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Abstract
Poultry raised without the use of antibiotics is becoming an increasingly popular option within the poultry meat market. The transition to a no antibiotics ever (NAE) production is accompanied by substantial knowledge gaps regarding the dynamics of the gut microbiota and the occurrence of enteric pathogens. The following study assessed the effect of supplementation with antibiotics in broiler chicken diets on the gut microbiota and incidence of foodborne pathogens. A microbiome comparative analysis between conventional and NAE broilers identified distinct shifts in gut microbial populations. Chicken raised without the use of antibiotics carried an intestinal microbiota with a lower species number but a higher taxonomic diversity. Furthermore, the abundance of beneficial genera Bifidobacterium, Ligilactobacillus, and Alistipes was higher in NAE raised chicken (P 0.05). Conventionally raised broilers harbored higher intestinal populations of Escherichia and Clostridium_P. Broilers from conventional farms also exhibited higher rates of Salmonella infection during early rearing stages (P 0.05), although no major differences were reported at the end of the grow-out cycle. Greater Campylobacter prevalence was observed on all farms, but the organism had a lower prevalence in farms with prolonged antibiotic administration (P 0.05). The pathogen exhibited its characteristic patterns of colonization and horizontal spread, reaching a 100% positive rate and intestinal microbial loads of 7 log10 CFU/g during early grow-out. In addition, differential abundance analysis of microbiome data showed a higher representation of Campylobacter in NAE broilers (P 0.05). The incidence of antimicrobial resistance (AMR) was higher among Salmonella isolates (76%) compared to that of Campylobacter (3.5%). However, the latter carried resistance to ciprofloxacin (1.2%), an antibiotic of clinical importance. This research identified important shifts in gut microbial community dynamics and foodborne pathogen prevalence associated with antibiotic administration within commercial poultry operations.