Creating a Fingerprint Database for Foodborne Pathogens
UNIVERSITY OF CALIFORNIA-DAVIS
PROBLEM
Efforts to identify and trace foodborne pathogens have traditionally relied on slow, 1940s technology to detect an outbreak or food contamination.
SOLUTION
Using DNA sequencing, a library of known pathogens is being built to rapidly determine the exact strain and source of outbreaks and food contamination for recalls.
FUNDING
Mars, Inc.
IBM
Department of Health and Human Services
Department of Defense
Agilent Technologies
Pacific Biosciences
Kapa Biosystems
Additional industry partners
RESEARCHERS
Bart C. Weimer, PhD, University of California, Davis
The genome of any organism can be used as a bar code, allowing quick identification of a particular strain. This is exceptionally important in food safety and public health efforts. If contamination is found on a food product—or, worse, someone contracts a bacterial infection—investigators need to know the pathogen and the potential sources of contamination along the food supply chain. The old way of doing things—growing bacteria—takes too long and cannot contain fast-moving outbreaks.
Dr. Bart Weimer and his team at UC Davis, School of Veterinary Medicine, are creating a massive database of genome signatures— collecting the “fingerprints” of 65,000 strains of Salmonella so far. The initiative, called the 100K Pathogen Genome Project, began as an innovative public-private-academic partnership. They have also partnered with international food safety agencies and universities to expand the database for global trade and traceability.
Their work enables public health agencies and the food industry to trace outbreaks to their source by comparing the genome of the pathogen to their database, which includes information on previously detected strains as well as their exact locations. The new approach swiftly provides conclusive evidence of the contamination source by processing millions of pieces of evidence.
“When foodborne illness outbreaks occur, the regulators and industry need to figure out traceability and accountability. Genomics has become so good that these attribution questions are now gone.”