You might have heard about the Center for Disease Control (CDC) and US Food and Drug Administration (FDA) sharing information about the Whole Genome Sequencing (WGS). What is this exactly and what does it mean for food safety and the food industry?


WGS is a technique that allows scientists to determine the exact DNA fingerprint of biological cells by learning the cell’s DNA base sequence. In doing so, they can learn a lot about the organism and its origin.


For example, if you find positives while testing for Listeria spp., your next step is to find out if you have Listeria monocytogenes or another Listeria. You could also go slightly further to determine if the listeria found is the same in other sampling sites, or if there are multiple strains. WGS allows for every accurate differentiation of strains, making it a useful tool for manufacturing locations when investigating repeat positives.

To date, regulatory has gained the most benefit from the new technology. In the USA, the FDA has started a program called GenomeTrakr, which attempts to identify the whole genome sequence of different pathogens isolated during plant inspections and foodborne illness outbreaks. According to the FDA, the GenomeTrakr network is the first distributed network of laboratories to utilize WGS for pathogen identification. It consists of public health and university laboratories that collect and share genomic and geographic data from foodborne pathogens. The generated data is housed in public databases at the National Center for Biotechnology Information, and is accessed by researchers and public health officials for real-time comparison and analysis. This program can speed up foodborne illness outbreak investigations and reduce foodborne illnesses and deaths.


A similar program at the CDC, PulseNet, is evolving from older techniques to WGS as well. This improvement advances the agencies’ ability to identify outbreaks and their causes, and as a result, minimize the size of an outbreak.


However, most have realized that the future is about analysis of large amounts of data to correlate illnesses. The graph shows the number of sequences added to the FDA GenomeTrakr since its inception. As you can see, the number is rapidly increasing; up to 1,000 new sequences are added each month. While the focus was originally on Listeria monocytogenes and Salmonella, the FDA and its partners are now sequencing pathogenic E. coli, Campylobacter, and other pathogens, as well as parasites and viruses.

WGS Graph 1 - Source FDA

Source: U.S. Food and Drug Administration (FDA)

The most useful application of WGS lets the CDC correlate different patient samples with isolated samples from the FDA to reduce the number of foodborne illness cases. The graph shows that after two years of WGS, the number of Listeria clusters detected has increased, while the median number of illnesses has decreased. It also shows that the number of cases linked to food sources has increased from 6 (pre-WGS) to 96 (WGS year 2).


WGS Graph 2 - Source CDC

Source: Centers for Disease Control (CDC)

By comparing the WGS of multiple patients’ foodborne pathogens, the CDC can question patients with food borne illness and similar WGS about the food they ate to find a link. This technique is very powerful for outbreak investigations.


The cost of the equipment is decreasing to allow more national and state labs to be equipped with this new tool. Currently there are 29 labs in the USA participating in the GenomeTrakr program, with the FDA hoping to add more.


For the food industry, this program would help epidemologists to narrow down the type of food that sourced an outbreak. It would also allow the FDA to more rapidly identify the source or manufacturing facility and potentially limit the number of cases.


This technique is being rolled out in many industrialized countries. We can expect them to begin sharing information among themselves to pinpoint the source when a suspected food is imported from a different country. There are nine labs outside of the USA, in Argentina, Australia, Canada, Denmark, Germany, and the United Kingdom, participating in the GenomeTrakr program.



You can find out more about PulseNet and WGS by going to the CDC website at www.CDC.gov.

To find out about how FDA is using WGS and the GenomeTrakr program, go to www.FDA.gov.

Author: Commercial Food Sanitation, Richard Brouillette.