Skip to main content
ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Research Project #427089

Research Project: Development of a Metagenomics-based Method for Improved Detection of Foodborne Pathogens

Location: Produce Safety and Microbiology Research

Project Number: 2030-42000-050-02-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 28, 2014
End Date: Jul 31, 2016

1. Identify and test the discriminatory power of gene signatures for Shiga toxin-producing Escherichia coli (STEC) to establish biomarkers that robustly distinguish STEC from innocuous relatives adapted to environmental niches; 2. Establish bioinformatics protocols that enable reliable detection of these biomarkers in produce-associated microbial community through sequence-based, culture-independent diagnostic tests; 3. Apply the developed method to characterize the interactions between produce-associated microbial communities and STECs under pre- and post-harvested conditions.

Biomarkers for Shiga toxin-producing Escherichia coli (STEC) will be generated by comparatively analyzing a large number STEC genomes with other E. coli genomes deposited in GenBank. A corresponding bioinformatics pipeline will be developed at GIT for accurate identification of STEC biomarkers in produce-associated metagenomic samples. The detection limit and sensitivity of the method will be evaluated using a “spiked” system on leafy greens, which will be carried out at the Agricultural Research Service. The interactions between STECs with produce-associated microflora under pre- and post-harvest conditions will be investigated using the developed metagenomic tools.