Antimicrobial resistance profiles in Escherichia coli isolated from whole-chicken carcasses from conventional, antibiotic-free, and organic rearing systems

Antimicrobial resistance (AMR) is a growing concern in human and animal health. Public discussions on these issues have contributed to an increased demand for antibiotic-free food. Studies comparing the antimicrobial resistance profiles of bacteria in foodstuffs originating from farming systems with restrictions on the use of antimicrobials are scarce. This study aimed to assess the antimicrobial resistance profiles of generic Escherichia coli isolated from whole chickens originating from farming systems with and without restrictions on the use of antimicrobials. For this purpose, three groups of E. coli strains were formed: (GC) from chickens reared in conventional production systems, without restriction on the use of antimicrobials (n=72); (GL) from chickens reared in farming systems certified as free of any antibiotic use (n=72); and (GO) from chickens from an organic farming system (n=72). Whole chicken units were individually rinsed as recommended by ISO 17604:2015, and E. coli was isolated from the rinse suspension. To evaluate the resistance profile, E. coli strains were tested against 12 antimicrobials using broth microdilution or disk diffusion tests. Eighty strains (40.7%) were found to be fully susceptible to the tested antimicrobials, and 23.6% were multidrug resistant. The highest frequencies of resistance were observed to tetracycline (GC=37,5%; GL=34,7%; GO=25%) and trimethoprim (GC=27,8%; GL=34,7%; GO=22,2%). In the case of multidrug resistant strains, GC presented 32% (n=23) of strains with multidrug resistance characteristics whereas the GL and GO groups presented 22% (n=16) and 17% (n=12), respectively. As for the totally susceptible strains, a frequency of 56% of Tsus strains was observed in the organic group, whereas this frequency was 33% in the GC and GL groups. Using GC as a reference, the Poisson regression model showed a higher occurrence of fully susceptible E. coli strains, as well as lower frequencies of multidrug resistance and resistance to ampicillin and nalidixic acid in GO. The GL group exhibited the lowest frequency of ampicillin resistance. These observations suggest that the lower selection pressure for antimicrobial use in the farming system may be reflected in the resistance profile of bacteria present in foodstuffs purchased by consumers.