{"id":{"repo_id":"buffalo","oai_identifier":"oai:ubir.buffalo.edu:10477/78498"},"canonical_url":"https://search.dev.ndltd.org/etd/buffalo/oai:ubir.buffalo.edu:10477/78498","repository":{"repo_id":"buffalo","name":"Buffalo","base_url":"https://ubir.buffalo.edu/oai/request"},"display":{"title":"Comprehensive Evaluation of Dairy Manure Management Strategies for the Removal of Antimicrobials and the Spread of Antimicrobial Resistance Genes","abstract":"Ph.D.","abstract_html":"Ph.D.","abstract_has_math":false,"creators":["Hurst, Jerod; 0000-0002-6667-7482"],"institution":"State University of New York at Buffalo","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Aga, Diana","Chemistry"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018-10-26T02:54:20Z","date_published":"2018-10-26T02:54:20Z","updated_at":"2026-07-27T19:05:09Z","subjects":["analytical chemistry","agriculture"],"languages":["eng"],"rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/10477/78498","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Aga, Diana","Chemistry"]},{"key":"dc:creator","label":"Author","values":["Hurst, Jerod; 0000-0002-6667-7482"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2018-10-26T02:54:20Z","2018","2018-06-06 09:09:47"]},{"key":"dc:publisher","label":"Institution","values":["State University of New York at Buffalo"]},{"key":"dc:type","label":"Dc Type","values":["Text","Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["analytical chemistry","agriculture"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/10477/78498"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Ph.D.","Environmental contamination by antimicrobials and dissemination of antimicrobial resistance genes (ARGs) through the excretion of administered antimicrobials in food-producing animals can potentially exacerbate the global issue of increased infections by antimicrobial resistant bacteria. Various mitigation strategies in large livestock operations for controlling the environmental dissemination of antimicrobials and ARGs exist, where manure treatment may provide the most direct strategy for removing residues prior to land application of manure for crop field fertilization. This research examined the occurrences of five antimicrobial classes and various ARGs present in dairy farms employing different manure management strategies. Residues of antimicrobials were analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS), while the prevalence of ARGs was investigated using quantitative polymerase chain reaction (qPCR), to elucidate potential relationships between ARG levels and antimicrobial use. Lastly, two novel manure treatment strategies were investigated for their potential to remove both antimicrobials and ARGs as technologically advanced mitigation strategies for combating antimicrobial resistance dissemination in agricultural environments.A comprehensive evaluation of antimicrobial occurrences present in dairy manure was explored in Chapter 2 to assess the efficiencies of 11 different dairy manure management systems at removing antimicrobial compounds across six collection dates. Of the four antimicrobial compounds detected among the large farm cohort, tetracyclines and sulfonamides were the only antimicrobial classes to be detected. Comparisons among the total tetracycline concentrations (ng/g DW) and tetracycline administration (mg) revealed no correlation, suggesting large variability in manure storage or manure sampling and warrants future research to investigate the possible discrepancies. Also, tetracycline residues were found to generally persist after each manure management system where anaerobic digestion effluent concentrations ranged from 167 to 4890 ng/g and composting treatments provided total concentrations ranging from 213 to 2430 ng/g after treatment. Sulfadimethoxine, one sulfonamide which provided detection along one treatment process, was not found to be significantly affected by manure treatment with anaerobic digestion and further long-term storage.Chapter 3 investigates the temporal and farm-based variability of 13 different ARGs conferring resistance mechanisms to sulfonamides, tetracyclines, beta-lactams, aminoglycosides, and macrolide antimicrobial classes. Farm dissimilarity in ARG prevalence was observed, suggesting each farm contains a unique resistome inherent in the microbial community. Temporal trends were observed using nMDS and targeted ARG data trends suggesting lower prevalence of ARGs during the winter months (December and March), possibly indicating bacterial population alterations during the colder months. It was also observed that the occurrences of ARGs generally did not correlate to the administration of tetracycline and beta-lactam antimicrobials, suggesting the presence of antimicrobials may contribute to ARG dissemination to a lesser extent than previously believed and other factors of bacterial selective pressure should be investigated. Manure from an antimicrobial-free farm was collected and studied to compare changes in ARG prevalence to that found in dairy manure collected from conventional farms that utilize antimicrobials. Antimicrobial-free manure provided positive detections for 6 of the 9 total ARGs investigated. Comparisons to antimicrobial-free manure revealed larger occurrences of ereB, OXA-2, and VEB-1 genes from manure collected from the conventional farms, suggesting these genes are affected the most by continual exposure to antimicrobials. Long-term storage manure was not found to contain significantly higher ARG prevalence values when compared to untreated manure.In Chapter 4, a novel liquid manure treatment technique known as Livestock Water RecyclingTM (LWR) was investigated for its potential to remove ionophore antimicrobials throughout the treatment process. An analytical method was developed for the sample extraction and analysis (via LC-MS/MS) of seven ionophore antimicrobials approved for use in the United States then applied to samples collected at a dairy farm with a newly installed LWR system. Two