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Education | Virtual

Event Title
Genome Trakr: How a Large Network of Sequencing Laboratories is Transforming Food Safety and Public Health

Thursday, July 13, 2017
12:00 p.m. -1:00 p.m., Eastern Standard Time (EST)

Presented by

Marc Allard, PhD
Research Microbiologist
FDA's Center for Food Safety and Nutrition
Webcast Lecture

Genome Trakr: How a Large Network of Sequencing Laboratories is Transforming Food Safety and Public Health

About the Presentation

Foodborne disease outbreaks are responsible for about 48 million illnesses, 325,000 hospitalizations, and 3,000 deaths every year in the U.S., according to CDC data. As the world becomes even more interconnected, FDA has recognized the urgency of creating new approaches and better tools to detect food contamination and stop outbreaks in their tracks.

The FDA-established GenomeTrakr is an innovative response to this global public health challenge that uses a cutting-edge technology called Whole Genome Sequencing (WGS).  This presentation will discuss the example of the 2015 Virginia sprout outbreak, where Whole Genome Sequencing (WGS) provided the lead.


In 2012, a pilot project, now a mature network called GenomeTrakr, was set up at the national level using WGS data to track foodborne outbreaks.  In this network, public health agencies collect and publicly share WGS data in real time. This high-resolution, rapidly growing database is being used in outbreak investigations at the state, national, and international level.

The GenomeTrakr network demonstrates how desktop WGS data can be used with traditional epidemiology for source tracking of foodborne pathogens. This new “open data” model enables greater transparency between federal/state agencies, our industry partners, academia, and international partners.

The high-resolution WGS data together with solid epidemiological evidence has dramatically enhanced our ability to identify the food source of current outbreaks for Listeria monocytogenes, for which the CDC is also contributing clinical isolates in real time. Understanding the root causes of foodborne contamination will help our academic, public health, and industry partners to develop preventative controls to make food safer globally.

About the Presenter

Dr. Marc W. Allard is a Senior Biomedical Research Services Officer in the Division of Microbiology in FDA’s Center for Food Safety and Nutrition. In 2008, Dr. he joined FDA, where he uses WGS of foodborne pathogens to identify and characterize outbreaks of bacterial strains, particularly Salmonella, E. coli, and Listeria.  He specializes in both phylogenetic analysis, as well as the biochemical laboratory methods that generate the WGS information.

Dr. Allard helped develop the first distributed network of laboratories that use WGS for pathogen identification and trace back, called the GenomeTrakr database, which is part of the NCBI Pathogen Detection web site. These tools are used daily for outbreak investigations.  Dr. Allard advises FDA on both WGS and phylogenetic methods as they apply to public health. 

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