{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/106393"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/106393","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Detection of antibiotic resistance genes in gardening composts","abstract":"Compost is an organic fertilizer widely used for gardening. To evaluate the risk of antibiotic resistance and potential pathogens in composts, two homemade composts, eight commercially available composts, and one immature swine mortality compost were collected and analyzed by high-throughput quantitative polymerase chain reaction (qPCR). One soil sample without a known application of compost or manure was used as the control. Five genes related to potential pathogenic bacteria including ftsZ and uidA of Escherichia coli, ttrC of Salmonella typhimurium, 23S rRNA gene of Enterococcus spp., and atpE of Mycobacterium spp. were absolutely quantified using standard curves. 95 antibiotic resistance genes (ARGs) were relatively quantified by comparing the abundance of the target gene with the abundance of the 16S rRNA gene. The relative abundance of target genes in each compost sample was then compared with that in control soil to get the enrichment condition of target genes in compost samples. Aminoglycoside resistance genes (aadA, aadA2, strB) were prevalent in all compost samples. Phenicol resistance gene floR was also enriched in all compost samples. For commercially available manure composts, tetracycline resistance gene tetW was enriched. But in homemade compost, tetW was under the detection limit. The immature swine mortality compost contained higher numbers of different ARG types with much higher concentrations (up to 510,000 fold). Five of eleven compost samples had potential pathogen genes detected, including both homemade composts, two commercially available manure composts, and the immature swine mortality compost. The atpE gene of Mycobacterium spp. was detected in all five positive samples. Immature swine mortality compost had ftsZ, uidA, and 23S rRNA gene detected. The results of this study suggest that though homemade composts had fewer ARGs detected than commercially available manure composts, more copies of atpE were detected in homemade composts. The immature swine mortality compost was the worst, which had the highest concentrations and the most variety of both ARGs and potential pathogen genes. Though ARGs and potential pathogen genes were detected in high abundance in this study, the actual risk of antibiotic resistance and pathogenic bacteria infection is not able to be fully evaluated. More studies on the viability of pathogenic bacteria and on the locations of ARGs are required to evaluate the actual health risk of different types of composts.","abstract_html":"Compost is an organic fertilizer widely used for gardening. To evaluate the risk of antibiotic resistance and potential pathogens in composts, two homemade composts, eight commercially available composts, and one immature swine mortality compost were collected and analyzed by high-throughput quantitative polymerase chain reaction (qPCR). One soil sample without a known application of compost or manure was used as the control. Five genes related to potential pathogenic bacteria including ftsZ and uidA of Escherichia coli, ttrC of Salmonella typhimurium, 23S rRNA gene of Enterococcus spp., and atpE of Mycobacterium spp. were absolutely quantified using standard curves. 95 antibiotic resistance genes (ARGs) were relatively quantified by comparing the abundance of the target gene with the abundance of the 16S rRNA gene. The relative abundance of target genes in each compost sample was then compared with that in control soil to get the enrichment condition of target genes in compost samples. Aminoglycoside resistance genes (aadA, aadA2, strB) were prevalent in all compost samples. Phenicol resistance gene floR was also enriched in all compost samples. For commercially available manure composts, tetracycline resistance gene tetW was enriched. But in homemade compost, tetW was under the detection limit. The immature swine mortality compost contained higher numbers of different ARG types with much higher concentrations (up to 510,000 fold). Five of eleven compost samples had potential pathogen genes detected, including both homemade composts, two commercially available manure composts, and the immature swine mortality compost. The atpE gene of Mycobacterium spp. was detected in all five positive samples. Immature swine mortality compost had ftsZ, uidA, and 23S rRNA gene detected. The results of this study suggest that though homemade composts had fewer ARGs detected than commercially available manure composts, more copies of atpE were detected in homemade