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Use of Metagenomic High‐Throughput Sequencing Technology and Robust Bioinformatics to Assess the Microbiome of Cattle, Their Environments, and Beef Products to Determine the Degree of Antimicrobial Resistance


<p>The objectives of this study were to use sophisticated molecular and statistical analysis methods to study evolutionary relationships and transmission of antimicrobial resistance genes among groups of organisms (microbiota) associated with cattle, beef, humans and the environments in which they cohabitate; and to determine the occurrence and abundance of microbes and genes in the cattle and beef product ecosystems by studying the microbiome of the beef production chain, with emphasis on the dissemination of antimicrobial resistance genetics.</p>

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<p>Antimicrobial resistance (AMR) is a pressing public health concern, and the use of antimicrobials in food animals has been posited as a major driver of increasing AMR. However, studies in this area have failed to provide reproducible, actionable results, largely due to the limitations of culture‐based microbiological methods that necessitate reliance on “indicator” bacteria to represent the complex ecology of 1,400+ microbial taxa present in the bovine gut. Shotgun metagenomics enables a more valid approach, and the goal of this project was to use such an approach to trace AMR during beef production.</p>

Geornaras, Ifigenia; Belk, Keith; Morley, Paul; Woerner, Dale
Colorado State University
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