Tracking Antibiotic Resistance throughout Agroecosystems

dc.contributor.authorWind, Lauren Leeen
dc.contributor.committeechairKrometis, Leigh-Anne H.en
dc.contributor.committeechairHession, W. Cullyen
dc.contributor.committeememberBadgley, Brian Douglasen
dc.contributor.committeememberPruden, Amyen
dc.contributor.departmentBiological Systems Engineeringen
dc.description.abstractWidespread use of antibiotics in livestock production can result in the dissemination of bacteria carrying antibiotic resistance genes (ARGs) to the broader environment. Within agroecosystems, ARGs can pose a risk to livestock handlers, farmers, and ultimately consumers. The overall goals of this dissertation are to examine the presence of resistance (antibiotic, metal) in agricultural soils and evaluate the most critical potential points of best management control of antibiotic resistance spread along the agricultural production chain. The relative impacts of agricultural practices, manure management, native soil microbiota, and type of crop grown and harvested on the agricultural resistome are multi-dimensional and cannot be captured via a single analytical technique or by focusing on one specific point in the agricultural process. Culture-, molecular "indicator"-, and next-generation sequencing- based methods were employed to characterize antibiotic resistance via taxonomic and functional profiles on the broader manure, soil, and vegetable surface microbial communities through 16S rRNA amplicon sequencing and shotgun metagenomics. Although antibiotic concentrations dissipated in the soil after 28 days after amendment application, antibiotic resistance presence was recoverable throughout the entire 120d growing season in the compost and manure amendments, the amended soil, and on vegetable surfaces. The addition of organic fertilizers increased antibiotic resistance presence compared to background levels. Further, metals and metal resistance were also measured in the amended soils and were found to be at greater levels in the inorganically fertilized soils compared to the manures and compost amended soils. Analysis of the widespread agroecosystem microbial community composition and broader metagenome has characterized varying genera profiles in the soil and on the vegetable surfaces and specific ARG and mobile genetic element (plasmid) co-occurrences. These co-occurrences highlight which ARGs may be most critical for future antibiotic resistance dissemination research. It is imperative to employ multiple methods when measuring agricultural resistance, as one method alone may miss significant patterns and lead to different best management recommendations. Linking the livestock manure, soil, and vegetable surface-associated ARBs, ARGs, resistomes, and microbiomes will help identify critical control points for mitigation of agricultural dissemination of antibiotic resistance to the environment and food production.en
dc.description.abstractgeneralBy 2050, it is estimated that antibiotic resistant infections will be the leading cause of death worldwide. It is important to consider human, animal, and environmental health when researching antibiotic resistance, which is known as a "One Health" approach. In this dissertation work, I focus on the environmental side of antibiotic resistance in our agricultural systems. Agriculture is a known source of antibiotic resistance due to its use of antibiotics in livestock as a treatment for illness, and in some instances, as a growth promoter. Over one growing season, I measured antibiotic resistance in an agricultural setting using many techniques. First, I analyzed the effects of inorganic (chemical) versus organic (manure and compost) fertilization on antibiotic resistance in the soil. I measured antibiotic resistance by growing antibiotic resistant bacteria, quantifying specific antibiotic resistant genes (ARGs) using DNA amplification, and quantifying all the ARGs in the soil using a next-generation sequencing (NGS) technique called shotgun metagenomics. I found that adding manure to the soil increases ARGs compared to background soil levels, and that composting in an effective management strategy in decreasing ARGs in the soil over time. Second, I analyzed the same effects of fertilization on metal resistance in the soil. I was able to use the same NGS dataset to measure metal resistance genes (MRGs). I found that adding inorganic chemical fertilizer increases MRGs in the agricultural soils compared to the organic (manure or compost) fertilizer. Additionally, I studied the microbes that live in the agricultural soils using another kind of NGS data specific for microbial identification. I found that although there were small differences between the microbial populations in the soil when fertilizers were added, they returned to similar composition over the growing season. Lastly, I measured antibiotic resistance and microbes throughout the entire agricultural system. I picked the point of fertilization (manure management), soil, and the lettuce surface to evaluate if antibiotic resistance spreads from the farm to the vegetable that ends up on a consumer's plate. I found that at each point antibiotic resistance is present, but at different levels. Composting reduces ARGs compared to raw manure. Agricultural soils may act as a natural buffer to antibiotic resistance. Lettuce plants grown in compost fertilized soils have less ARGs than lettuce plants grown in manure. There are many agricultural management practices that effectively reduce antibiotic resistance and using all of them plus many measurement methods will ultimately help farmers and consumers reduce antibiotic resistance in our agricultural systems.en
dc.description.degreeDoctor of Philosophyen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.subjectKeywords: antibiotic resistanceen
dc.subjectantibiotic resistance genes (ARGs)en
dc.subjectantibiotic resistomeen
dc.subjectantibiotic resistant bacteria (ARB)en
dc.subjectmetal resistance genes (MRGs)en
dc.titleTracking Antibiotic Resistance throughout Agroecosystemsen
dc.typeDissertationen Systems Engineeringen Polytechnic Institute and State Universityen of Philosophyen


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