Date of Award

Summer 2020

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biological Sciences

First Advisor

Hristova, Krassimira R.

Second Advisor

Campbell, James

Third Advisor

Maki, James


Antimicrobial resistance (AMR) is a ubiquitous global health issue driven by the overuse and misuse of antimicrobial compounds in healthcare and veterinary medicine. Both natural and built environments have been recognized as reservoirs of antimicrobial resistant bacteria, genes, and pathogens but the factors that drive increases in their abundance are not well understood, especially in natural environments. The primary goal of this work is to characterize the ecological drivers of antimicrobial resistance in freshwater ecosystems impacted by intensive livestock farms, known contributors of environmental resistance. Kewaunee County, Wisconsin served as an ideal study site for the investigation of the impact of intensive livestock farming on environmental antimicrobial resistance as the county is home to 15 dairy and one beef concentrated animal feeding operations (CAFOs) and more than 200 smaller farms. Manure, a known reservoir of antimicrobial resistance genes (ARGs) and bacteria (ARB) is collected from these farms and used as cropland fertilizer which can enter waterways through runoff events. Surveys of Kewaunee County freshwater ecosystems determined that ARGs from multiple classes of antibiotics increase temporally, corresponding with the manure fertilization period and concentrations agricultural pollutants in Kewaunee County. Manure application and runoff also serve as repeated ecological disturbances for sediment microbial communities in Kewaunee County. Sediment microbial community composition and function are significantly altered by manure runoff and do not return to a pre-disturbance state within five months post-disturbance. Additionally, resistance patterns and evolutionary history of Escherichia coli from Kewaunee County manure and freshwater ecosystems are most similar to one another, indicating possible transmission of bacteria between these two sources. Experimental investigations were used to identify whether the microbial community or nutrients from manure are the primary driver of increased antimicrobial resistance in freshwater sediments. Nutrients from manure were identified as the primary driver of increased antimicrobial resistance in sediments by fundamentally altering the microbial community structure to allow microorganisms that correlate with ARGs to proliferate. These results indicate that sterile manure increases ARGs in sediments, suggesting nutrient loads are a primary driver of AMR in natural environments and necessitating a review of manure fertilization practices.

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