Whole Genome Sequencing and its applications for Food Safety

Whole Genome Sequencing for Food Safety: Opportunities, Benefits and Challenges. A peer-reviewed knowledge paper by the International Association for Food Protection (IAFP) published in Food Protection Trends. https://www.foodprotection.org/publications/food-protection-trends/archive/2026-01-whole-genome-sequencing-for-food-safety-opportunities-benefits-and-challenges/

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Whole Genome Sequencing (WGS) is increasingly used by public health and regulatory agencies to detect foodborne disease outbreaks, identify outbreak sources, and, less commonly, to assess food industry’s regulatory compliance status. WGS application appears most prevalent in US, Canada, many parts of Europe, Australia and New Zealand, as compared to other countries and specifically most low and middle income countries.

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The use of WGS by the food industry is more limited and typically focuses on very specific applications where benefits have been determined to outweigh potential risks of WGS use, including regulatory, legal and reputational risks due to use and sharing of WGS data and attribution of WGS data to a specific firm. Broader industry adoption is further hampered by hurdles such as lack of trained personnel to properly interpret WGS findings and/or the ability to put the findings into context of enterprise risk.

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Ultimately, global public health will benefit from the use of WGS and the sharing of normalized and standardized data provided that the risks to the private sector can be appropriately and reasonably identified and mitigated, and that global WGS infrastructure is enhanced and further harmonized.

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To that end SSAFE developed a peer-reviewed knowledge paper with Dr. Martin Wiedmann of Cornell University and Melanie Neumann of Neumann Advisory Services that is intended to:

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• Enhance the understanding of how the food industry, regulatory and public health agencies use whole genome sequencing (WGS) to identify and characterize foodborne pathogens;
• Highlight key technical, regulatory, legal and business risks and benefits in using and sharing WGS data;
• Raise awareness of certain adoption challenges, particularly in the private sector; and
• Offer practical risk mitigation considerations to help set the stage for further discussions between the public and private sectors across the globe to foster increased and effective use of WGS and sharing of WGS data to improve food safety.

Specifically, this paper aims to:

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1. Define key terms and overarching principles related to WGS to enhance industry understanding and help set the stage for further discussions between the public and private sectors.
2. Provide a technical overview of the use of WGS by the food industry, regulatory authorities, public health agencies and academia in the United States and selected countries where WGS has been adopted to notable levels.
3. Summarize key benefits of WGS use and data sharing in enhancing food safety.
4. Summarize key challenges and risks of WGS use and data sharing (with a focus on the private sector) and discuss possible risk mitigation considerations.
5. Provide recommendations for future consideration by both public and private sectors for fostering greater industry adoption of WGS testing and data sharing.

The paper has been peer reviewed by the International Association for Food Protection (IAFP) and published in Food Protection Trends, Vol 46, No. 1, p. 8–32. You can download the document directly from IAFP at https://www.foodprotection.org/publications/food-protection-trends/archive/2026-01-whole-genome-sequencing-for-food-safety-opportunities-benefits-and-challenges/ or by completing your information in the download box on this page.

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