Foodborne Illness

November 11, 2019
Est. Reading: 3 minutes

Foodborne illnesses are not only an unpleasant personal experience for millions of Americans each year, they’re a logistical concern for businesses, with the potential to drive and keep people (and their dollars) away for good. As our food supply becomes increasingly global, the ability to accurately and quickly identify the source of any pathogen causing a foodborne illness has become exponentially more difficult. To ensure the safety of what we eat, the Food and Drug Administration (FDA) plans to build upon its early success with digital technology and whole-genome sequencing for its New Era of Smarter Food Safety.

Whole-genome sequencing

At its simplest, a genome is the information a cell needs to create an organism. Since an organism’s genome is as unique as a fingerprint, sequencing that genome is the first step in being able to quickly identify just what is making a person sick. Scientists generate the sequence by gathering samples of a particular food in a sterile environment, mashing it up, and conducting the genome analysis. The result is the fingerprint for that specific entity.

The problem is, having this information on hand at the local level is useful only under very limited circumstances. For instance, it would be enough if a group of people became ill after eating a single meal with food sourced locally, in a single sitting at a single event. With a few calls, it might be possible to identify the food causing the illness and take steps to keep it from being shipped to new locations.

More common is the case in which a number of people with nothing in common at first become ill within days of one another. Making a match between the pathogen causing the illness and the pathogen in each food involved is still fairly straightforward – if everything is sourced locally. But what if some of the food comes from sources across the globe? How are the fingerprints for those foods going to be of use in stopping the spread of the illness to additional locations when there is no way to readily communicate with other localities?


So, to bring whole-genome information into play on a global scale, the FDA created a United States-based open-source distributed network of labs in 2013. The result is GenomeTrakr – the stuff of foodie-sci-fi. It makes whole-genome sequences from foods around the world available globally. Any health agency, anywhere on the network, can upload data from a pathogen causing illness in their locality and receive information about entities that match or closely approximate that sequence. In effect, the power of the digital fingerprinting and related DNA sampling now in use in law enforcement  can be put to work for foodborne illness outbreaks by either making a match or reporting that the match is likely to be found within a certain cluster of “related” genome sequences. This game-changing use of whole-genome sequencing has already helped to halt the spread of global foodborne pathogens several times.

A digital framework

But global genome sequencing is still not all that is needed to safeguard the food supply – and your health. Being able to readily access a whole-genome sequence  can tell you which food is the culprit, but how do you know where the food originated, what path it took from field to plate, and where any additional product is currently located on its journey from field to plate?

The FDA’s remedy to this part of the challenge is to digitize the records kept at each step of a food’s journey through the global system. Rather than filling out a paper form that remains local or creating a paper-based dossier that travels with a food shipment, each step along the way will be documented in a globally accessible, digital format. The result will be a system that complements the GenomeTrakr by making it possible to trace the source of a foodborne pathogen to its point of origin in minutes rather than weeks or months.

Why does it matter? It matters because ready access to the genome, the origin, and the trail it traveled will make it possible to stop the flow of this food through the system: It will keep additional people from becoming ill.

A blueprint

As the first step in the FDA’s Strategic Blueprint for this New Era of Smarter Food Safety, agencies and companies from all parts of the food sector met in October to discuss the logistics of the new approach and offer input.  Considerations ranging from ownership of the data to concerns about data transfer were among the many raised. These issues are not not only vital to the integrity of the data in the system, but will also result in a system we can count on when we sit down to eat.

Published on The Spoon

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