Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems

The aim of this study was to investigate the microbial composition, and the profiles of antimicro-bial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production sys-tems (CO), certified antimicrobial-free intensive produc-tion systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses accord-ing to a cross-sectional study design. Shot-gun metage-nomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha-and beta-microbial diversity, the abundance of some taxa dif-fered significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212; blaOXA-275 and ompA), aminoglycosides (aph(30)-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lin-cosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson = s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.

Automated summary

This study investigated the microbial composition, abundance of antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) in retail chicken carcasses from different production systems. Although there were no differences in microbial diversity, certain taxa, including spoilage-associated organisms, showed significant differences across the groups. The co-resistome comprised 29 shared ARGs, and their abundance was lower in chicken carcasses from certified antimicrobial-free intensive production systems (AF) and certified organic production systems with restricted antimicrobial use (OR) compared to conventional intensive production systems (CO). Transposases were the most abundant MGEs, with a higher abundance in CO compared to OR.