Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems.
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.
Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
Noelle R
NR
Noyes
Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
Xiang
X
Yang
Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
Lyndsey M
LM
Linke
Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
Roberta J
RJ
Magnuson
Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada.
Shaun R
SR
Cook
Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada.
Rahat
R
Zaheer
Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
Hua
H
Yang
Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
Dale R
DR
Woerner
Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
Ifigenia
I
Geornaras
Department of Population Medicine &Diagnostic Sciences, Cornell University, Ithaca, NY, USA.
Jessica A
JA
McArt
Centre for Food-borne, Environmental Zoonotic Infectious Diseases, Public Health Agency of Canada, University of Saskatoon, Saskatchewan, Canada.
Sheryl P
SP
Gow
Department of Computer Sciences, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA.
Jaime
J
Ruiz
Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Denver, CO, USA.
Kenneth L
KL
Jones
Department of Computer Sciences, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA.
Christina A
CA
Boucher
Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB, Canada.
Tim A
TA
McAllister
Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
Keith E
KE
Belk
Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
Paul S
PS
Morley
D000818:Animals; D044822:Biodiversity; D002170:Canada; D002417:Cattle; D016000:Cluster Analysis; D004352:Drug Resistance, Microbial; D058751:Livestock; D008372:Manure / Q000382:microbiology*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D012988:Soil Microbiology; D014481:United States; D014866:Waste Products; D062065:Wastewater / Q000382:microbiology*
D008372:Manure; D014866:Waste Products; D062065:Wastewater