Define a suite of molecular technologies that will provide rapid (two-day) analyses of foodborne pathogens for precise comparison of clinical and foodborne isolates from on-going outbreaks. In order to capture and share data on surveillance and outbreak strains, a web-based user interactive database system that integrates these data-types with biological data (phenotypes, biomarkers, etc.) will be developed. This project will help to better ensure a timely and effective response by FDA to protect the public health and economic welfare of the country.CFSAN scientists have developed a suite of new technologies that can be applied to enteric foodborne bacterial outbreak analysis with a focus on establishing important food-clinical linkage attributes. These technologies enable rapid (two-day) genome-scale interrogation of outbreak strains and include (i.) genotyping with custom DNA microarray designs, (ii.) optical genome mapping for discrimination of large scale DNA insertions-deletions, and (iii.) identifying and sub-typing with panels of informative single nucleotide polymorphisms (SNPs) derived from whole genome sequence comparisons. As a compendium, a newly developed database platform, the Pathogen Annotated Tracking and Resource Network (PATRN, <a href=http://www.patrn.net/ target=”_blank”> www.patrn.net/patrn</a>), was developed for central storage and comparative real-time assessment of resultant data including important metadata of newly acquired outbreak strains in our continuously growing strain repository. For at least one of these technologies (microarray), the extensive in-house experience and comparative analysis of internal array data collected and analyzed from more than 500 unique isolates of E. coli and Shigella has been streamlined into a compact design intended for field use using signature sequences for sub-typing. Collectively, these advancements will undoubtedly improve food safety and potentially reduce economic impacts to the food industry by providing enhanced tools that redefine molecular epidemiology for trace back and source-tracking.A. Identify strains using optical mapping of whole genomes for precise comparison of clinical and foodborne isolates6/1/2010Completed6/30/2010B. Develop the PATRN (Pathogen Annotated Tracking Resource Network) database and initiate data curation and loading9/30/2010Completed9/30/2010C. Identify and differentiate strains using DNA microarrays for strain genotyping and profiling12/1/2010Completed12/1/2010D. Establish and maintain a strain repository for the permanent and secure storage of reference and outbreak strains12/30/2010Completed12/30/2010E. Identify strains using single-nucleotide polymorphisms (SNPs) and other gene markers from genomic sequence analysis of foodborne pathogens6/1/2011Completed6/30/2011F. With genomic data from our other high-resolution techniques/profiling, develop a streamlined next-generation custom microarray design using genomic signatures (genes, SNPs, molecular serotyping) for rapid identification of enteric foodborne pathogens with focus on field deployment6/15/2011Completed6/30/2011 http://www.fda.gov/AboutFDA/Transparency/track/ucm206221.htmFDA-TRACK CFSAN Dashboard਍††਍਍਍਍਍਍਍