Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy

Simple Summary Antibiotic resistance represents an emergent threat for animals, humans, and the environment. Food-producing animals are directly involved in the dissemination and maintenance of resistant bacteria and their genetic determinants. The genes responsible for resistance mechanisms in bacteria can be located at the chromosomal level or in extra-chromosomal mobile genes, and are transferrable to other bacteria by different modalities. The use of antibiotics in livestock can exercise a selective pressure on resistance determinants and their persistence in intestinal microbiota. In this respect, poultry farming represents a potential driver of resistance genes as these genes can reach the environment or the food chain from poultry litter. In this study, litter samples from conventional flocks (where antibiotics are allowed only for therapeutic purposes) and antibiotic-free farms (where these molecules are excluded) are screened for some resistance genes against antibiotics routinely used in veterinary practice (tetracyclines, aminoglycosides, lincomycin), along with some critically/highly important antibiotics exclusively intended for humans (chloramphenicol, colistin, vancomycin, carbapenems). The results showed the presence of several resistance genes in poultry litter from both farming systems. Interestingly, the highest positivity was observed for tetracycline genes in antibiotic-free flocks, raising some concerns about the role of alternative farming systems in the reduction in antibiotic resistance in food-producing animals. Antimicrobial resistance is a complex and widespread problem threatening human and animal health. In poultry farms, a wide distribution of resistant bacteria and their relative genes is described worldwide, including in Italy. In this paper, a comparison of resistance gene distribution in litter samples, recovered from four conventional and four antibiotic-free broiler flocks, was performed to highlight any influence of farming systems on the spreading and maintenance of resistance determinants. Conventional PCR tests, targeting the resistance genes related to the most used antibiotics in poultry farming, along with some critically important antibiotics for human medicine, were applied. In conventional farms, n. 10 out of n. 30 investigated genes were present in at least one sample, the most abundant fragments being the tet genes specific for tetracyclines, followed by those for aminoglycosides and chloramphenicol. All conventional samples resulted negative for colistin, carbapenems, and vancomycin resistance genes. A similar trend was observed for antibiotic-free herds, with n. 13 out of n. 30 amplified genes, while a positivity for the mcr-1 gene, specific for colistin, was observed in one antibiotic-free flock. The statistical analysis revealed a significant difference for the tetM gene, which was found more frequently in the antibiotic-free category. The analysis carried out in this study allowed us to obtain new data about the distribution of resistance patterns in the poultry industry in relation to farming types. The PCR test is a quick and non-expensive laboratory tool for the environmental monitoring of resistance determinants identifying potential indicators of AMR dissemination.