Header graphic for print

Food Safety News

Breaking news for everyone's consumption

Genome Sequencing of 100,000 Foodborne Pathogens Underway

New database will speed up outbreak investigations

Over the past three years, scientists at the U.S. Food and Drug Administration have conducted whole genome sequencing on over hundreds of foodborne pathogens to get a detailed map of their DNA. Now, with the help of university researchers and a private company, they’re expanding that figure to 100,000.

The initiative, aptly titled “The 100K Genome Project,” is a private-public collaboration between FDA, the University of California Davis and Agilent, a testing technology company.

By developing this new database, FDA hopes to help health officials cut down on the time it takes to identify the source of an outbreak.

Right now, investigators are able to identify clusters of illnesses by uploading pathogens isolated from different individuals to the government-maintained PulseNet database. But the information in PulseNet can only tell which cases are related. It does not provide the genetic details needed to figure out what food the bug is coming from.

For that, investigators must question victims to see whether they ate a common food in the days preceding their illnesses.

“Humans tend to move around a lot and they don’t have a good memory of what they ate, so getting good information from humans is really hard,” explains Steven Musser, Director of the Office of Regulatory Science at FDA’s Center for Food Safety and Applied Nutrition.

Musser, 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 perhaps even the food on which it was found.

“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,” he explained in an interview with Food Safety News.

This new database will be comprised mostly of genetic information on pathogens isolated from food, he says, so if a human isolate is uploaded and matches a pathogen already in the database, investigators will know what region, or even business, the matching food sample came from.

FDA has evidence that this system will work. Of the 500 strains it has already sequenced – which will constitute the foundation of the new database – one 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.

While this connection was made after the outbreak had ended, Musser says that in the future, with a working database already in place, these links could be made while outbreaks are still ongoing, and could help officials identify contaminated food sooner.

The project is expected to increase the number of foodborne pathogens currently sequenced by 100 times said an FDA spokesperson.

UC Davis, whose labs will conduct the sequencing, has the capacity to sequence 1,000 pathogens per week, says Musser.

“This important project will harness the cutting-edge technology of genome sequencing to advance our understanding of and response to foodborne outbreaks,” said FDA Commissioner Margaret A. Hamburg, M.D. in a statement Thursday.

© Food Safety News