Food safety and quality
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Whole Genome Sequencing (WGS) and food safety

Current activities

  • FAO facilitates an informal network of developing countries to share information, knowledge and experience in using WGS for food safety management. Participating countries include: Bangladesh, Bhutan, Botswana, China, Egypt, Ghana, India, Iran, Mauritius, Mongolia, Mozambique, Namibia, Philippines, Sudan, Tanzania, Thailand, Vietnam (as of 1 August 2018, 20 people from 17 countries are participating). Contact [email protected] to join the network.
  • FAO supports non-profit technical initiatives working on WGS and food safety, such as Global Microbial Identifier and PulseNet International.
    • Global Microbial Identifier (GMI): FAO, together with its partner agencies such as WHO and OIE, is sitting in the steering committee of GMI to ensure all countries, including developing countries and transition countries, will benefit from this potentially powerful technology that is applicable to food safety management.
    • PulseNet International: PulseNet International is a global laboratory network dedicated to foodborne disease surveillance and outbreak detection. This international network envisions the standardised use of WGS to identify and subtype foodborne bacterial pathogens worldwide, replacing traditional methods. Standardized methods for analyzing foodborne disease WGS data are required for international comparability in a timely and consistent manner. Furthermore, freely available bioinformatic tools and databases are necessary so that all countries can use these internationally standardized methods in real time. FAO regularly attends the PulseNet technical meetings to support their initiatives to design and build the system that has a potential in being converted into an internationally standardized system. Currently, analysis schemes are being validated by this partnership for application to foodborne pathogens Listeria, Salmonella, E. coli, Shigella, and Campylobacter. Additional activities are presently focused on ensuring the availability of the tools to all countries in a sustainable manner.

Past activities

General information

Genome sequencing can identify microorganisms with previously unknown accuracy; this unsurpassed capability together with declining operating costs will fundamentally change food safety management in the years to come. Genome sequencing is already established in the areas of plant/animal breeding, and in animal health to understand and characterize the pathogenicity of viruses. In the area of outbreak investigation of food-borne illness, certain high-income countries demonstrated great success in quickly and precisely targeting the source of the outbreak and limit the negative impact of the outbreak on public health and on trade.

Outside high-income countries, the level of understanding regarding benefits and implications concerning the use of genome sequencing in the area of food safety significantly varies. Particularly for developing countries, there are capacity, regulatory and resource implications to be considered. While several industralized countries have been moving forward with the technology, information on potential benefits, possible drawbacks, relevant challenges and considerations need to be analysed, with careful attention to developing and transitional countries with possibly limited capacity and resources.

It is a role of FAO's to keep all Members informed on the latest scientific developments in the food and agriculture sectors, and provide technical assistance to those who need it.

Key outputs

For more information, please contact [email protected].