Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut

Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of treatment and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR), due to their antimicrobial properties, and the ability of bacteria to evolve resistance to these drugs.. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons. In this study, we use metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. Additionally, we explore the mobile fraction of the resistome, the total of ARGs in a sample, investigating ARGs identifying investiARGs with the potential to disseminate within and beyond farm settings. Our findings reveal significant variation in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identify 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans. Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.