Controlling for herd type (antimicrobial-free versus conventional), each antimicrobial-bacterial species combination yielded unique combinations of risk factors; however, housing type, history of rhinitis, farm ventilation, and history of swine flu were significant in more than one model. A variety of herd-level practices were associated with the prevalence of antimicrobial resistance on swine farms. Further studies are encouraged when considering interventions for antimicrobial resistance on both antimicrobial-free and conventional farms.