Browsing by Author "Wind, Lauren Lee"

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    Persistence of Culturable Antibiotic Resistant Fecal Coliforms From Manure Amended Vegetable Fields
    Wind, Lauren Lee (Virginia Tech, 2017-06-14)
    The reduced efficacy of antibiotics in treating common infections is one of the most pressing health concerns of the 21st Century. Increasing evidence links the widespread use of antibiotics in livestock production to the transfer of bacteria carrying antibiotic resistance genes to the broader environment. It is therefore critical to understand the persistence and dissemination of resistance in agricultural soils to understand potential threats to consumers. The goal of this large-scale agricultural field experiment was to identify the effects of crop (lettuce, radish) and fertilizer type (inorganic, compost, raw manure) on the incidence and persistence of antibiotic-resistant fecal coliforms, a common family of fecal indicator bacteria used to track the environmental spread of antibiotic resistance. Soil samples were collected eight times over a 120-day period and analyzed for fecal coliforms utlizing a suite of MacConkey agars supplemented with different antibiotics (ceftazidime, clindamycin, erythromycin, sulfamethoxazole, and tetracycline). Given the number of samples with resistant fecal coliform concentrations below the limit of detection, analyses to identify the effects of soil treatment and crop relied on Zero-inflated Poisson Regressions. Antibiotic-resistant culturable fecal coliforms were recoverable from soils across all treatments immediately following application, though persistence throughout the experiment varied by antibiotic. Sulfamethoxazole- and tetracycline-resistant fecal coliforms were nondetectable after Day 1; this was expected, as the cattle supplying the manure amendments were not treated with these antibiotics or similar analogs. Clindamycin- and erythromycin-resistant fecal coliforms were nondetectable after 42 days but rebounded on Day 90 in the soil; both of these drugs were of the same antibiotic class as the ones used to treat the dairy cattle during the manure collection period. Ceftazidime-resistant fecal coliform levels were consistently high throughout the duration of the growing season. No statistical differences were observed between root and aboveground crops. Results suggest that soils amended with raw or composted dairy manure are at risk of contamination with antibiotic resistant fecal coliforms; however, composting decreased the antibiotic resistant fecal coliform levels of the macrolide (erythromycin) and lincosamide (clindamycin) antibiotic classes administered to the dairy cattle (cephapirin and pirlimycin).
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    Tracking Antibiotic Resistance throughout Agroecosystems
    Wind, Lauren Lee (Virginia Tech, 2021-01-12)
    Widespread 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.