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ARS Home » Plains Area » Lincoln, Nebraska » Agroecosystem Management Research » Research » Publications at this Location » Publication #318214

Title: Metagenomics and other Methods for Measuring Antibiotic Resistance in Agroecosystems

Author
item Durso, Lisa

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 7/28/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary: There is no standard method for measuring antibiotic resistance in environmental samples, and no definition of what constitutes “resistance” in environmental bacteria. Our understanding, therefore, of the types and amounts of resistance that are present on farms and in manure-impacted environments, depends to some degree of what methods we use to measure this parameter. We review metagenomic tools used to address questions regarding the types and taxonomic distribution of antibiotic resistance genes in cattle feces, water, and soil, along with other common culture-based and culture-independent methods used to track and quantify antibiotic resistance on farms, and provide examples from research projects that use these tools. By more precisely defining how antibiotic resistance is measured we can better assess the impacts that agricultural best management practices have on the specific types of antibiotic resistant bacteria and antibiotic resistance genes that are most important for animal and human health.

Technical Abstract: Background: There is broad concern regarding antibiotic resistance on farms and in fields, however there is no standard method for defining or measuring antibiotic resistance in environmental samples. Methods: We used metagenomic, culture-based, and molecular methods to characterize the amount, types and taxonomic distribution of antibiotic resistant bacteria and antibiotic resistance genes in cattle feces, water, and soil Results: Assessment of whether one site has more resistance than another depends heavily on the specific parameter chosen to assess resistance. Metagenomic studies reveal that antibiotic resistance genes are common in agricultural, human, and coastal-marine metagenomes, but although the types of resistance are fairly consistent across habitats, there are differences in the kinds of bacteria that likely carry the resistance genes. Culture-based studies in native Nebraska prairies support the idea that antibiotic resistance is ubiquitous in soil, even in non-agricultural sites. Phenotypic and genotypic characterization of prairie soils highlight that resistance can vary even in samples collected from the same prairie, and provide specific examples of how resistance changes depending on what gene or bacteria is measured. Conclusions: By more precisely defining how antibiotic resistance is measured we can better assess the impacts that agricultural best management practices have on the specific types of antibiotic resistant bacteria and antibiotic resistance genes that are most important for animal and human health.