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A Novel Bioinformatics Pipeline for 18S rRNA Amplicon-based Detection of Protozoan Parasites in Shellfish

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dc.contributor.advisor Feng, Zeny
dc.contributor.advisor Shapiro, Karen
dc.contributor.author DeMone, Catherine
dc.date.accessioned 2020-01-03T19:56:39Z
dc.date.available 2020-01-03T19:56:39Z
dc.date.copyright 2019-11
dc.date.created 2019-12-04
dc.date.issued 2020-01-03
dc.identifier.uri http://hdl.handle.net/10214/17701
dc.description.abstract Zoonotic, pathogenic protozoa are a serious public health concern. Three common species, Cryptosporidium parvum, Giardia enterica, and Toxoplasma gondii have been detected in commercial oysters. Current methods of detecting protozoa in shellfish are not standardized and few are able to simultaneously identify multiple species of interest. Here we present a bioinformatics pipeline to process 18S rRNA amplicons extracted from oyster matrices for the purpose of detecting protozoan pathogens. The pipeline was successfully applied for detection of G. enterica cysts and C. parvum and T. gondii oocysts spiked into whole oyster homogenates and hemolymph. These results indicate that 18S rRNA metabarcoding coupled with the validated pipeline could be tested for monitoring wild oysters contaminated with protozoan pathogens. While this study focused on detecting three parasites of interest, the multispecies identification abilities of this method make it an ideal screening tool for a broad range of protozoan pathogens in shellfish. en_US
dc.description.sponsorship Natural Sciences and Engineering Research Council (NSERC), Canada Excellence Research Chairs (CERC), University of Guelph Department of Mathematics and Statistics, University of Guelph Bioinformatics graduate program en_US
dc.language.iso en en_US
dc.rights Attribution-NonCommercial-ShareAlike 4.0 International *
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/4.0/ *
dc.subject metabarcoding en_US
dc.subject 18S rRNA en_US
dc.subject zoonotic protozoa en_US
dc.subject shellfish en_US
dc.subject bioinformatics en_US
dc.title A Novel Bioinformatics Pipeline for 18S rRNA Amplicon-based Detection of Protozoan Parasites in Shellfish en_US
dc.type Thesis en_US
dc.degree.programme Bioinformatics en_US
dc.degree.name Master of Science en_US
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