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 (ARG) 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 (ABR) 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 ARG (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR. 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 µg kg -1, respectively) followed by broiler chickens (2.9 x 10 -4 and 1.7 x 10 -4 µg kg -1, respectively), swine (0.22 x 10 -4 and 0.20 x 10 -4 µg kg -1, respectively) and beef cattle (0.19 x 10 -4 and 0.02 x 10 -4 µg kg -1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg -1) than for other animal species (1.8-0.06 µg kg -1), while chlortetracycline, lincomycin, and oxytetracycline ABR 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 (ARM) and ARG.