Genome Sequencing of 100,000 Foodborne Pathogens Underway

The U.S. Food and Drug Administration, along with the help of university researchers and a private company, have announced that they will be conducting genome sequencing on 100,000 foodborne pathogens. Known as “The 100K Genome Project,” the FDA and the Unversity of California Davis and Agilent will be developing this new database wit the hope of creating a system to allow health officials to cut down the time it takes to identify the source of an outbreak. As of present time, investigators identify clusters of illnesses by uploading pathogens isolated from different individuals to the government-mainted PulseNet database. However, this database can only tell which cases are related, and cannot provide specific genetic details that are needed to figure out where the illness is coming from.



Steven Musser, Director of the Office of Regulatory Science at FDA’s Center for Food Safety and Applied Nutrition, who is working on the genome sequencing project, says this new database will supplement PulseNet by providing high-resolution data, such as where an organism was found, whether it is resistant to any antibiotics and may even be able to identify the food source. “In terms of resolution it would be sort of like looking at the stars with the Hubble space telescope versus looking at them with binoculars,” explains Musser. The FDA already has evidence that this system will work. One of the 500 strains that has already been sequenced was a strain of Salmonella Bareilly isolated from India that turned out to be the very same strain that caused an outbreak linked to raw tuna product this spring. The plant that processed the tuna implicated in that outbreak was only six miles from where the sample analyzed by FDA was found.

I hope this helps with the control and regulation of products that go on recall due to diseases and outbreaks. As a blueberry farmer, I know how easily one plant can cause trouble to the entire farm due to the inability to successfully locate where the disease is coming from. During the recent lettuce E. coli outbreak, many products that were not infected had to be taken off of the shelves due to the inability to successfully locate the source of the outbreak. With this new genome sequencing project, I hope that cases like these will no longer exist.