Comparative metagenomics in livestock production antimicrobial resistance

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Lee, Catrione
University of Lethbridge. Faculty of Arts and Science
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Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry
Antimicrobial resistance is a global health problem. It affects people suffering from infections and is also able to jeopardize livestock food security. With the rise of this problem, steps have been taken to reduce the use of antimicrobials in livestock production. “Raised Without” antimicrobial livestock production has been described to reduce antimicrobial resistance by removing the selective pressure which would reinforce resistance gene conservation in bacterial genomes. This thesis’ goal was to investigate the extent to which this statement is true. First, optimization of several different methods was used to detect resistance genes and associate them with mobile genetic elements to determine their transferability potential. Taking those methods and applying them to a beef cattle dataset revealed that an absence of antimicrobial use is likely not the cause of differences observed in antimicrobial resistance gene and microbiota abundance. Macrolide resistance genes are more likely to be stably conserved than tetracycline resistance genes. Expanding that analysis to include broiler chickens and swine both raised with and without antimicrobials, revealed there to be no difference between antimicrobial management practices unless at specific antimicrobial resistance gene group-levels.
Antimicrobial resistance , Antimicrobials , Microbiota , Cattle , Swine , Broiler chickens , Livestock production