The use of disinfectant in barn cleaning alters microbial composition and increases carriage of Campylobacter jejuni in broiler chickens

To maintain food safety and flock health in broiler chicken production, biosecurity approaches to keep chicken barns free of pathogens are important. Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection; FD) and may wash with water (water-wash; WW) throughout the year. However, many producers use FD after each flock, assuming a greater efficacy of more stringent cleaning protocols, although little information is known regarding how these two cleaning practices affect pathogen population and gut microbiota. In the current study, a cross-over experiment over four production cycles was conducted in seven commercial chicken barns to compare WW and FD. We evaluated the effects of barn cleaning method on the commercial broiler performance, cecal microbiota composition, pathogen occurrence and abundance, as well as short-chain fatty acid concentrations in the month-old broiler gut. The 30-day body weight and mortality rate were not affected by the barn cleaning methods. The WW resulted in a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis p = 0.05, and unweighted-UniFrac; adonis p = 0.01), with notable reductions in Campylobacter jejuni occurrence and abundance. In addition, the WW group had increased cecal acetate, butyrate and total short-chain fatty acid concentrations, which were negatively correlated with C. jejuni abundance. Our results support the use of WW over FD to enhance the activity of the gut microbiota and potentially reduce zoonotic transmission of C. jejuni in broiler production without previous disease challenges.