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Title:Detection of antibiotic resistance genes in gardening composts
Author(s):Mao, Yuqing
Advisor(s):Nguyen, Thanh Huong
Department / Program:Civil & Environmental Eng
Discipline:Environ Engr in Civil Engr
Degree Granting Institution:University of Illinois at Urbana-Champaign
antibiotic resistance
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.
Issue Date:2019-12-11
Rights Information:Copyright 2019 Yuqing Mao
Date Available in IDEALS:2020-03-02
Date Deposited:2019-12

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