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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.


Binary heatmap of resistance mechanisms and classes identified in fecal, soil and wastewater samples collected from a US and a Canadian (CA) feedlot.Black‚ÄČ=‚ÄČabsent, red‚ÄČ=‚ÄČpresent.
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f6: Binary heatmap of resistance mechanisms and classes identified in fecal, soil and wastewater samples collected from a US and a Canadian (CA) feedlot.Black‚ÄČ=‚ÄČabsent, red‚ÄČ=‚ÄČpresent.

Mentions: No significant resistome differences were observed between US and Canadian feedlot samples, which may indicate that diet did not have a major impact (NMDS Stress‚ÄČ=‚ÄČ0.11 and 0.04, ANOSIM R‚ÄČ=‚ÄČ0.02 and 0.05, and ANOSIM P‚ÄČ=‚ÄČ0.31 and 0.26 for the mechanism and class levels, respectively). Diversity, richness and sequencing depth also did not differ significantly. However, descriptive results show differences, indicating that lack of statistical difference could stem from low study power (Fig. 6). Canadian samples contained reads that aligned to 12 classes and 30 mechanisms of resistance. In comparison, reads aligning to 6 classes and 11 mechanisms of resistance were identified in US feedlot samples. Previous studies have shown that diet significantly impacts the cattle fecal microbiome, which could impact the resistome6263. While the US feedlot fed a corn-based and the Canadian feedlot a barley-based ration, antimicrobial use in these feedlots was largely similar (both feedlots administered in-feed tylosin) and this uniformity may have overpowered the influence of diet and microbial composition, leading to a lack of difference between samples.


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)

Binary heatmap of resistance mechanisms and classes identified in fecal, soil and wastewater samples collected from a US and a Canadian (CA) feedlot.Black‚ÄČ=‚ÄČabsent, red‚ÄČ=‚ÄČpresent.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Binary heatmap of resistance mechanisms and classes identified in fecal, soil and wastewater samples collected from a US and a Canadian (CA) feedlot.Black‚ÄČ=‚ÄČabsent, red‚ÄČ=‚ÄČpresent.
Mentions: No significant resistome differences were observed between US and Canadian feedlot samples, which may indicate that diet did not have a major impact (NMDS Stress‚ÄČ=‚ÄČ0.11 and 0.04, ANOSIM R‚ÄČ=‚ÄČ0.02 and 0.05, and ANOSIM P‚ÄČ=‚ÄČ0.31 and 0.26 for the mechanism and class levels, respectively). Diversity, richness and sequencing depth also did not differ significantly. However, descriptive results show differences, indicating that lack of statistical difference could stem from low study power (Fig. 6). Canadian samples contained reads that aligned to 12 classes and 30 mechanisms of resistance. In comparison, reads aligning to 6 classes and 11 mechanisms of resistance were identified in US feedlot samples. Previous studies have shown that diet significantly impacts the cattle fecal microbiome, which could impact the resistome6263. While the US feedlot fed a corn-based and the Canadian feedlot a barley-based ration, antimicrobial use in these feedlots was largely similar (both feedlots administered in-feed tylosin) and this uniformity may have overpowered the influence of diet and microbial composition, leading to a lack of difference between samples.

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.