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U.S. Department of Health and Human Services

About FDA

Early-Stage Pathogen Identification

Description: Use new omics technologies and pattern-recognition algorithms to analyze omic data for early-stage pathogen identification and to study how to improve food protection. As part of this process, a food pathogen research database is being designed with partners at the Virginia Bioinformatics Institute.

Definition: Antibiotic resistance developed from agribusiness use of antibiotics in the food chain is a continuing problem, especially with Salmonella. NCTR scientists have used DNA microarray technology to identify genes responsible for mitigating drug resistance in different species of Salmonella.

The ability of this high-data density analyses to rapidly detect hundreds of antimicrobial resistance genes can be beneficial to the FDA, state, and other federal agencies for analyzing patters of drug resistance in Salmonella and observing emerging drug-resistant species of Salmonella.

Public Health Outcome: Identification and molecular characterization of potential bacteria contaminants in foods, feed, clinical samples, and other FDA-regulated products.

1. Needs Assessment Survey

Reason for Study Cancellation: The principal investigator has left NCTR. Management determined that given limited resources, completion of the manuscript is not in the best interest of DPNM.

Briefing Status: COMPLETED

Prior Briefing Status: ON TRACK

Milestone DescriptionMilestone DateMilestone StatusMilestone Completion Date

a. Conduct and complete a needs assessment survey of existing Salmonella databases

5/1/2010

(9/1/2010)

Completed 8/15/2010

b. Complete draft publication describing needs assessment

5/1/2010

(11/1/2010)

(4/30/2011)

(11/1/2011)

Completed Canceled

c. Complete the peer review (NCTR and other FDA researchers) of draft publication

7/30/2011

(1/30/2012)

Completed Canceled

d. Obtain NCTR director approval of the draft publication via the document tracking system

5/31/2010

(11/1/2010)

(7/30/2011)

(2/28/2012)

Completed Canceled

e. Submit final publication on needs assessment survey results to scientific journal

9/30/2011

(3/31/2012)

Completed Canceled

2. High-Throughput Analyses of Pathogens

Reason for Study Cancellation: Due to reorganization and as a way to streamline reporting, this program measure was retired.

Briefing Status: COMPLETED

Prior Briefing Status: ON TRACK

Milestone DescriptionMilestone DateMilestone StatusMilestone Completion Date

a. Obtain additional PFGE data from the CDC (1)

4/30/2010

(12/31/2010)

Completed 5/1/2011

b. Continue survey and develop concept paper for high throughput analyses project

6/1/2010

(4/1/2011)

Completed 6/15/2011

c. Complete protocol for pilot project on high throughput analyses of pathogens

6/30/2010

(9/1/2010)

(8/1/2011)

(10/1/2011)

(1/1/2012)

Completed Canceled

d. Obtain NCTR Center Director approval on the protocol

11/1/2010

(10/1/2011)

(12/1/2011)

(7/1/2012)

Completed Canceled

e. Conduct research

N/A

Completed Canceled

f. Complete the assessment of research findings

9/1/2011

Completed Canceled

g. Complete the draft publication(s)

12/1/2011

Completed Canceled

h. Complete the peer review (NCTR and other FDA researchers) of draft publication

1/1/2012

Completed Canceled

i. Obtain NCTR director approval of the draft publication via the document tracking system

N/A

Completed Canceled

j. Submit final publication reporting on results from the high throughput analyses of pathogens

3/1/2012

Completed Canceled

Footnotes

  • (1) PFGE is an electrophoretic technique than can resolve the length of large DNA fragments by stimulating migration via altering the angle of the voltage source with respect to the gel. Depending on the gradient of the voltage, DNA fragments will respond differently according to nucleotide composition, thereby providing greater resolution than typical electrophoretic techniques that do not vary the direction of voltage application.

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.

Glossary

pathogen

an agent that causes disease

PFGE

Pulsed Field Gel Electrophoresis

CDC

Center for Disease Control

protocol

description of a study's objectives, approach and design, procedures, etc.

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.