Chromosomal integration of a bcrRABD-carrying integrative and conjugative element increases bacitracin resistance in Clostridium perfringens following restrictions in antimicrobial use in Canadian broiler chickens

Abstract Background In response to the threat of antimicrobial resistance, the Chicken Farmers of Canada banned the prophylactic use of Category II antimicrobials in 2018, thereby increasing the reliance on bacitracin to prevent necrotic enteritis in broiler chickens. This study hypothesised that the significant increase in bacitracin use, a Category III antibiotic, following the ban may have increased the prevalence of bacitracin-resistant Clostridium perfringens isolates. Methods Using genomic analyses, we correlated phenotypic resistance to bacitracin of C. perfringens clinical isolates from the pre-ban ( n = 77) and post-ban ( n = 54) periods with the presence of different bacitracin resistance genes. Results The prevalence of bacitracin-resistant C. perfringens isolates was significantly higher ( p < 0.005) in the post-ban period (48.1%) than in the pre-ban period (23.4%). Genomic analyses revealed the presence of the bcrB and bcrC genes in all isolates, and the bcrA , bcrD and bcrR genes in resistant isolates only. The locus bcrRABD was detected in all resistant isolates and was found to be located on integrative and conjugative elements. Conclusions Our results illustrate that the increased use of bacitracin in Canadian broiler chickens has led to a greater prevalence of C. perfringens resistance to this antimicrobial agent.