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Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems.

Noyes NR, Yang X, Linke LM, Magnuson RJ, Cook SR, Zaheer R, Yang H, Woerner DR, Geornaras I, McArt JA, Gow SP, Ruiz J, Jones KL, Boucher CA, McAllister TA, Belk KE, Morley PS - Sci Rep (2016)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.

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.

No MeSH data available.


Related in: MedlinePlus

A comparison of fecal samples collected from calves and adult cattle.(A) NMDS ordination of fecal sample resistomes from calf vs. adult cattle. (B) Proportion of all aligned reads that aligned to ARGs within different resistance classes, in adult cattle versus calf feces. MDR = Multi-drug resistant mechanisms; MLS = Macrolide-lincosamide-streptogramin.
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f1: A comparison of fecal samples collected from calves and adult cattle.(A) NMDS ordination of fecal sample resistomes from calf vs. adult cattle. (B) Proportion of all aligned reads that aligned to ARGs within different resistance classes, in adult cattle versus calf feces. MDR = Multi-drug resistant mechanisms; MLS = Macrolide-lincosamide-streptogramin.

Mentions: The resistome of fecal samples collected from preweaned dairy calves was different from that of mature cattle of all types (Stress = 0.11 and 0.03, ANOSIM R = 0.28 and 0.41, ANOSIM P = 0.05 and 0.02 at the mechanism and class levels, respectively, Fig. 1). Shannon’s diversity and richness at the mechanism and class levels were both lower in adult cattle compared to calf feces (Kruskal-Wallis P = 0.02 and 0.05 for richness and P = 0.09 and 0.09 for Shannon’s diversity, respectively). A descriptive comparison of dairy calf and adult dairy cow feces reflects this same pattern (Fig. 2), suggesting that production system (i.e., beef versus dairy) was not confounding this comparison and that the resistome of adult cattle feces is less diverse than that of calves. In addition, sequencing depth and DNA quantity and quality were not significantly different between samples collected from calves and samples collected from adult cattle, providing further evidence that resistome differences between these samples were not artifactual. Previous studies in calves have documented significant changes in fecal microbial diversity and composition as calves moved from milk-fed to weaning4243 and these changes could be driving resistome composition.


Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems.

Noyes NR, Yang X, Linke LM, Magnuson RJ, Cook SR, Zaheer R, Yang H, Woerner DR, Geornaras I, McArt JA, Gow SP, Ruiz J, Jones KL, Boucher CA, McAllister TA, Belk KE, Morley PS - Sci Rep (2016)

A comparison of fecal samples collected from calves and adult cattle.(A) NMDS ordination of fecal sample resistomes from calf vs. adult cattle. (B) Proportion of all aligned reads that aligned to ARGs within different resistance classes, in adult cattle versus calf feces. MDR = Multi-drug resistant mechanisms; MLS = Macrolide-lincosamide-streptogramin.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837390&req=5

f1: A comparison of fecal samples collected from calves and adult cattle.(A) NMDS ordination of fecal sample resistomes from calf vs. adult cattle. (B) Proportion of all aligned reads that aligned to ARGs within different resistance classes, in adult cattle versus calf feces. MDR = Multi-drug resistant mechanisms; MLS = Macrolide-lincosamide-streptogramin.
Mentions: The resistome of fecal samples collected from preweaned dairy calves was different from that of mature cattle of all types (Stress = 0.11 and 0.03, ANOSIM R = 0.28 and 0.41, ANOSIM P = 0.05 and 0.02 at the mechanism and class levels, respectively, Fig. 1). Shannon’s diversity and richness at the mechanism and class levels were both lower in adult cattle compared to calf feces (Kruskal-Wallis P = 0.02 and 0.05 for richness and P = 0.09 and 0.09 for Shannon’s diversity, respectively). A descriptive comparison of dairy calf and adult dairy cow feces reflects this same pattern (Fig. 2), suggesting that production system (i.e., beef versus dairy) was not confounding this comparison and that the resistome of adult cattle feces is less diverse than that of calves. In addition, sequencing depth and DNA quantity and quality were not significantly different between samples collected from calves and samples collected from adult cattle, providing further evidence that resistome differences between these samples were not artifactual. Previous studies in calves have documented significant changes in fecal microbial diversity and composition as calves moved from milk-fed to weaning4243 and these changes could be driving resistome composition.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.

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.

No MeSH data available.


Related in: MedlinePlus