Food safety authorities may soon be able to match pathogens to a particular region much like detectives match crime scene evidence with the DNA of a suspect.
The Food and Drug Administration, the University of California-Davis, Agilent Technologies Inc. and the Centers for Disease Control and Prevention will work together to create a public database of 100,000 food pathogen genomes.
The genomic sequencing will be coordinated by UC-Davis and will be housed at the National Institutes of Health’s National Center for Biotechnology Information.
Tests made possible by the database are expected to have the potential to reduce the typical public health response time foodborne disease outbreak to days instead of weeks, said one official connected to the project.
Steve Musser, director of the office of regulatory science at the FDA’s Center for Food Safety and Nutrition and lead FDA official in the database effort, said the industry will also have access to the database.
“Industry has always asked for more information during tracebacks and now they should have the same information we do,” Musser said.
Musser said the technology would likely have allowed investigators to know that the salmonella Saintpaul outbreak in 2008 was caused by peppers and not tomatoes. Florida tomato industry representatives said that misstep cost them more than $100 million.
Researchers already have looked at a lot of preliminary genomics data on several different types of salmonella related to outbreaks, he said.
“In all cases those have shown geographic resolution and we could tell what part of the country or the world a particular organism came from,” he said.
The environmental conditions of various regions and also patterns related to other microbes living in the environment influence the genomics of specific bacteria pathogens, Musser said.
The real power of the database will be priority samples, such as salmonella, E. coli, or listeria isolated from different places in the world so authorities will be able to quickly determine where each pathogen came from, he said.
“We would like to link bacteria to certain regions of the world or the U.S.,” Musser said.
The ability to determine exactly where the bacteria came from is not fully explored yet, he said.
“We can tell the difference between East Coast, Midwest and Western Coast of the U.S.,” he said. “Whether we can do north south and countrywide is not determined yet.”
It may take five years to input all 100,000 genomes in the database, he said.
“We think probably before that we will start having significant amounts of data to start making predictions earlier,” Musser said.
Musser said there is much hope that the database tool could help FDA target resources more effectively.
“Right now it can take months to figure out where a particular contaminant is coming from in a food, but we really need to close that down to days,” Musser said.
The data could help prevent collateral damage to food producers during an outbreak investigation.
“If we know for example that a particular organism can be linked to something from outside the U.S., then that won’t impact U.S. growers,” he said.
Where federal authorities would have previously warned against eating a particular commodity because of an outbreak investigation, they could change their advisory to the implicated commodity in a particular region.
“That would have real value to industry,” he said.
As part of its efforts for the collaboration, UC-Davis is forming a consortium to support the 100K Genome Project. The consortium participants will draw from a variety of agencies, including federal, state and local public health laboratories, food manufacturers, industries and academic organizations, according to a news release from the FDA. Organizations interested in the collaboration effort can contact Bart Weimer, UC-Davis program director at firstname.lastname@example.org.