Food pathogen genome database to aid in investigations - The Packer

Food pathogen genome database to aid in investigations

07/18/2012 03:35:00 PM
Tom Karst

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.”

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