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U.S. Department of Health and Human Services

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Sequencing-based analytical methods for microbial contaminant detection

Description: A suite of methodologies will be developed for culture independent diagnostics applied directly to foods or their culture enrichments. This project will treat genomic sequencing as an analytical tool using state-of-the-art high-throughput Illumina MiSeq platforms available in field laboratories. In addition, it will enhance or replace front-end analyses for pathogen detection while further integrating such emerging new technology into the field component. Furthermore, it can be used to comprehensively reassess and improve standard culture-based methods. Collectively, these advancements will undoubtedly improve food safety and potentially reduce economic impacts to the food industry by providing an integrated solution based on a unified, single technology for the spectrum of microbial detection to strain subtyping.

Briefing Status: ON TRACK

Prior Briefing Status: ON TRACK

Milestone DescriptionMilestone DateMilestone StatusMilestone Completion Date
A. Establish metagenomic limits of detection of enteric pathogens in hazard commodity pairings
i. Shiga toxin producing E. coli (STEC) in fresh produce, specific initial focus on spinach 4/1/2016
Completed 9/1/2016
ii.Foodborne virus (HAV and norovirus) on fresh produce (berries and tomatoes) 8/1/2016
Completed 12/1/2017
iii. Salmonella in fresh produce with an initial focus on cilantro 8/1/2017
Completed 12/31/2016
B. Identify minimum enrichment timeframes for BAM culture protocols using sequencing analytics to detect =10 cfu.
i. Identify minimal timeframe for pre-enrichment and enrichment steps in BAM method for STEC detection on fresh produce. 9/1/2016
Completed 3/1/2016
ii. Determine the optimal enrichment time for detection of Salmonella in produce using the BAM method with an initial focus on cilantro. 9/1/2016
Completed 3/1/2016
C. Stratify BAM culture protocols using metagenomics sequencing analytics inform/improve culture media additive performance for BAM protocols.
i. Investigate performance of suggested BAM medium additives for E. coli detection and suggest recommendations. 9/1/2017
Completed 11/1/2017
ii. Evaluate BAM Salmonella enrichment broths to improve Salmonella detection in fresh produce with an initial focus on cilantro. 9/1/2016
Completed 7/1/2016
D. Investigate metagenomic commercial solution(s) for enteric pathogen signature depth.
i. Determine specificity for CosmosID discrimination of STEC pathogens 1/1/2017
Completed 4/1/2017
ii. Determine specificity of CosmosID for detection of Salmonella in produce with an initial focus on cilantro 9/1/2017
Completed 4/1/2017
E. Dietary supplement safety containing live microbial ingredients
i. Generate whole genome sequence reference database for market products 12/1/2018
Completed 12/1/2018
ii. Continue adding microbial DNA sequences to the whole genome sequence reference database 12/1/2023
On Track
iii. Conduct metagenomic surveillance of live dietary supplements for off-label contaminants 12/1/2023
On Track

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.