About FDA
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.
| Milestone Description | Milestone Date | Milestone Status | Milestone 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 (12/1/2017) |
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 (12/1/2017) |
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. Conduct metagenomic surveillance of live dietary supplements for off-label contaminants |
|
Ongoing |
Key Projects Legend
| Milestone Status | Definition |
|---|---|
| Not Yet Started | Work for specific milestone has not yet been started. |
| Completed | Milestone and/or overall project is completed. |
| On Track | Milestone - On track for completion by milestone deadline. Quarter status - Project is on track for completion based on overall milestone status. |
| On Hold | Milestone - On hold, but deadline for completion has not passed. Quarter status - Project is on hold, based on overall milestone status. |
| Delayed | Milestone - Delayed as it has not been completed and deadline has passed. Quarter status - Project is delayed based on overall milestone status. |
