Over two and a half years, researchers at the University of Nottingham analysed microbiomes from chickens, carcasses and environments. The resulting network of correlations between livestock, environments, microbial communities and antimicrobial resistance suggests multiple routes for improving antimicrobial resistance surveillance in livestock production.
The findings also show that a core subset of the chicken gut microbiome, featuring clinically relevant bacteria and antibiotic resistance genes correlates with AMR profiles of E. coli, colonizing the gut. Notably, this core, which contains clinically high transmissible ARGs shared by chickens and environments, is influenced by environmental temperature and humidity, and correlates with antimicrobial usage.
In many countries, chickens are housed in sheds that do not have an effective climate control system, and therefore experience substantial temperature and humidity variations. The study results indicate that the core features of the gut microbial community and resistome, found to be correlated with resistance in E. coli, are also correlated with changes in temperature and humidity in chicken housing.