FDA Assesses Impact of Whole Genome Sequencing Program.Sharing Whole Genome Sequencing with the World.GenomeTrakr: Pushing Back the Frontiers of Outbreak Response.Video overview of how foodborne pathogens are isolated from a food sample and sequenced.Includes updates on the number of pathogens sequenced 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 to better understand the environmental conditions associated with the contamination of agricultural products and to help develop new rapid methods and culture independent tests. The FDA Foods Whole Genome Sequencing Staff is coordinating efforts by public health officials to sequence pathogens collected from foodborne outbreaks, contaminated food products, and environmental sources. GenomeTrakr: Using Genomics to Identify Food Contamination 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.įDA’s foods program has been utilizing whole genome sequencing since 2008.

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. 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. 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. 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. 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. Its ability to differentiate between even closely related organisms allows outbreaks to be detected with fewer clinical cases and provides the opportunity to stop outbreaks sooner and avoid additional illnesses. 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. This type of testing has traditionally been done using methods such as PFGE, but there are some strains of Salmonella spp. 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. These can then be compared to clinical isolates from patients. The most basic application of this technology to food safety is using it to identify pathogens isolated from food or environmental samples.

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. This in turn allows us to differentiate between organisms with a precision that other technologies do not allow. Whole genome sequencing reveals the complete DNA make-up of an organism, enabling us to better understand variations both within and between species.

Proactive Applications of Whole Genome Sequencing Technology.

How FDA Uses Whole Genome Sequencing for Regulatory Purposes.

GenomeTrakr: Using Genomics to Identify Food Contamination.

Multi-Agency Use of Whole Genome Sequencing for Food SafetyįDA, CDC, USDA, and NCBI publish report about the adoption of whole genome sequencing for foodborne illness outbreak investigations and the public health benefits it offers.

Gene sequence definition