Whole-Genome Sequencing for Food Safety

Whole-genome sequencing (WGS) is a molecular technology or process that determines the complete DNA sequence of an organism. Sequencing the complete DNA of a foodborne pathogen, such as Salmonella, Listeria, E. coli, etc., plays an important role in public health protection. Historically, several molecular subtyping methodologies have been employed for this. But the methods were time consuming and expensive to use in foodborne illness outbreak surveillance systems. The new rapid sequencing methods (often referred as next-generation sequencing) that use WGS deliver results at low cost and turn time with wide applications that were previously not possible.


The information obtained from WGS helps investigators quickly identify the bacterial strain responsible for foodborne illness outbreaks. The data are reliable, efficient, and capable of providing location specificity. Other specific advantages are that it is easy to use and inexpensive; identifies the source of foodborne illness outbreak; helps in identification of related cases; helps in monitoring/tracking the transmission route; provides other useful information such as antibiotic resistance, virulence characteristics, serotype, etc.; helps in identifying the risks associated with these pathogens in our food; helps in determining intervention strategies.


FDA is using WGS to link pathogens isolated from food and facility to human illness. FDA is spearheading the network of laboratories that can sequence the whole genome of foodborne pathogens collected from contaminated food products and environmental samples and upload the information in the open-access platform GenomeTrakr, a collaboration among FDA, public health, and university laboratories.

When the WGS of a pathogen isolated from food or environmental swab samples is available, GenomeTrakr checks the PulseNet database to identify possible links to DNA fingerprints from patients. These sequences (from source and patient) are compared, and the database will show if other people are sick from the same strain, and if this has been isolated from a specific food or manufacturing facility. Once a cluster is identified, PulseNet works with laboratory and epidemiological investigation teams at CDC, federal food regulatory agencies, and state and local health departments to determine the source and causal microorganism responsible. Depending on this result, FDA will take appropriate corrective actions such as recalling the products, stopping further distribution, issuing public notices/alerts, and overseeing the company’s corrective action plan.


WGS technology has been successfully used in foodborne illness investigations by FDA, FSIS, and CDC. It provides a strong scientific platform for investigators to connect the dots in the case of an outbreak and to come up with intervention strategies to stop outbreaks sooner. In the future, food manufacturers should expect that any isolate obtained from a food or environmental swab sample will undergo WGS. The data will be stored in the GenomeTrakr database to be trackable in the event of a food safety crisis. Hence, it is vital for food manufacturers to be aware of this technology and its regulatory applications in foodborne illness outbreak surveillance.

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