Antibiotic susceptibility and resistance genes in Escherichia coli from broilers reared in a low-antibiotic-use production system

Antimicrobial resistance (AMR) is a major global concern for animal and human health. This study investigated the occurrence and patterns of AMR in Escherichia coli (E. coli) isolated from Swedish broiler flocks reared under low-antibiotic-use conditions. During routine necropsy examinations of 80 broilers from 40 flocks with increased mortality associated with colibacillosis, liver samples were collected for bacteriological analysis. E. coli isolated from the liver were classified as clinical E. coli. In addition, boot sock samples were taken to collect feces from the litter of 60 broiler flocks with no signs of disease or increased mortality. E. coli isolates (n = 109) obtained from boot sock samples were classified as non-clinical E. coli. Susceptibility to 15 antibiotics was assessed using broth microdilution, and resistance-associated genes and mutations were identified through whole-genome sequencing (WGS). Overall resistance was low, with all isolates susceptible to 9 of the 15 tested antibiotics: meropenem, azithromycin, amikacin, gentamicin, tigecycline, ceftazidime, cefotaxime, chloramphenicol, and colistin. Resistance was significantly more frequent in non-clinical than clinical isolates for the six antibiotics with detected resistance (P < 0.05) 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 with 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%). The results of this study indicate that in low-antibiotic-use production systems, factors beyond direct antibiotic use-such as horizontal gene transfer, vertical transmission, and environmental contamination-may contribute to AMR dissemination. Higher AMR rates in non-clinical isolates suggest that these isolates may serve as reservoirs of resistance genes. This highlights the importance of monitoring commensal E. coli and farm environments to support AMR mitigation and sustainable broiler production.