Comprehensive analysis of antimicrobial resistance dynamics in broiler and duck production systems

This study provides a comprehensive analysis of antimicrobial resistance (AMR) dynamics in broiler and duck production systems, focusing on resistance diversity, abundance, and associated microbial taxa across the rearing phases (starter, grower, and finisher). A total of 3,669 distinct AMR types were identified, with broilers exhibiting a slightly broader spectrum (1,918 types) compared to ducks (1,747 types). Host-specific AMRs accounted for 25.3% (592 types) in broilers and 18% (421 types) in ducks, while 56.7% (1,326 of 2,339 types) of AMRs were shared across both hosts. AMR diversity declined significantly from the starter to finisher phases in both birds, with broilers experiencing a 641-type reduction compared to a 308-type reduction in ducks. However, AMR frequencies increased by the time they reached the finisher phase in both broilers and ducks, exhibiting significantly higher values compared to those observed in the starter phase (p < 0.0001). Thirteen poultry core high-resistance carrier (HRC) species were identified, shared between both hosts, indicating a poultry core microbiome with high resistance potential. Broiler-specific HRCs exhibited a significantly higher (p = 0.035) relative abundances (0.08) compared to duck-specific HRCs (0.003), despite a smaller number of unique species. Environmental and biological samples revealed significant microbial overlaps, with diagnostic panels identifying 15 biomarker species in broiler environments and 9 in duck environments, each strongly correlated with poultry-core HRCs (correlation coefficient > 0.7). Notably, host-specific patterns in differentially abundant resistance markers were observed, with penam resistance dominating in ducks (log2 reads: 19.46 for tet(36)) and macrolide resistance in broilers (log2 reads: 8.89 for msrA).