Microbial characterization of irrigation waters using rapid, inexpensive and portable next generation sequencing technologies

New microbial detection approaches such as next generation sequencing (NGS) are being increasingly applied for tracing microbial contaminants entering the food chain. The produce industry can directly benefit from these powerful new approaches, such as shotgun metagenomics, which allow for the rapid identification of all the bacterial, viral, fungal, and protozoan pathogens in water, soil, or product samples in a single assay, thereby eliminating the need for many different detection assays. Ultimately, these novel approaches will be able to reduce the time and cost of not just food safety surveillance but also plant pathogen surveillance programs by combining everything into a single rapid assay. However, the application of these new NGS approaches need to be verified and validated for use by the produce industry. The goal of this project is to investigate two NGS technologies (Illumina iSeq100 and Oxford Nanopore MinION) that offer slightly different approaches for pathogen detection, and identify the benefits and limitations of each, verify the results, and validate the technologies for use by the produce industry. To accomplish this project, we have the following objectives: (1) Evaluate the detection limits of the iSeq100 and MinION sequencing technologies for three bacterial pathogens, two viral pathogens, and one protozoan pathogen in agricultural waters of varying quality. (2) Use shotgun metagenomics to characterize the microbial communities of agricultural waters from several Southwest regions using the “gold standard” of large amounts of Illumina sequencing and compare to the portable MinION technology. (3) Conduct whole genome sequencing, shotgun metagenomic, MinION and iSeq100 workshops/trainings for the produce industry. The results of this study will provide recommendations and guidelines to the produce industry regarding the proper implementation of iSeq100 and MinION technologies in food safety surveillance programs.