Feed the Future
This project is part of the U.S. Government's global hunger and food security initiative.

Global Collaboration to Fight Foodborne Illness Using Whole Genome Sequencing Technology

We all need to eat food to survive. However, food can easily be contaminated with foodborne hazards during production, processing, shipping, distribution and preparation. According to the World Health Organization, 600 million people fall ill and 420,000 die, globally, after eating contaminated food every year. The food industry should routinely monitor the environment around food products, from field to fork, to prevent foodborne contaminations. Usually, the food industry, especially the small one, uses traditional microbiological methods to monitor the environment. Molecular-based methods obtain more precise views of the hygienic state of these environments. Pulsed-field gel electrophoresis (PFGE), a molecular-based method, has been widely used by the large food industry during the past decade.

Whole Genome Sequencing (WGS) is a novel, state of-the-art, rapid and accurate molecular-based technology that can be universally used to detect and identify pathogenic bacteria that cause foodborne disease outbreaks. Briefly, the steps of a bacterial WGS are: a) obtaining a pure culture of the bacteria, b) DNA extraction, c) library preparation and amplification, d) DNA sequencing, e) data analysis and f) biological interpretation.

WGS can differentiate between bacterial strains that the PFGE method does not allow. For example, PFGE is unable to differentiate between some strains of Salmonella spp. The ability of WGS to differentiate between organisms allows for faster detection of outbreaks. The faster the source of contamination is identified, the faster the harmful food can be removed from the market and the more illnesses and deaths can be prevented. WGS also has the ability to pair a foodborne pathogen’s genomic information with its geographic location; the genomic information of a pathogenic species is different from one geographic area to another. And that is a powerful tool in tracking down the root source of contamination, especially in multi-ingredient food products (such as salad, hamburger, pizza, etc.) where ingredients can come from different countries.

International organizations, including the World Health Organization and the Food and Agriculture Organization, have been working to promote the use of WGS among the international community. The Centers for Disease Control and Prevention (CDC), the US Food and Drug Administration (FDA), the United States Department of Agriculture - Food Safety and Inspection Service (USDA-FSIS) and other international public health and regulatory agencies (Public Health England, European Center for Disease Prevention and Control) have already begun sequencing foodborne pathogen isolates. The FDA encourages the food industry to use WGS, as the rapid release of WGS data allows the food industry to react faster. The FDA is also leading an international effort to build a network of laboratories. Six years ago, the FDA started an international network of laboratories called GenomeTrakr, a real time public database sequencing microbial foodborne pathogens, which assembles large genetic sequence information. This database can help investigators determine how and where these pathogens got into the food supply so preventative measures can be taken to prevent this from happening again in the future.

The cost of WGS technology has been significantly reduced over the last 15 years. In 2003, the cost of the first human genome sequence  bacterial genomes are roughly 1,000 times smaller than the human genome (about three billion base pairs)  was about $500 million. The cost of sequencing a microbial genome in 2009 was around $1,500 and is currently under $50. In the future it is expected to be even cheaper and more cost-effective for public health agencies to use WGS to respond and prevent foodborne diseases as the sequencing technology continues to improve.

A global collaboration between developed and developing countries is a must to fight foodborne pathogens. It is important for developing countries to understand the basics of WGS technology as well as its applications. Developed countries should make sure that developing countries continue to stay informed on advances in WGS technology. Developed countries should also provide technical and financial assistance to the developing countries to be able to effectively use WGS technology which will have profound impacts on global food safety and quality.