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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

Specific resistance classes drive separation of soil from fecal and wastewater resistomes.NMDS ordination of fecal (black), soil (red) and wastewater (green) samples based on normalized counts of alignments aggregated at the resistance class level. Biplot coordinates of resistance classes are labeled with the class name, and show that aminoglycoside, phenicol and spectinomycin resistances differentiate the soil from the fecal and wastewater resistomes.
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f5: Specific resistance classes drive separation of soil from fecal and wastewater resistomes.NMDS ordination of fecal (black), soil (red) and wastewater (green) samples based on normalized counts of alignments aggregated at the resistance class level. Biplot coordinates of resistance classes are labeled with the class name, and show that aminoglycoside, phenicol and spectinomycin resistances differentiate the soil from the fecal and wastewater resistomes.

Mentions: Ordination biplot results indicated that aminoglycoside, spectinomycin, phenicol and tetracycline resistance classes strongly influenced separation of soil samples from wastewater and feces (Fig. 5). Phenicol and spectinomycin resistance classes were not identified in adult cattle fecal samples, and reads aligning to aminoglycoside ARGs were less abundant in adult cattle fecal samples compared to soil samples (log-fold change = −4.6, adjusted P < 0.0001). Reads aligning to genes that confer tetracycline resistance–which were highly abundant in all samples–were more abundant in adult feces than in soil (log-fold difference = 1.50, adjusted P < 0.0001). This difference was driven overwhelmingly by the abundance of ribosomal protection proteins in feces, as major facilitator superfamily (MFS) efflux pumps were less abundant in feces compared to soil (log-fold difference = −2.1, adjusted P < 0.001). This pattern of tetracycline resistance mechanism differentiation between soil and feces has been observed in a comparison of human gut samples and agricultural soils55. Beta-lactam resistance alignments were also more abundant in feces and soil than in wastewater. Beta-lactams have been shown to degrade relatively quickly in the environment, and this could account for significantly lower levels in wastewater if antimicrobial drug residues influence the density of beta-lactam ARGs in this environment56.


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)

Specific resistance classes drive separation of soil from fecal and wastewater resistomes.NMDS ordination of fecal (black), soil (red) and wastewater (green) samples based on normalized counts of alignments aggregated at the resistance class level. Biplot coordinates of resistance classes are labeled with the class name, and show that aminoglycoside, phenicol and spectinomycin resistances differentiate the soil from the fecal and wastewater resistomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Specific resistance classes drive separation of soil from fecal and wastewater resistomes.NMDS ordination of fecal (black), soil (red) and wastewater (green) samples based on normalized counts of alignments aggregated at the resistance class level. Biplot coordinates of resistance classes are labeled with the class name, and show that aminoglycoside, phenicol and spectinomycin resistances differentiate the soil from the fecal and wastewater resistomes.
Mentions: Ordination biplot results indicated that aminoglycoside, spectinomycin, phenicol and tetracycline resistance classes strongly influenced separation of soil samples from wastewater and feces (Fig. 5). Phenicol and spectinomycin resistance classes were not identified in adult cattle fecal samples, and reads aligning to aminoglycoside ARGs were less abundant in adult cattle fecal samples compared to soil samples (log-fold change = −4.6, adjusted P < 0.0001). Reads aligning to genes that confer tetracycline resistance–which were highly abundant in all samples–were more abundant in adult feces than in soil (log-fold difference = 1.50, adjusted P < 0.0001). This difference was driven overwhelmingly by the abundance of ribosomal protection proteins in feces, as major facilitator superfamily (MFS) efflux pumps were less abundant in feces compared to soil (log-fold difference = −2.1, adjusted P < 0.001). This pattern of tetracycline resistance mechanism differentiation between soil and feces has been observed in a comparison of human gut samples and agricultural soils55. Beta-lactam resistance alignments were also more abundant in feces and soil than in wastewater. Beta-lactams have been shown to degrade relatively quickly in the environment, and this could account for significantly lower levels in wastewater if antimicrobial drug residues influence the density of beta-lactam ARGs in this environment56.

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