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Use of Shotgun Metagenomic NGS Combined with a Previously developed Bioinformatics Pipeline vs. Traditional Culture/Screening Diagnostics to Evaluate Ecology of AMR and Diagnose Salmonella spp. in Cattle Feces Before and After Cetiiofur Metaphylaxis


The overarching goal of this study was to develop and validate a dual‐purpose metagenomics pipeline for pathogen detection and resistome analysis of cattle feces in the early part of the feeding period. One objective under this goal was to utilize shotgun metagenomics to understand the impact of metaphylactic macrolide (tulathromycin) exposure on the resistome of cattle in the early feeding period. The second objective was to develop an approach for identifying Salmonella enterica in shotgun metagenomic data and to compare this approach to culture based results.

Noyes, Noelle; Morley, Paul; Jones, K; Boucher, C; Belk, Keith
Colorado State University
Virginia Polytechnic Institute and State University
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