Prevalence and Risk Factors for Antimicrobial Resistance on U.S. Dairy Operations

Antimicrobial resistance has become a major public health concern and animal agriculture is often implicated as a source of resistant bacteria. The primary objective of this study was to determine prevalence of antimicrobial resistance in Salmonella and E. coli from healthy animals on dairy farms in Pennsylvania. Confidence intervals (CI) of farm prevalence were calculated for resistance and the comparisons between different animal groups were adjusted for within-farm clustering. The secondary objective was to identify potential risk factors associated with antimicrobial resistance. In particular, we investigated the correlations between previous antimicrobial use and current resistance in E. coli using multiple logistic regression models. A total of 444 composite manure samples were collected from 80 herds in Pennsylvania. Four age and production groups were included: pre-weaned calves, post-weaned calves, dry cows, and lactating cows. E. coli (n=2370) and Salmonella (n=1095), when isolated from the manure composite samples (n=444), were screened for resistance on antimicrobial supplemented agar. Isolates of interest were further essayed against 14 antimicrobials using a broth microdilution method. Salmonella was isolated from at least one composite manure sample from 51 (67%) farms with 99% being pan-susceptible, and was detected more frequently in lactating cows and dry cows than pre- and post-weaned calves. The most prevalent Salmonella serogroups were K, C1 and C2. Among the E. coli isolates, resistance was more frequently detected in pre-weaned and post-weaned calves than in dry and lactating cows for all 14 antimicrobials tested (P < 0.05). Multi-drug resistance (resistant to ≥3 antimicrobial classes) in E. coli was detected in 66 farms (83%) and was detected more often in pre-weaned calves (P < 0.05). The bla_CTX-M and bla_CMY genes were found in cephalosporin-resistant E. coli from 5% and 35% of the farms surveyed, respectively. A number of risk factors, including antimicrobial use, were found to be associated with an increased likelihood of resistance in E. coli, and these associations were not limited to the same antimicrobial classes. The results of this study showed dairy farms, especially pre-weaned calves and their environment, are significant reservoirs for antimicrobial resistance, and antimicrobial use may aggravate the resistance problem.