Abundance and diversity of the faecal resistome and microbiome in broilers

Antimicrobial resistance (AMR) is a growing problem, posing a threat to human and animal health. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands continuous surveillance in livestock and in humans. Although there are numerous studies to determine the fecal carriage of antibiotic-resistant bacteria in broiler flocks, there is a lack of comprehensive metagenomic research targeting the resistome in broilers in Türkiye. The aim of this study was to investigate the microbial composition and the profiles of antimicrobial resistance genes (ARGs, resistome) in three selected broiler farms in Hatay, using a shotgun metagenomics approach. The microbiota of broilers from Flock A and C was dominated by Bacillota (formerly Firmicutes) (46.83% and 43.87%, respectively), whereas Flock B exhibited a high relative abundance of Pseudomonadota (formerly Proteobacteria) (82.5%). At the genus level, Brachybacterium, Escherichia, and Ligilactobacillus were significantly more abundant in Flocks A, B, and C, respectively. It was also noticed that the most abundant KEGG pathways belonged to metabolism and genetic information processing. Furthermore, xenobiotics biodegradation and metabolism pathways were more abundant in Flock B than in Flocks A and C. Similarly, a higher ARG diversity was observed in Flock B. A total of 137 ARGs were identified, comprising different resistance mechanisms. The MLS23S gene, conferring macrolide resistance through a 23S rRNA gene mutation, was the predominant ARG in all flocks. These findings provide a baseline characterization of the broiler gut resistome, highlighting the importance of metagenomic surveillance in poultry production despite the unavailability of farm-level antimicrobial usage records.