ionophore antimicrobials, monensin and lasalocid, were detected in separated manure solids and separated manure liquids form the dairy farm. Monensin concentrations when adsorbed onto solid manure fractions ranged from 220 to 1,200 ng/g and was not substantially removed among each individual treatment step. Monensin was the only ionophore detected in the separated liquid fractions of manure, where concentrations were reduced from 42 ng/mL to 7 ng/mL after reverse osmosis treatment providing an average percent removal for three sample collections of 85%. Lasalocid was only detected when adsorbed onto solid manure fractions, but was not significantly reduced among the individual treatment steps of the LWR system.Chapter 5 investigated the efficacy for a solid manure treatment technique known as a Bedding Recovery UnitTM (BRU) for removing both antimicrobials and ARGs during a short-term composting procedure (24 hours). Two antimicrobials were detected, oxytetracycline and sulfadimethoxine, where their removal behaviors differed after treatment. Oxytetracycline was observed to have a 45% removal of the parent antimicrobial compound while sulfadimethoxine was not shown to be significantly changed when comparing the solid manure influent to the solid manure effluent. Conversely, ARGs were shown to be reduced after the short-term composting procedure with removal values of 75%, 98%, and 94% for sul1, tetO, OXA-1 respectively. The int1 gene, which has been linked to horizontal gene transfer, was also investigated for the possible removal capabilities where it was shown to have a 60% reduction in the normalized gene copies after BRU treatment of the solid manure. These results indicate the efficiency of the BRU system for removing ARGs, however antimicrobial compounds in general were not removed to the same extent suggesting antimicrobials have higher stability compared to ARGs under aerobic conditions suggesting different treatment conditions are needed for efficient mitigation during manure treatment.Lastly, Chapter 6 examines the detection of beta-lactam antimicrobials in dairy manure by using either indirect enzyme-linked immunosorbent assay (ELISA) or by LC-MS/MS analysis. An indirect ELISA method was utilized to act as a screening tool for the detection of beta-lactams, where two separate kits were evaluated (beta-lactam class specific and ceftiofur specific). In studying the occurrences of beta-lactams by ELISA, the majority of the samples did not show positive detections. The few samples that showed positive detections were not confirmed by LC-MS/MS, which suggest that there may be interfering matrix components that bind to the antibodies used in the ELISA method resulting in false positives. An LC-MS/MS method was developed to increase the selectivity of detections, where a solid-liquid extraction procedure was also validated. This LC-MS/MS method was applied to study the degradation of beta-lactams present in fresh manure where significant degradation occurred over a 14-day period. Estimated half-lives of beta-lactams ranged from 2.2 to 4.5 days, assuming a pseudo-first order degradation rate indicating beta-lactams (if excreted from the cow unmetabolized) are quickly degraded in manure matrix."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Comprehensive Evaluation of Dairy Manure Management Strategies for the Removal of Antimicrobials and the Spread of Antimicrobial Resistance Genes"]}]}],"canonical_facts":{"dc:contributor":["Aga, Diana","Chemistry"],"dc:creator":["Hurst, Jerod; 0000-0002-6667-7482"],"dc:date":["2018-10-26T02:54:20Z","2018","2018-06-06 09:09:47"],"dc:description":["Ph.D.","Environmental contamination by antimicrobials and dissemination of antimicrobial resistance genes (ARGs) through the excretion of administered antimicrobials in food-producing animals can potentially exacerbate the global issue of increased infections by antimicrobial resistant bacteria. Various mitigation strategies in large livestock operations for controlling the environmental dissemination of antimicrobials and ARGs exist, where manure treatment may provide the most direct strategy for removing residues prior to land application of manure for crop field fertilization. This research examined the occurrences of five antimicrobial classes and various ARGs present in dairy farms employing different manure management strategies. Residues of antimicrobials were analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS), while the prevalence of ARGs was investigated using quantitative polymerase chain reaction (qPCR), to elucidate potential relationships between ARG levels and antimicrobial use. Lastly, two novel manure treatment strategies were investigated for their potential to remove both antimicrobials and ARGs as technologically advanced mitigation strategies for combating antimicrobial resistance dissemination in agricultural environments.A comprehensive evaluation of antimicrobial occurrences present in dairy manure was explored in Chapter 2 to assess the efficiencies of 11 different dairy manure management systems at removing antimicrobial compounds across six collection dates. Of the four antimicrobial compounds detected among the large farm cohort, tetracyclines and sulfonamides were the only antimicrobial classes to be detected. Comparisons among the total tetracycline concentrations (ng/g DW) and tetracycline administration (mg) revealed no correlation, suggesting large variability in manure storage or manure sampling and warrants future research to investigate the possible discrepancies. Also, tetracycline residues were found to generally persist after each manure management system where anaerobic digestion effluent concentrations ranged from 167 to 4890 ng/g and composting treatments provided total concentrations ranging from 213 to 2430 ng/g after treatment. Sulfadimethoxine, one sulfonamide which provided detection along one treatment process, was not found to be significantly affected by manure treatment with anaerobic digestion and further long-term