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Browsing Theses and Dissertations by Subject "AMR"

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    Shotgun metagenomic and 16S rRNA gene sequencing investigation of antimicrobial resistance in the beef supply chain
    (Colorado State University. Libraries, 2019) Weinroth, Margaret, author; Belk, Keith E., advisor; Metcalf, Jessica L., committee member; Morley, Paul S., committee member; Yang, Hua, committee member
    Antibiotic resistant bacterial infections are a growing public health issue. In food producing animals, there is a concern that using antibiotics will increase the risk of antibiotic resistance (AMR) on meat products, thus increase consumers' risk of acquiring AMR infections via meat consumption. However, in order to mitigate these risks, there are several areas of livestock production where more data are needed to understand current communities of AMR genes (resistomes) and how antibiotics influence associated cattle microbiomes. In order to obtain more information about these communities, three experiments were conducted: (A) a characterization of market cow resistome and microbiomes, (B) the effect of region and tylosin exposure on feedlot cattle, and (C) the characterization of liver purulent material from feedlot cattle. All three of the studies were conducted utilizing shotgun metagenomics for resistome analysis and 16S rRNA amplicon sequencing for microbiome analysis. Both culture-free methods used in these studies were chosen because AMR is an ecological concern in microbial communities and resistance genes are not exclusively harbored in culturable bacteria. In the first study, market cows were selected as the population of interest because, while a fifth of beef produced in the U.S. is from market cows, past studies have been more focused on feedlot cattle. Findings from the market cows study highlighted that the resistome of bovine trimmings was impacted by slaughter facility over the production system the cows were raised in. In the second study, cattle were raised in three different geographical regions, and within each geographical region pens were either fed or not fed tylosin—a common macrolide antibiotic for the prevention of liver abscesses. In addition to the scoring of liver abscesses in these pens of cattle at harvest, pen floor feces and soil were collected. These data revealed no significant differences in resistome composition between different antibiotic group exposures, but geographical region affected the resistome. Finally, aliquots of liver purulent material of a subset of cattle in the aforementioned experiment were collected for characterization in the third study. While tylosin is used to reduce liver abscesses in feedlot cattle, and it has been postulated that fusobacterium necrophorum is the causative organism of liver abscesses, the mode of action in which tylosin reduced abscesses is not known, nor has fusobacterium necrophorum introduction into livers resulted in 100% incidence of liver abscesses. To gain a more complete understanding of the cause of liver abscesses, purulent material was evaluated with 16S rRNA amplicon sequencing. Fusobacterium was identified in all abscesses along with many other phyla, demonstrating a polymicrobial bacterial community. All three of these studies further contributed to the understanding of resistome and microbiome dynamics as a result of antibiotic exposure. Across studies, geographical region and facility of slaughter were seen to contribute more to resistome composition changes in both feces and colon content and bovine trimmings than antibiotic exposure.
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    ItemOpen Access
    The effect of tylosin exposure or exclusion on liver abscess prevalence, fecal pathogen populations, and the microflora of finished beef products from feedlot cattle
    (Colorado State University. Libraries, 2018) Weissend, Carla Jane, author; Martin, Jennifer, advisor; Belk, Keith, committee member; Bryant, Tony, committee member; Metcalf, Jessica, committee member; Weir, Tiffany, committee member
    There is great pressure to reduce use of, and find alternatives to, antibiotics in animal production. More than 70% of feedlot cattle in 1000+ head lots are currently exposed to tylosin phosphate, a macrolide antibiotic used for the reduction and prevention of liver abscesses. As such, its potential removal from cattle feeding strategies could have a marked impact on both the economics of the beef industry and food safety. Additionally, little is known about the effect of tylosin exposure or exclusion on the microbiome of finished beef products. In light of these facts, a blinded, randomized, controlled field trial was conducted to evaluate the impact on the prevalence of liver abscesses and the characterization of the microbiome of feces, liver abscesses, carcasses, and finished beef products through 16S rRNA gene sequencing and shotgun sequencing from feedlot cattle with and without exposure to tylosin. Overall, liver abscess rates were lower among cattle exposed to tylosin. However, there were no differences among treatment groups for any of the sample types, suggesting that removal of tylosin from current feeding strategies will not upend the safety of the beef supply. The information gained in this study will provide valuable insight as the search for alternative feeding strategies to antibiotics continues.