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

dc.contributor.advisorFeng, Zeny
dc.contributor.advisorShapiro, Karen
dc.contributor.authorDeMone, Catherine
dc.date.accessioned2020-01-03T19:56:39Z
dc.date.available2020-01-03T19:56:39Z
dc.date.copyright2019-11
dc.date.created2019-12-04
dc.date.issued2020-01-03
dc.degree.grantorUniversity of Guelphen_US
dc.degree.nameMaster of Scienceen_US
dc.degree.programmeBioinformaticsen_US
dc.description.abstractZoonotic, 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.sponsorshipNatural Sciences and Engineering Research Council
dc.description.sponsorshipCanada Excellence Research Chairs
dc.description.sponsorshipUniversity of Guelph Department of Mathematics and Statistics
dc.description.sponsorshipUniversity of Guelph Bioinformatics graduate program
dc.identifier.urihttp://hdl.handle.net/10214/17701
dc.language.isoenen_US
dc.publisherUniversity of Guelphen_US
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjectmetabarcodingen_US
dc.subject18S rRNAen_US
dc.subjectzoonotic protozoaen_US
dc.subjectshellfishen_US
dc.subjectbioinformaticsen_US
dc.titleA Novel Bioinformatics Pipeline for 18S rRNA Amplicon-based Detection of Protozoan Parasites in Shellfishen_US
dc.typeThesisen_US

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