About FDA

Description: 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.

Accomplishment: 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, www.patrn.net/patrn), 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.