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Investigating Antimicrobial Resistance In Fresh Produce Using Quantitative Pcr And Whole Genome Sequencing
Date of Award
Nutrition and Food Science
Fresh produce is increasingly recognized as a source of pathogenic bacteria, antimicrobial-resistant bacteria, and antimicrobial resistance genes (ARGs). However, limited studies have been conducted on antimicrobial resistance (AMR) in fresh produce. The current investigation was aimed to gather information about the prevalence and abundance of ARGs associated with fresh produce. A total of 48 vegetable samples, which included 21 leafy greens and 27 root vegetables, were collected from three Detroit urban gardens that received no animal manure or waste-water. Total DNA was extracted from vegetable rinse. We targeted blaTEM, IntI-1, sul2, and tetM due to their high prevalence in the environment and high relevance to clinical outcomes. The relative abundance of ARGs was determined using quantitative PCR method, and the ARG profile was obtained using whole genome sequencing (WGS) of bacterial isolates in the selected vegetable samples. The relative abundance of blaTEM, IntI-1, sul2, and tetM was 2.09 X10-3, 9.17 X 10-2, 4.92 X10-3, and 3.52 X10-3, respectively. IntI-1, a gene marker for class 1 integron, showed higher abundance than the other three genes (p < 0.05, t-test). One of two E.coli isolates showed resistance phenotype to ampicillin. Enterococcus isolates showed resistance phenotype to different antimicrobials including streptomycin, ampicillin, erythromycin, and ciprofloxacin. WGS data showed multiple multidrug efflux pump genes and beta-lactamase gene, ampC in E.coli. Enterococcus isolates carried efflux pump genes, Macrolides-lincosamides-streptogramines (MLS) resistance genes and tetracycline resistance genes. In terms of mobile genetic elements (MGE), prophage was identified in E.coli, and Tn916 transposon was observed in all Enterococcus. Together with the high abundance of IntI-1 in vegetables, the data suggest the importance of MGE in disseminating AMR in fresh produce. The observation of AMR phenotypes and ARGs in locally-grown fresh produce indicates that fresh produce may serve as a potential vehicle of AMR microorganisms to cause food safety outcomes.
Amarasekara, Nirosha Ruwani, "Investigating Antimicrobial Resistance In Fresh Produce Using Quantitative Pcr And Whole Genome Sequencing" (2019). Wayne State University Theses. 837.