Temperature, humidity and both bacterial species abundance and the presence of antibiotic resistance genes (ARGs) 7, 8, 9 can influence bacterial infection in broilers 10. External events such as changes in diet, temperature and stress 4, 5 may result in the colonization of new resident species or AMR transfer between species 6. Antibiotic use, even at low levels, alters and expands the gut resistome in livestock 2, and the microbial community can shape antimicrobial resistance (AMR) phenotypes 3. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.Īntimicrobial use in poultry production in China is five times higher than the international average 1. Temperature and humidity in the barns were also correlated with ARG presence. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread.
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