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U.S. Department of Health and Human Services

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GenomeTrakr Program

Description: The GenomeTrakr Program is creating a sustainable network of public health laboratories using whole genome sequencing (WGS) to investigate foodborne illness outbreaks and attribute illnesses to specific food products, processing or farming practices, or geographic regions. The program is changing the way that foodborne illnesses are investigated, allowing authorities to investigate small illness clusters before there is a chance to sicken large numbers of people. The network is linked by a common, publically-accessible database that uses a common sequencing platform, with common laboratory and quality control procedures, common on-board training and a common metadata (sample information) standard. Since 2012, the network has expanded to 10 state health and agriculture laboratories, one commercial lab servicing the food industry, and one international lab. The network has built a database of over 10 thousand and 4 thousand Salmonella and Listeria monocytogenes genomes respectively from real time surveillance and historical collections. This database has supported multiple foodborne illness outbreak investigations and is fundamentally changing the way that outbreak investigations are conducted.

Accomplishment: As of October 1, 2018, the milestones of the GenomeTrakr network key project were completed. Work continues to harmonize international standards for Whole Genome Sequencing in collaboration with the International Standards Organization (ISO) and international organizations. These international standards continue to evolve as science and use of WGS technology advance. For more information about the GenomeTrakr program, please visit:https://www.fda.gov/food/foodscienceresearch/wholegenomesequencingprogramwgs/ucm363134.htm

Briefing Status: Completed

Prior Briefing Status: Completed

Milestone DescriptionMilestone DateMilestone StatusMilestone Completion Date
A. Develop FDA Trak-n-trace program (FDA compliance/CORE)
i. Develop hands-on genomic workbench to support compliance/enforcement strategies and Coordinated Outbreak Response and Evaluation (CORE) activities. 10/31/2018
Completed 10/31/2018
a. Develop software tools for genomic compliance workbench. 10/31/2016
Completed 11/30/2017
b. Test and evaluate software tools with compliance test cases. 10/31/2017
Completed 7/1/2018
c. Implement/deploy genomics tools for compliance/enforcement and outbreak investigations. 10/31/2018
Completed 10/31/2018
ii. Adapt Genomic information management system (GIMS) to employ metadata tracking to link WGS data to critical investigation metadata. 10/31/2017
Completed 7/1/2018
iii. Develop minimum quality control standards for state network in collaboration with CDC. 10/31/2016
Completed 6/30/2017
iv. Harmonize international standards for WGS in collaboration with International Organization of Standardization (ISO) and international organizations. 10/31/2018
Completed 10/1/2018
v. Develop international proficiency standards and program in collaboration with Global Microbial Identifier (GMI) group. 10/31/2017
Completed 9/30/2017
B. Develop a single WGS-based workflow for full Salmonella outbreak strain characterization.
i. Develop WGS Serotyping approach for Salmonella outbreak strain characterization. 10/31/2018
Completed 9/30/2017
a. Adapt SeqSero software to develop method for serotyping Salmonella pathogens. 10/31/2016
Completed 9/30/2017
b. Evaluate Seek-sero method for serotyping Salmonella pathogens. 10/31/2017
Completed 9/30/2017
c. Validate Seek-sero method for serotyping Salmonella pathogens. 10/31/2017
Completed 10/31/2017
d. Implement/deploy Seek-sero method for serotyping Salmonella pathogens. 10/31/2018
Completed 7/15/2018
ii. Integrate CVM-developed WGS anti-microbial resistance (AMR) screening tool- accurate correlation analysis between AST (phenotypic) (CVM lead). 10/31/2018
Completed 8/1/2018
a. Validate WGS AMR/AST tool. 10/31/2016
Completed 12/31/2017
b. Implement/deploy WGS AMR/AST tool. 10/31/2018
Completed 8/1/2018
iii. Integrate WGS microbial characterization tools (i-iii) into single WGS predictive software tool for outbreak/isolate strain characterization 10/31/2018
Completed 10/1/2018
a. Consolidate WGS outbreak characterization scripts or plug-ins into single dashboard toolbox for pathogen characterization. 10/31/2018
Completed 10/1/2018
b. Implement/deploy WGS microbial characterization tool for pathogen characterization. 10/31/2018
Completed 10/1/2018

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.