composts. The immature swine mortality compost was the worst, which had the highest concentrations and the most variety of both ARGs and potential pathogen genes. Though ARGs and potential pathogen genes were detected in high abundance in this study, the actual risk of antibiotic resistance and pathogenic bacteria infection is not able to be fully evaluated. More studies on the viability of pathogenic bacteria and on the locations of ARGs are required to evaluate the actual health risk of different types of composts.","abstract_has_math":false,"creators":["Mao, Yuqing"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Environ Engr in Civil Engr","degree_department":null,"school":null,"contributors":["Nguyen, Thanh Huong"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-03-02T22:18:17Z","date_published":"2020-03-02T22:18:17Z","updated_at":"2026-07-22T22:24:47Z","subjects":["compost","antibiotic resistance"],"languages":["en"],"rights":["Copyright 2019 Yuqing Mao"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/106393","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Nguyen, Thanh Huong"]},{"key":"dc:creator","label":"Author","values":["Mao, Yuqing"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-03-02T22:18:17Z","2022-03-03T10:15:13Z","2019-12-11","2019-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Environ Engr in Civil Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["compost","antibiotic resistance"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Yuqing Mao"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/106393"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Compost is an organic fertilizer widely used for gardening. To evaluate the risk of antibiotic resistance and potential pathogens in composts, two homemade composts, eight commercially available composts, and one immature swine mortality compost were collected and analyzed by high-throughput quantitative polymerase chain reaction (qPCR). One soil sample without a known application of compost or manure was used as the control. Five genes related to potential pathogenic bacteria including ftsZ and uidA of Escherichia coli, ttrC of Salmonella typhimurium, 23S rRNA gene of Enterococcus spp., and atpE of Mycobacterium spp. were absolutely quantified using standard curves. 95 antibiotic resistance genes (ARGs) were relatively quantified by comparing the abundance of the target gene with the abundance of the 16S rRNA gene. The relative abundance of target genes in each compost sample was then compared with that in control soil to get the enrichment condition of target genes in compost samples. Aminoglycoside resistance genes (aadA, aadA2, strB) were prevalent in all compost samples. Phenicol resistance gene floR was also enriched in all compost samples. For commercially available manure composts, tetracycline resistance gene tetW was enriched. But in homemade compost, tetW was under the detection limit. The immature swine mortality compost contained higher numbers of different ARG types with much higher concentrations (up to 510,000 fold). Five of eleven compost samples had potential pathogen genes detected, including both homemade composts, two commercially available manure composts, and the immature swine mortality compost. The atpE gene of Mycobacterium spp. was detected in all five positive samples. Immature swine mortality compost had ftsZ, uidA, and 23S rRNA gene detected. The results of this study suggest that though homemade composts had fewer ARGs detected than commercially available manure composts, more copies of atpE were detected in homemade composts. The immature swine mortality compost was the worst, which had the highest concentrations and the most variety of both ARGs and potential pathogen genes. Though ARGs and potential pathogen genes were detected in high abundance in this study, the actual risk of antibiotic resistance and pathogenic bacteria infection is not able to be fully evaluated. More studies on the viability of pathogenic bacteria and on the locations of ARGs are required to evaluate the actual health risk of different types of composts.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2021-12-01","The student, Yuqing Mao, accepted the attached license on 2019-12-10 at 21:39.","The student, Yuqing Mao, submitted this Thesis for approval on 2019-12-10 at 21:54.","This Thesis was approved for publication on 2019-12-11 at 12:46.