Antibiotic resistance, antimicrobial residues, and bacterial community diversity in pasture-raised poultry, swine, and beef cattle manures

Animal manure can be a source of antibiotic-resistant genes (ARGs) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABRs) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine, and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARGs (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR (real-time PCR). Results indicated that the ARG abundances (Sul1 [P < 0.05] and TetA [P < 0.001]) were higher in layer hen manures (16.5 x 10(-4) and 1.4 x 10(-4) mu g kg(-1), respectively) followed by broiler chickens (2.9 x 10(-4) and 1.7 x 10-4 mu g kg(-1), respectively), swine (0.22 x 10(-4) and 0.20 x 10(-4) mu g kg(-1), respectively) and beef cattle (0.19 x 10(-4) and 0.02 x 10(-4) mu g kg(-1), respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 mu g kg(-1)) than for other animal species (1.8 to 0.06 mu g kg(-1)), while chlortetracycline, lincomycin, and oxytetracycline ABRs were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic-resistant microorganisms (ARMs) and ARG.