Longitudinal mapping of microbiome and antibiotic resistance dynamics in the yellow-feathered broiler production chain

Abstract Yellow-feathered broilers (YFBs), an important Asian protein source, undergo extended rearing and multi-stage supply chains that may promote microbiota succession and antibiotic resistance gene (ARG) dissemination, posing One Health risks. Through longitudinal tracking of 57 YFBs across farm (days 1, 31, and 57), slaughterhouse (day 59), and retail (day 60) stages, integrating 16S rRNA sequencing, metagenomics, machine learning, and Bayesian modeling, we characterized microbial and ARG dynamics. Farm-associated Enterococcus faecalis MAGs contained lsa(A) and vanR , with model-based inference supporting stage-associated diffusion from feces to evisceration carcasses (Bayes factor > 100; mean rate = 1.07). At slaughter, MAGs assigned to Algoriella xinjiangensis and containing predicted blaB -like beta-lactamase genes, annotated as encoding BlaB/IND/MUS family subclass B1 metallo-beta-lactamases, were enriched on carcasses and remained detectable at retail. Cold-chain logistics were associated with model-inferred ARG flow and possible contamination exchange across slaughterhouse and retail stages. Pre-chilling emerged as a pivotal control point associated with marked microbiota and ARG restructuring. This first comprehensive production-chain mapping identifies cold chain-associated contamination-exchange risks and pre-chilling as a priority intervention target for mitigating ARG dissemination in global poultry systems.