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

Authors: Rothrock, Michael; Min, Byeng Ryel; Castleberry, Bobbie - Lana; Waldrip, Heidi; Parker, David; Brauer, David; PITTA, DIPTA - University Of Pennsylvania; INDUGU, NAGARAJU - University Of Pennsylvania

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/3/2021
Publication Date: 5/4/2021
Citation: Rothrock Jr, M.J., Min, B., Castleberry, B., Waldrip, H., Parker, D.B., Brauer, D.K., Pitta, D., Indugu, N. 2021. Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures. Journal of Animal Science. https://doi.org/10.1093/jas/skab144
DOI: https://doi.org/10.1093/jas/skab144

Interpretive Summary: 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. Bacteria in an animal’s gastrointestinal tract or in the environment after land application of manure exposed to antibiotic residues (ABR) have been recognized as potential sources of antimicrobials and ARG, which can affect environmental, animal and human health. Consequently, we need to understand the environmental impact of antibiotic use in animal production; however, first we must collect essential background information on microbiome diversity and ABR/ARG content in feces from different types of livestock and different production systems. Therefore, scientists from USDA-ARS at Bushland, TX, USDA/ARS, Athens, GA, and University of Pennsylvania, PA, analyzed the effects of pasture-raised livestock and poultry systems on changes in microbiome diversity and the presence of ABR and ARG (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) that contained a diverse range of animal types: pasture-raised poultry (broiler and layer), swine and beef cattle. Results indicated that the Sul1 and TetA ARG in layer hen manure were the highest, followed by broiler chickens, swine and beef cattle. Additionally, fecal microbial richness and abundances differed significantly both among farms and specific species of animal. These data indicate that the microbial diversity, ABR, and ARG concentrations in feces varied from farm-to-farm and from animal type-to-animal type.

Technical Abstract: 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 types: 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 Sul1 (P < 0.05) and TetA (P < 0.001) ARG in layer hen manure were the highest (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 Tet 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, oxytetracycline and sulfachloropyridazine ABR were similar among animal types. There were interactions (P < 0.01) between farms and animal types for fecal pH and concentrations of total carbon, magnesium, sulfur, copper and lead across animal types. Furthermore, fecal microbial richness and abundances differed significantly (P < 0.01) both among farms and specific species of animal. Animal types, total carbon (C), total nitrogen (N), and fecal mineral contents were negatively correlated with fecal TetA concentrations, while fecal pH, ABR (chlortetracycline, lincomycin and tetracycline) and C/N ratios were positively correlated with fecal TetA concentrations. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal type-to-animal type. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic resistant microorganisms (ARM) and AGR.