Rovira Sanz, Pablo, authorBelk, Keith, advisorMorley, Paul, committee memberSchmidt, John, committee memberYang, Hua, committee member2017-09-142019-09-122017https://hdl.handle.net/10217/183928In recent years, consumer demand for natural and organic foods has increased, partly due to concerns about the use of antimicrobials in food producing animals. The aim of this study was to evaluate antimicrobial resistance (AMR) in beef feedlot and dairy cattle raised without use of antibiotics compared to cattle raised in conventional (CONV) production. Three research projects were conducted to accomplish that general goal. In the first study, a conventional feedlot, natural feedlot, conventional dairy and organic dairy were visited to collect cattle feces, wastewater from lagoons and soil where the wastewater was applied. After DNA extraction, sequencing, and processing, metagenomic reads were aligned to reference databases for identification of antibiotic resistance genes (ARGs; i.e. the resistome) and bacteria (microbiome). Resistome composition was influenced by rearing method, cattle type, and type of sample. Most mechanisms of resistance affected by rearing method were enriched (P < 0.05) in conventional samples. Resistome differences were greatest for wastewater samples by rearing method but with contradictory results that suggested an impact of effluent management on wastewater resistome. Resistance to tetracycline and macrolide-lincosamide-streptogramin classes were more abundant in feces of feedlot cattle than in dairy cattle (P < 0.05); whereas resistance to beta-lactams was greatest in feces of dairy cattle (P < 0.05). Resistome and microbiome of feces differed (P < 0.05) between wastewater and soil samples. Results indicated that ARGs are widespread in beef feedlot and dairy cattle farms even in those with restricted antibiotic use. In the second study, feces from RWA (n=36) and CONV (n=36) cattle lots were recovered from colons at a commercial beef processing plant. Samples were equally distributed by month and production protocol over one year (3 samples/production protocol/month). After extracting DNA from individual samples, composite samples were prepared by mixing DNA from each lot into a single composite sample (N = 72) and sequencing the composites on an Illumina platform. Metagenomic reads were processed similarly to those in experiment 1for identification of ARGs and bacteria. Resistomes of CONV and RWA cattle were significantly different by season. In general, mechanisms conferring resistance to beta-lactams, tetracyclines, multi-drug and macrolides were more prevalent (P < 0.05) in feces from CONV colons than in RWA colons. In the third study, a systematic review and meta-analysis was performed to assess the relationship between antimicrobial use (AMU) and antimicrobial resistance (AMR) in feedlot cattle. After conducting a literature search and screening reported studies, 32 studies were selected for use that addressed AMR in Escherichia coli, Enterococcus, Salmonella, Campylobacter, and Mannheimia haemolytica. Overall, 60% (95% CI: 26% to 88%) of the observational studies and 50% (95% CI: 30% to 70%) of the controlled trials reported a positive association between AMU and AMR. Meta-analysis provided evidence for an increase in average relative risk (RR) associated with antibiotic use. Isolates recovered from treated cattle were 2.5 times (95% confidence interval: 1.7 – 3.5) as likely to display antibiotic resistance compared to isolates recovered from unexposed animals. Risk of resistance increases with animal defined daily doses (DDDs). More comprehensive studies that consider the relationship between antibiotic use in cattle and antibiotic resistant bacteria in humans are needed as a part of a farm to fork approach to tackle antimicrobial resistance.born digitaldoctoral dissertationsengCopyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.bacteriametagenomicsantimicrobial resistanceresistance genescattleText