Fig.1. Scanning electron microscope image of Campylobacter jejuni bacteria, a top cause of bacterial food-related gastrointestinal illness in the United States (Credit: De Wood, Pooley, USDA, 2008).
Every year, foodborne illnesses kill nearly 2 million people around the world. These illnesses are caused by harmful bacteria, viruses, parasites, or chemical substances and present a very real danger to food security and health care. Food safety is the topic of the World Health Organization’s (WHO) World Health Day, today on April 7, with the slogan "From farm to plate, make food safe." In an effort to promote food safety, the WHO released guidelines to prevent food contamination that can create a vicious cycle of disease and malnutrition.
Although foodborne disease outbreaks are a huge problem -- affecting millions of people and costing billions of dollars to address -- some organizations are taking the problem down to the molecular level. A collaboration between 26 federal, state, and university labs promises to speed up outbreak response through the DNA analysis of common foodborne pathogens.
Identifying 100,000 pathogens
The University of California, Davis, Agilent Technologies, and the U.S. Food and Drug Administration (FDA) together hope to complete the ambitious task of sequencing the entire genomes of 100,000 types of foodborne pathogens. This work will be the foundation for the GenomeTrakr network, which has already done whole genome sequencing on more than 10,500 Salmonella spp. isolates and 2,700 Listeria spp. isolates. Their genome database, hosted by the National Center for Biotechnology Information (NCBI), offers the ability for researchers and public health officials to distinguish between different strains and even trace back to the exact pathogen type after an outbreak.
The use of whole genome sequencing has already halted food disease outbreaks, including a 2012 salmonella outbreak which sickened 258 people. GenomeTrackr and other gene databases offer immediate traceability in strains, which allow healthcare professionals to rapidly respond to an outbreak.
DNA sequencing, museums, and healthcare
In addition to tracing a pathogen to its source, sequence databases offer great opportunities in food security, species conservation, and biodiversity studies. For example, recent analysis of the International Center for Tropical Agriculture (CIAT) seed repository found 30 bean varieties able to survive and thrive in a warmer world. Increasingly inexpensive and requiring only a small amount sample material, sequencing offers researchers the ability to return to collections and extract DNA from specimens and collections previously thought to be unusable. Although GenomeTrackr still has many genomes to sequence, this effort is a powerful tool in the global fight for food safety.
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