Whole Genome Sequencing Program (WGS)

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Whole genome sequencing reveals the complete DNA make-up of an organism, enabling us to better understand variations both within and between species. This in turn allows us to differentiate organisms with a precision that other technologies do not allow. FDA is using this technology to perform basic foodborne pathogen identification during foodborne illness outbreaks and applying it in novel ways that have the potential to help reduce foodborne illnesses and deaths over the long term both in the U.S and abroad.

The most basic application of this technology to food safety is using it to identify pathogens isolated from food or environmental samples. These can then be compared to clinical isolates from patients. If the pathogens found in the food or food production environment match the pathogens from the sick patients, a reliable link between the two can be made, which helps define the scope of a foodborne illness outbreak. This type of testing has traditionally been done using methods such as PFGE, but there are some strains of Salmonella spp. that PFGE is unable to differentiate. Whole genome sequencing performs the same function as PFGE but has the power to differentiate virtually all strains of foodborne pathogens, no matter what the species.

However the most promising and far reaching public health benefit may come from pairing a foodborne pathogen’s genomic information with its geographic location and applying the principles of evolutionary biology to determine the relatedness of the pathogens. Why? Because, the genomic information of a species of foodborne pathogen found in one geographic area is different than the genomic information of the same species of pathogen found in another area. Knowing the geographic areas that pathogens are typically associated with can be a powerful tool in tracking down the root source of contamination for a food product, especially multi-ingredient food products whose ingredients come from different states or countries. The faster public health officials can identify the source of contamination, the faster the harmful ingredient can be removed from the food supply and the more illnesses and deaths that can be averted. To realize this goal FDA is spearheading an international effort to build a network of laboratories that can sequence the genomes of foodborne pathogens and then upload the genomic sequence of the pathogen and the geographic location from which the pathogen was gathered into a publicly accessible database. As the size of the database grows, so will its strength as a tool to help focus and speed investigations into the root cause of illnesses.

FDA’s foods program has been utilizing whole genome sequencing since 2008.

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GenomeTrakr: Using Genomics to Identify Food Contamination

The CFSAN Genomics team is coordinating efforts by State and Federal public health officials to sequence pathogens collected from foodborne outbreaks, contaminated food products and environmental sources. The genome sequences are archived in an open-access genomic reference database called GenomeTrakr, 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 from ingesting the Salmonella Montevideo pathogen. 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 confirm that the spice coatings (red and black pepper rub) were the source of the contamination at the New England facility.

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

See a list of recent outbreaks

Page Last Updated: 08/29/2014
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