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

Abstract

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 β-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%), blaTEM-1B, and sul2 (24.3%, each), which are responsible for resistance to tetracyclines, aminoglycosides, β-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 blaTEM (29.7%), blaCTX m (13.5%), and blaCMY (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.