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ARS Home » Midwest Area » Ames, Iowa » National Laboratory for Agriculture and The Environment » Agroecosystems Management Research » Research » Publications at this Location » Publication #341113

Research Project: MANAGING AGRICULTURAL WATER QUALITY IN FIELDS AND WATERSHEDS: NEW PRACTICES AND TECHNOLOGIES

Location: Agroecosystems Management Research

Title: Improving monitoring of erythromycin ribosome methylase genes in swine and cattle manures with gene targeted approaches

Author
item Choi, Jinlyung - Iowa State University
item Luby, Elizabeth - Iowa State University
item Soupir, Michelle - Iowa State University
item Smith, S - Iowa State University
item Cole, James - Michigan State University
item Tift, Leo - Michigan State University
item Moorman, Thomas - Tom
item Douglass, Elizabeth - Beth
item Howe, Adina - Iowa State University

Submitted to: Symposium Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 4/27/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Macrolide antibiotics are often used in feed for animal industry to prevent diseases. Resistance to these antibiotics is associated with erythromycin ribosome methylase genes (erm genes), which were first discovered in Staphylococcus aureus. The erm gene confers resistance by methylating rRNA at the active site and reduces antibiotic binding and has been used as an estimate of potential antibiotic resistance in animals, manure, and environmental samples. To detect erm genes in environmental samples, primers have been designed for gene targets for PCR and qPCR approaches that focus on specific genera, mainly Enterococcus. In this study, we evaluate previously published primers for ermB, ermC, and ermF genes in capturing the diversity of erm genes in manure metagenomes. We identify phylogenetic clusters of erm biodiversity that are abundant in manure metagenomes but would be missed with current primer targets. We designed novel primers to target these clades and can increase the detection of erm genes in swine and cattle manures from 45% to 79% in swine manures and 46% to 64% in cattle manures. The results of this study suggest that current assays may be underestimating erm genes in manure samples. Using metagenomes to guide primer design, we can improve our ability to detect and quantify erm genes, especially in animal production systems, for targeted gene assays.