Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia

Simple Summary Antimicrobial resistance (AMR) is a major concern for animal and human health. The use of antimicrobials is the main factor contributing to the development of AMR in food-producing animals but is unlikely to be the only factor. It is important to determine if antimicrobial use in a feedlot setting contributes to the overall resistance burden and what proportion of animals may already harbour resistant bacteria at feedlot entry. This project aimed to assess the level of AMR in E. coli isolated from beef cattle in South Australia at two time points, the entry and exit (at slaughter) from the beef feedlot. AMR frequency in E. coli isolated from entry compared to exit increased for tetracycline (0 to 17.8%), ampicillin (0.7 to 5.4%), streptomycin (0.7 to 4.7%), and sulfisoxazole (0 to 3.9%). Therefore, the regular inspection of these bacteria and their resistance determinants in food animals would be crucial to tracking changes in AMR and applying control mechanisms. This study investigated the antimicrobial resistance (AMR) profile of fecal Escherichia coli isolates from beef cattle (n = 150) at entry and exit from an Australian feedlot. Sample plating on MacConkey agar and Brilliance ESBL agar differentiated generic from extended-spectrum beta-lactamase (ESBL)-producing E. coli, respectively. Resistance profiles were determined by minimum inhibitory concentration (MIC) testing and further analyzed by whole-genome sequencing (WGS). At entry, the prevalence of antimicrobial resistance to amoxicillin/clavulanic acid, ampicillin, streptomycin, and trimethoprim/sulfamethoxazole was very low (0.7%, each). At the exit, the resistance prevalence was moderate to tetracycline (17.8%) and low to ampicillin (5.4%), streptomycin (4.7%), and sulfisoxazole (3.9%). The most common AMR genes observed in phenotypically resistant isolates were tet(B) (43.2%), aph(3 '')-Ib and aph(6)-Id (32.4%), bla(TEM-1B), and sul2 (24.3%, each), which are responsible for resistance to tetracyclines, aminoglycosides, beta-lactams, and sulfonamides, respectively. The ESBL-producing E. coli were recovered from one sample (0.7%) obtained at entry and six samples (4.0%) at the exit. The ESBL-producing E. coli harbored bla(TEM) (29.7%), bla(CTX m) (13.5%), and bla(CMY) (5.4%). The resistance phenotypes were highly correlated with resistance genotypes (r >= 0.85: p < 0.05). This study demonstrated that E. coli isolated from feedlot beef cattle can harbour AMR genes, but the low incidence of medically important resistance reflected the prudent antimicrobial use in the Australian industry.