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Title: Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: prospects and challenges

item LUBY, ELIZABETH - Iowa State University
item Ibekwe, Abasiofiok - Mark
item ZILLES, JULIE - University Of Illinois
item PRUDEN, AMY - Virginia Tech

Submitted to: Journal of Environmental Quality
Publication Type: Review Article
Publication Acceptance Date: 9/19/2015
Publication Date: 3/1/2016
Citation: Luby, E., Ibekwe, A.M., Zilles, J., Pruden, A. 2016. Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: prospects and challenges. Journal of Environmental Quality. 45:441-453. doi: 10.2134/jeq2015.07.0367.

Interpretive Summary: The successful assessment of antibiotic resistance in agricultural ecosystems with molecular methods depends on focused research questions, appropriate application of molecular methods combined with other measurements to address current technological questions. One key question is the continued development of DNA techniques and associated data analysis methods for detecting and quantifying antibiotics and antibiotic-resistant genes in the environment, and how these new approaches may help in reducing the transfer of antibiotics and antibiotic-resistant bacteria from the environment to human. This review looks at the new methodological frontiers in the development of standard protocols and gene targets for monitoring antibiotic resistance in the environment, which would facilitate large-scale environmental monitoring efforts and cross-study comparisons. This review supports a recent executive order issued by the White House calling for a national strategy to combat antibiotic resistant bacteria as well as FSIS, EPA, FDA, USDA, and different federal and state agencies that are involved in antibiotic resistance work.

Technical Abstract: Agricultural ecosystems are of special interest for monitoring the potential for antibiotic resistance to spread through the environment and contribute to human exposure. Molecular methods, which target DNA, RNA, and other molecular components of bacterial cells, present certain advantages for characterizing and quantifying markers of antibiotic resistance and their horizontal gene transfer. However, molecular methods are also subject to limitations that are not always clearly addressed or taken into consideration in the interpretation of scientific data. The purpose of this review is to provide an overview of existing molecular methods for tracking antibiotic resistance in agricultural ecosystems, define their strengths and weaknesses, and recommend a path forward for future applications of molecular methods and standardized reporting in the literature. This will guide research along the farm-to-fork continuum and support comparability of the growing number of studies in the literature in a manner that informs management decisions and policy development.