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U.S. Department of Health and Human Services


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Whole Genome Sequencing Program (WGS)

August 1, 2013

Person in lab

Since 2008, research scientists at FDA’s Center for Food Safety and Applied Nutrition (CFSAN) have used whole genome sequencing (WGS) to investigate food contamination and foodborne illness outbreaks.

Knowing the exact order of molecules in an organism’s genome allows FDA researchers to quickly and accurately identify specific strains of pathogens (such as Salmonella, E. coli and Listeria disclaimer icon) in foods that make people ill.

Once the pathogen responsible for the illness is identified, researchers can trace it back to where the original contamination occurred. These trace back investigations help improve the safety of our food supply. Genomic data also helps identify which food products need to be recalled, protecting consumers from harmful products.

On this page:

Genome Trakr: Using Genomics to Identify Food Contamination

The CFSAN Genomics team is coordinating efforts by State and Federal public health to sequence pathogens collected from foodborne outbreaks, contaminated food products and environmental sources. The genome sequences will be archived in an open-access genomic reference database called Genome Trakr, that can be used to find the contamination sources of current and future outbreaks.

 How Outbreak Investigators Use Genomic Data

In 2009-2010, nearly 300 people in 44 states and the District of Columbia became ill with Salmonella Montevideo. Investigators were puzzled because the standard tracking procedures, such as food consumption questionnaires, suggested spiced salami was the culprit. However, conventional lab methods could not tell the difference between bacteria samples from the suspected spiced salami and samples of contaminated pistachios (involved in a previous investigation at a New England processing facility). Which food had really caused this outbreak – the pistachios, the salami, or the spice coating on the salami?

By using genomic data, scientists were able to trace the contamination back to the spice coatings (red and black pepper rubs) used in the production of salami at the suspected facility. Subsequently, the FDA issued several recalls of meat products containing contaminated black or red pepper.

Read FDA’s article in The New England Journal of Medicine (March 2011) about how genome sequencing helped resolve a salmonellosis outbreak. disclaimer icon

Find archived data from such investigations

Monitoring Food Safety

Many food processing plants have resident Salmonella and Listeria strains, but safe food-handling practices should prevent those bacteria from contaminating products that reach consumers. Collecting samples and cataloging whole genome sequences from food production sites can help monitor compliance with FDA’s rules and safe food-handling practices. Subsequent samples, either from routine testing or from an outbreak, can then be matched to genomic databases for identification and trace back.

Read about another food contamination investigation: Salmonella Enteritidis found in eggs disclaimer icon

Learn about the Coordinated Outbreak Response & Evaluation (CORE) network’s role in food safety

Find out more about how government responds to food illness outbreaks at www.FoodSafety.gov.

See a list of recent outbreaks