AMR in E. coli from low-antibiotic use broiler production

Objectives Antimicrobial resistance (AMR) is a major global threat to both human and animal health. This study investigated the occurrence and patterns of AMR in clinical and non-clinical Escherichia coli isolates from broiler flocks raised under low antibiotic use conditions. Methods Clinical isolates (n = 80) were collected at necropsy from the livers of broiler chickens in 40 flocks with increased mortality due to colibacillosis. Non-clinical isolates (n = 109) were obtained from the litter using sock samples from 60 flocks with normal mortality. Susceptibility to 15 antibiotics was assessed using broth microdilution, and whole-genome sequencing was conducted to identify resistance-associated genes and mutations. Results Overall resistance was low, with all isolates susceptible to 9 of the 15 tested antibiotics, including meropenem, azithromycin, amikacin, gentamicin, tigecycline, ceftazidime, cefotaxime, chloramphenicol, and colistin. Resistance was significantly more frequent in non-clinical than in clinical isolates and was strongly correlated with the presence of known AMR genes or mutations. Among clinical isolates, 93.7% were fully susceptible to all tested antibiotics, compared to 49.5% of non-clinical isolates. The highest resistance rates were observed in non-clinical isolates against ampicillin (34%), sulfamethoxazole (32.1%), and trimethoprim (28.4%). Conclusions Higher AMR rates in non-clinical isolates compared to clinical isolates suggest that commensal E. coli may serve as reservoirs of resistance genes. Since antibiotics are rarely used in Swedish broiler production, these findings suggest that factors beyond direct antibiotic use—such as horizontal gene transfer, vertical transmission, and environmental contamination—may contribute to AMR dissemination.