In-the-field detection and molecular characterization of parasites on fresh produce using next generation sequencing

The main goal of this project will be to develop an in-the-field portable DNA sequencing platform for the simultaneous detection and genotyping of foodborne protozoan parasites contaminating fresh produce. The use of this new technology will allow for much faster and more accurate results during foodborne illness outbreak investigations or in parasite surveillance studies, and will fill large knowledge gaps that currently exist. This information will allow for the development of more accurate risk assessments, guidelines and polices associated with parasites on foods. The specific objectives of this project include 1) optimizing the extraction of target DNA from fresh produce, and evaluating DNA library preparation systems for their compatibility with the minION sequencer; 2) optimizing the bioinformatic analysis of real-time sequence data generated by the minION; and 3) using whole genome sequencing on multiple geographic isolates of Cyclospora in order to identify markers for genotype/subtype discrimination.