Applications of Whole Genome Sequencing in food safety management

Recent advances in Whole Genome Sequencing (WGS) technology have the potential to play a significant role in the area of food safety. WGS provides rapid identification and characterization of microorganisms, including antimicrobial resistance (AMR), with a level of precision not previously possible. With the rapidly declining cost of this technology, WGS applications in food safety management, including the opportunities it provides for enhanced integration of information from other sectors, such as human and animal health, could contribute to enhanced consumer protection, trade facilitation, nutrition and food security. However, the level of understanding of the concepts and potential use of WGS in food safety management vary among countries. This document aims to take the first steps in addressing these gaps, and providing answers to some of the questions which food safety officials (particularly those in developing countries) need to ask and consider if they are to make informed decisions about WGS and its potential value in food safety management in their context. Four real-life case studies are presented to highlight key benefits and potential drawbacks of WGS in food safety management. Benefits and drawbacks are explained in detail, including the issues related to global data sharing. The document discusses challenges in employing WGS within the regulatory framework in both developed and developing countries, and highlights considerations for countries with limited capacity and resources. A simple exercise to enable developing countries to assess the feasibility of incorporating WGS into national food control systems through a step-by-step approach is described. While WGS can significantly contribute to improving food safety management, it still relies on the appropriate interpretation of laboratory data in the context of epidemiological evidence; WGS alone will not suffice. Despite the challenges, WGS is poised to become standard methodology in some places for the identification and characterization of foodborne pathogens. Finding appropriate mechanisms for data sharing will be an important element of its application. In all of this, there is a strong need at the global level to ensure that situations in developing countries are fully taken into account, and that the technology advances in an appropriate direction, in order for WGS to become an effective tool for all.