storage.Chapter 3 investigates the temporal and farm-based variability of 13 different ARGs conferring resistance mechanisms to sulfonamides, tetracyclines, beta-lactams, aminoglycosides, and macrolide antimicrobial classes. Farm dissimilarity in ARG prevalence was observed, suggesting each farm contains a unique resistome inherent in the microbial community. Temporal trends were observed using nMDS and targeted ARG data trends suggesting lower prevalence of ARGs during the winter months (December and March), possibly indicating bacterial population alterations during the colder months. It was also observed that the occurrences of ARGs generally did not correlate to the administration of tetracycline and beta-lactam antimicrobials, suggesting the presence of antimicrobials may contribute to ARG dissemination to a lesser extent than previously believed and other factors of bacterial selective pressure should be investigated. Manure from an antimicrobial-free farm was collected and studied to compare changes in ARG prevalence to that found in dairy manure collected from conventional farms that utilize antimicrobials. Antimicrobial-free manure provided positive detections for 6 of the 9 total ARGs investigated. Comparisons to antimicrobial-free manure revealed larger occurrences of ereB, OXA-2, and VEB-1 genes from manure collected from the conventional farms, suggesting these genes are affected the most by continual exposure to antimicrobials. Long-term storage manure was not found to contain significantly higher ARG prevalence values when compared to untreated manure.In Chapter 4, a novel liquid manure treatment technique known as Livestock Water RecyclingTM (LWR) was investigated for its potential to remove ionophore antimicrobials throughout the treatment process. An analytical method was developed for the sample extraction and analysis (via LC-MS/MS) of seven ionophore antimicrobials approved for use in the United States then applied to samples collected at a dairy farm with a newly installed LWR system. Two ionophore antimicrobials, monensin and lasalocid, were detected in separated manure solids and separated manure liquids form the dairy farm. Monensin concentrations when adsorbed onto solid manure fractions ranged from 220 to 1,200 ng/g and was not substantially removed among each individual treatment step. Monensin was the only ionophore detected in the separated liquid fractions of manure, where concentrations were reduced from 42 ng/mL to 7 ng/mL after reverse osmosis treatment providing an average percent removal for three sample collections of 85%. Lasalocid was only detected when adsorbed onto solid manure fractions, but was not significantly reduced among the individual treatment steps of the LWR system.Chapter 5 investigated the efficacy for a solid manure treatment technique known as a Bedding Recovery UnitTM (BRU) for removing both antimicrobials and ARGs during a short-term composting procedure (24 hours). Two antimicrobials were detected, oxytetracycline and sulfadimethoxine, where their removal behaviors differed after treatment. Oxytetracycline was observed to have a 45% removal of the parent antimicrobial compound while sulfadimethoxine was not shown to be significantly changed when comparing the solid manure influent to the solid manure effluent. Conversely, ARGs were shown to be reduced after the short-term composting procedure with removal values of 75%, 98%, and 94% for sul1, tetO, OXA-1 respectively. The int1 gene, which has been linked to horizontal gene transfer, was also investigated for the possible removal capabilities where it was shown to have a 60% reduction in the normalized gene copies after BRU treatment of the solid manure. These results indicate the efficiency of the BRU system for removing ARGs, however antimicrobial compounds in general were not removed to the same extent suggesting antimicrobials have higher stability compared to ARGs under aerobic conditions suggesting different treatment conditions are needed for efficient mitigation during manure treatment.Lastly, Chapter 6 examines the detection of beta-lactam antimicrobials in dairy manure by using either indirect enzyme-linked immunosorbent assay (ELISA) or by LC-MS/MS analysis. An indirect ELISA method was utilized to act as a screening tool for the detection of beta-lactams, where two separate kits were evaluated (beta-lactam class specific and ceftiofur specific). In studying the occurrences of beta-lactams by ELISA, the majority of the samples did not show positive detections. The few samples that showed positive detections were not confirmed by LC-MS/MS, which suggest that there may be interfering matrix components that bind to the antibodies used in the ELISA method resulting in false positives. An LC-MS/MS method was developed to increase the selectivity of detections, where a solid-liquid extraction procedure was also validated. This LC-MS/MS method was applied to study the degradation of beta-lactams present in fresh manure where significant degradation occurred over a 14-day period. Estimated half-lives of beta-lactams ranged from 2.2 to 4.5 days, assuming a pseudo-first order degradation rate indicating beta-lactams (if excreted from the cow unmetabolized) are quickly degraded in manure matrix."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/10477/78498"],"dc:language":["eng"],"dc:publisher":["State University of New York at Buffalo"],"dc:rights":["Users of works found in University at Buffalo Institutional Repository (UBIR) are responsible for identifying and contacting the copyright owner for permission to reuse. University at Buffalo Libraries do not manage rights for copyright-protected works and cannot assist with permissions.","Copyright retained by author."],"dc:subject":["analytical chemistry","agriculture"],"dc:title":["Comprehensive Evaluation of Dairy Manure Management Strategies for the Removal of Antimicrobials and the Spread of Antimicrobial Resistance Genes"],"dc:type":["Text","Dissertation"]},"updated_at":"2026-07-27T19:05:09Z"}