Abstract
It has been proposed that livestock production effluents such as wastewater, airborne dust and manure increase the density of antimicrobial resistant bacteria and genes in the environment. The public health risk posed by this proposed outcome has been difficult to quantify using traditional microbiological approaches. We utilized shotgun metagenomics to provide a first description of the resistome of North American dairy and beef production effluents, and identify factors that significantly impact this resistome. We identified 34 mechanisms of antimicrobial drug resistance within 34 soil, manure and wastewater samples from feedlot, ranch and dairy operations. The majority of resistance-associated sequences found in all samples belonged to tetracycline resistance mechanisms. We found that the ranch samples contained significantly fewer resistance mechanisms than dairy and feedlot samples, and that the resistome of dairy operations differed significantly from that of feedlots. The resistome in soil, manure and wastewater differed, suggesting that management of these effluents should be tailored appropriately. By providing a baseline of the cattle production waste resistome, this study represents a solid foundation for future efforts to characterize and quantify the public health risk posed by livestock effluents.
Highlights
Medically important[14,15]
Pre-weaned dairy calves are most commonly treated for respiratory disease and diarrhea, with phenicols, cephalosporins, macrolides, sulfonamides, tetracyclines and aminoglycosides all used in approximately the same proportions[16]. Given these use practices and evidence that antimicrobial drug residues in livestock effluent can contribute to elevated antimicrobial resistance (AMR) levels, it is important to improve our understanding of how current management systems may impact AMR transmission to the public
A conventional and an organic dairy were chosen to investigate the impact of antimicrobial use practices on the resistome; a US and a Canadian feedlot were chosen to explore the impact of diet (US feedlots typically feed corn-based diets, while Canadian feedlots utilize barley); and a cow-calf ranch was selected to compare resistome differences between intensive and extensive production systems
Summary
Medically important[14,15]. Macrolides, which are classified as critically important, are the second most commonly administered antimicrobial[13,15]. Pre-weaned dairy calves are most commonly treated for respiratory disease and diarrhea, with phenicols, cephalosporins, macrolides, sulfonamides, tetracyclines and aminoglycosides all used in approximately the same proportions[16] Given these use practices and evidence that antimicrobial drug residues in livestock effluent can contribute to elevated antimicrobial resistance (AMR) levels, it is important to improve our understanding of how current management systems may impact AMR transmission to the public. Pan-microbial approaches enable access to this microbial resistance ecology and provide information on how livestock production practices influence the density and composition of ARGs (i.e., the resistome[26]). With this insight, practical mitigation strategies can be proposed to minimize the flow of ARGs into aquatic, terrestrial and atmospheric ecosystems. A conventional and an organic dairy were chosen to investigate the impact of antimicrobial use practices on the resistome; a US and a Canadian feedlot were chosen to explore the impact of diet (US feedlots typically feed corn-based diets, while Canadian feedlots utilize barley); and a cow-calf ranch was selected to compare resistome differences between intensive (i.e., feedlot) and extensive (i.e., pastured) production systems
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