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<ol><li> 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</li> <li> Establish bioinformatics protocols that enable reliable detection of these biomarkers in produce-associated microbial community through sequence-based, culture-independent diagnostic tests </li><li>Apply the developed method to characterize the interactions between produce-associated microbial communities and STECs under pre- and post-harvested conditions</li>
<p>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.</p>