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U.S. Department of Health and Human Services

About FDA

New Technologies for Outbreak Strain Analysis

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.

Milestone DescriptionMilestone DateMilestone StatusMilestone Completion Date

A. Identify strains using optical mapping of whole genomes for precise comparison of clinical and foodborne isolates


Completed 6/30/2010

B. Develop the PATRN (Pathogen Annotated Tracking Resource Network) database and initiate data curation and loading


Completed 9/30/2010

C. Identify and differentiate strains using DNA microarrays for strain genotyping and profiling


Completed 12/1/2010

D. Establish and maintain a strain repository for the permanent and secure storage of reference and outbreak strains


Completed 12/30/2010

E. Identify strains using single-nucleotide polymorphisms (SNPs) and other gene markers from genomic sequence analysis of foodborne pathogens


Completed 6/30/2011

F. 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 deployment


Completed 6/30/2011

Key Projects Legend

Milestone StatusDefinition
Not Yet StartedWork for specific milestone has not yet been started.
CompletedMilestone and/or overall project is completed.
On TrackMilestone - On track for completion by milestone deadline. Quarter status - Project is on track for completion based on overall milestone status.
On HoldMilestone - On hold, but deadline for completion has not passed. Quarter status - Project is on hold, based on overall milestone status.
DelayedMilestone - Delayed as it has not been completed and deadline has passed. Quarter status - Project is delayed based on overall milestone status.


Note: The data provided on this website is produced on an ongoing basis for performance management purposes and is subject to change due to updates of preliminary estimates, corrections, or other reasons. In addition, FDA may change the type or amount of data provided on this website at any time. Information marked as "Completed" may include measures and/or key projects for which activities are ongoing but no longer tracked as part of FDA-TRACK.