Finding needles in the haystack: development and application of next generation sequencing for detection of protozoan pathogens in shellfish

Principal Investigator: J. Trenton McClure
Co-Investigators: Karen Shapiro (University of Guelph) & Spencer Greenwood

Detection of parasites in food and water is a significant public health challenge. Current approaches commonly target single organisms, and screening for pathogens requires separate testing for multiple microorganisms, with substantial costs and labor. In contrast, next generation sequencing (NGS) can profile total microbial communities. However, the application of this innovative technology in environmental matrices or food remains challenging, including obstacles such as the relatively low concentrations of pathogens combined with an abundance of resident microorganisms that compete during the sequencing process.

The overall goal of this project is to develop an NGS assay for detection of three protozoan pathogens commonly implicated in food- and water-borne infections: Cryptosporidium spp., Giardia spp., and Toxoplasma gondii. Preliminary trials will infect artificial seawater and oyster tissues with parasite “cocktails” for method optimization and validation. Subsequent testing will use field-collected oysters from Prince Edward Island during the 2018 harvest season. The overall objective is to provide preliminary data that validates NGS as an effective tool for pathogen detection in environmental matrices. These results will prove essential for securing future extramural funding to support long-term research that uses this technology to investigate the drivers of parasite transmission in food and water.