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14781 on 2020-02-28 at 17:24:21","Made available in DSpace on 2020-03-02T22:18:17Z (GMT). No. of bitstreams: 4 MAO-THESIS-2019.pdf: 660124 bytes, checksum: 4fa8cc4237eaf486e6a590c814413c85 (MD5) AppendixB-2-??CT values for antibiotic resistance genes.xlsx: 54452 bytes, checksum: 20651d2b18f3d4617af6b63978210ace (MD5) AppendixC-2-?CT values for antibiotic resistance genes.xlsx: 51688 bytes, checksum: edc9ecf0414419d35e06bfeaee65a459 (MD5) LICENSE.txt: 4207 bytes, checksum: 912c420218d3233e81b52926d58f2bce (MD5) Previous issue date: 2019-12-11","Embargo set by: Seth Robbins for item 113936 Lift date: 2022-03-02T22:18:25Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only Restriction Lifted for Item 113936 on 2022-03-03T10:15:13Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Detection of antibiotic resistance genes in gardening composts"]}]}],"canonical_facts":{"dc:contributor":["Nguyen, Thanh Huong"],"dc:creator":["Mao, Yuqing"],"dc:date":["2020-03-02T22:18:17Z","2022-03-03T10:15:13Z","2019-12-11","2019-12"],"dc:description":["Compost is an organic fertilizer widely used for gardening. To evaluate the risk of antibiotic resistance and potential pathogens in composts, two homemade composts, eight commercially available composts, and one immature swine mortality compost were collected and analyzed by high-throughput quantitative polymerase chain reaction (qPCR). One soil sample without a known application of compost or manure was used as the control. Five genes related to potential pathogenic bacteria including ftsZ and uidA of Escherichia coli, ttrC of Salmonella typhimurium, 23S rRNA gene of Enterococcus spp., and atpE of Mycobacterium spp. were absolutely quantified using standard curves. 95 antibiotic resistance genes (ARGs) were relatively quantified by comparing the abundance of the target gene with the abundance of the 16S rRNA gene. The relative abundance of target genes in each compost sample was then compared with that in control soil to get the enrichment condition of target genes in compost samples. Aminoglycoside resistance genes (aadA, aadA2, strB) were prevalent in all compost samples. Phenicol resistance gene floR was also enriched in all compost samples. For commercially available manure composts, tetracycline resistance gene tetW was enriched. But in homemade compost, tetW was under the detection limit. The immature swine mortality compost contained higher numbers of different ARG types with much higher concentrations (up to 510,000 fold). Five of eleven compost samples had potential pathogen genes detected, including both homemade composts, two commercially available manure composts, and the immature swine mortality compost. The atpE gene of Mycobacterium spp. was detected in all five positive samples. Immature swine mortality compost had ftsZ, uidA, and 23S rRNA gene detected. The results of this study suggest that though homemade composts had fewer ARGs detected than commercially available manure composts, more copies of atpE were detected in homemade composts. The immature swine mortality compost was the worst, which had the highest concentrations and the most variety of both ARGs and potential pathogen genes. Though ARGs and potential pathogen genes were detected in high abundance in this study, the actual risk of antibiotic resistance and pathogenic bacteria infection is not able to be fully evaluated. More studies on the viability of pathogenic bacteria and on the locations of ARGs are required to evaluate the actual health risk of different types of composts.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2021-12-01","The student, Yuqing Mao, accepted the attached license on 2019-12-10 at 21:39.","The student, Yuqing Mao, submitted this Thesis for approval on 2019-12-10 at 21:54.","This Thesis was approved for publication on 2019-12-11 at 12:46.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14781 on 2020-02-28 at 17:24:21","Made available in DSpace on 2020-03-02T22:18:17Z (GMT). No. of bitstreams: 4 MAO-THESIS-2019.pdf: 660124 bytes, checksum: 4fa8cc4237eaf486e6a590c814413c85 (MD5) AppendixB-2-??CT values for antibiotic resistance genes.xlsx: 54452 bytes, checksum: 20651d2b18f3d4617af6b63978210ace (MD5) AppendixC-2-?CT values for antibiotic resistance genes.xlsx: 51688 bytes, checksum: edc9ecf0414419d35e06bfeaee65a459 (MD5) LICENSE.txt: 4207 bytes, checksum: 912c420218d3233e81b52926d58f2bce (MD5) Previous issue date: 2019-12-11","Embargo set by: Seth Robbins for item 113936 Lift date: 2022-03-02T22:18:25Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only Restriction Lifted for Item 113936 on 2022-03-03T10:15:13Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/106393"],"dc:language":["en"],"dc:rights":["Copyright 2019 Yuqing Mao"],"dc:subject":["compost","antibiotic resistance"],"dc:title":["Detection of antibiotic resistance genes in gardening composts"],"dc:type":["text"],"thesis:degree_discipline":["Environ Engr in Civil Engr"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:47Z"}