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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.


Soil samples are significantly more diverse and rich than wastewater.Dotplots showing Shannon’s diversity and richness at the mechanism and class levels, separated by system (beef vs. dairy) and colored by sample matrix, i.e., feces (black), soil (red) and wastewater (blue). Bolded text within each panel indicates which matrices differed based on Nemenyi post-hoc pairwise comparisons (WW = wastewater). Diversity and richness were not significantly different between beef and dairy at any level.
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f4: Soil samples are significantly more diverse and rich than wastewater.Dotplots showing Shannon’s diversity and richness at the mechanism and class levels, separated by system (beef vs. dairy) and colored by sample matrix, i.e., feces (black), soil (red) and wastewater (blue). Bolded text within each panel indicates which matrices differed based on Nemenyi post-hoc pairwise comparisons (WW = wastewater). Diversity and richness were not significantly different between beef and dairy at any level.

Mentions: The resistome composition of feces, soil and wastewater were significantly different at the mechanism and class levels (NMDS Stress = 0.11 and 0.06, ANOSIM R = 0.34 and 0.30, and ANOSIM P = 0.001 and 0.001, respectively). Shannon’s diversity and richness were significantly higher in soil versus wastewater at the mechanism and class levels; however, soil samples received significantly more sequencing reads than water samples, and this could account for such differences53. Shannon’s diversity but not richness was significantly higher in soil versus feces at the mechanism and class levels (Fig. 4), and sequencing depth was comparable between the two matrices. The difference between soil and fecal diversity is especially interesting given that pen floors in dairies and feedlots are often a mixture of dried, compacted feces and underlying soil, rather than undisturbed soil matrix. In this context, the differentiation of “soil” (i.e., compacted feces) from fresh feces could stem from simple mixing of the two components, or from changes that occur within the soil-fecal matrix over time and under varying environmental exposures, as has been shown in E. coli54. Indeed, the fecal collection in this study focused on collection of recently voided fecal pats, in which exposure to aerobic conditions was of relatively short duration. Therefore, the environmental milieu to which the fecal and soil samples were exposed was likely very different.


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)

Soil samples are significantly more diverse and rich than wastewater.Dotplots showing Shannon’s diversity and richness at the mechanism and class levels, separated by system (beef vs. dairy) and colored by sample matrix, i.e., feces (black), soil (red) and wastewater (blue). Bolded text within each panel indicates which matrices differed based on Nemenyi post-hoc pairwise comparisons (WW = wastewater). Diversity and richness were not significantly different between beef and dairy at any level.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Soil samples are significantly more diverse and rich than wastewater.Dotplots showing Shannon’s diversity and richness at the mechanism and class levels, separated by system (beef vs. dairy) and colored by sample matrix, i.e., feces (black), soil (red) and wastewater (blue). Bolded text within each panel indicates which matrices differed based on Nemenyi post-hoc pairwise comparisons (WW = wastewater). Diversity and richness were not significantly different between beef and dairy at any level.
Mentions: The resistome composition of feces, soil and wastewater were significantly different at the mechanism and class levels (NMDS Stress = 0.11 and 0.06, ANOSIM R = 0.34 and 0.30, and ANOSIM P = 0.001 and 0.001, respectively). Shannon’s diversity and richness were significantly higher in soil versus wastewater at the mechanism and class levels; however, soil samples received significantly more sequencing reads than water samples, and this could account for such differences53. Shannon’s diversity but not richness was significantly higher in soil versus feces at the mechanism and class levels (Fig. 4), and sequencing depth was comparable between the two matrices. The difference between soil and fecal diversity is especially interesting given that pen floors in dairies and feedlots are often a mixture of dried, compacted feces and underlying soil, rather than undisturbed soil matrix. In this context, the differentiation of “soil” (i.e., compacted feces) from fresh feces could stem from simple mixing of the two components, or from changes that occur within the soil-fecal matrix over time and under varying environmental exposures, as has been shown in E. coli54. Indeed, the fecal collection in this study focused on collection of recently voided fecal pats, in which exposure to aerobic conditions was of relatively short duration. Therefore, the environmental milieu to which the fecal and soil samples were exposed was likely very different.

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.