Effects of pulsed in-feed antimicrobials on chicken fecal resistome

Abstract Background: Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect the fecal resistome. Here we used metagenomic approach to investigate the effects of pulsed antimicrobial administration on chicken fecal resistome. Chickens received three 5-day-course of alone/combined antimicrobials at therapeutic dose, including amoxicillin, chlortetracycline and florfenicol. Chicken feces was collected on T0 (before treatment), T5 (after first treatment), T10 (after second treatment), T15 (after third treatment) at the chicken age of 40 days that are ready for slaughter. Results: Tetracycline resistance gene and polymyxin resistance gene only responded to chlortetracycline and amoxicillin, respectively. The tetracycline resistance gene tetC significantly increased from T0 to T15 in chlortetracycline group. The multidrug resistance gene acrB, acrF, mdtA, mdtK and CRP only occurred significant increase in amoxicillin group (P<0.05). Klebsiella significantly decreased from T0 to T10 in florfenicol group, while significantly increased from T0 to T15 in chlortetracycline group (P<0.05). Amoxicillin did not lead significant change to Klebsiella. Escherichia was always the major host for multidrug resistance genes. ARG-harboring Escherichia increased mainly due to the antimicrobial selection for β-lactam, tetracycline, chloramphenicol resistance genes they harbored. Conclusions: The results indicated that the effects induced by amoxicillin, chlortetracycline and florfenicol significantly shaped the fecal microbiome and resistome. We provided a comprehensive insight into antimicrobial-mediated alteration of chicken fecal microbiome and resistome. These findings will give suggests to veterinarian for combating antimicrobial resistance in broiler chicken production.