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United States Department of Agriculture

Agricultural Research Service

Research Project: Environmentally Sound Manure Management for Reduction of Gas Emissions, Nutrients, and Pathogens

Location: Agroecosystem Management Research

Title: Distribution and quantification of antibiotic resistance genes and bacteria across agricultural and non-agricultural metagenomes

Authors
item Durso, Lisa
item Miller, Daniel
item Wienhold, Brian

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 24, 2012
Publication Date: November 2, 2012
Repository URL: http://handle.nal.usda.gov/10113/57132
Citation: Durso, L.M., Miller, D.N., Wienhold, B.J. 2012. Distribution and quantification of antibiotic resistance genes and bacteria across agricultural and non-agricultural metagenomes. PLoS One [online]. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048325.

Interpretive Summary: The issue of antibitoic resistance is of concern to consumers, and scientists. One area of particular concern is the transfer of antibitoic resistance through the food chain, especially for foods of animal origin. While a broad conceptual framework has been worked out describing how use of antibitoics in food animals has the potential to adversely impact human health, many of the specific details remain unknown. A number of studies have measured antibiotic resistance in animal production environments, and the general public perception is that agricultural environments have more antibiotic resistance than natural and non-agricultural environments. We have tested this hypothesis by counting the numbers and kinds of antibiotic resistance genes from 26 environments, including natural and agricultural samples. In addition, we were interested in determining what bacteria are likely carrying the antibiotic resistance genes, and if there are differences in the kinds of antibiotic resistant bacteria in agricultural and natural settings. Genes coding for antibiotic resistance were found in all samples, including agricultural and human samples, as well as costal-marine habitats such as Chesapeake Bay and Key West, and minimally-impacted samples like the Sargasso Sea and Antarctic Lakes. Agricultural, human, and coastal-marine samples have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural samples compared to marine and Antarctic samples.

Technical Abstract: There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described and few details are known about how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.

Last Modified: 10/31/2014
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