Whole genome sequencing (WGS) has revolutionized our understanding of and ability to combat foodborne illnesses by transforming routine surveillance, outbreak detection, outbreak response, and source identification. WGS plays a crucial role in enhancing surveillance efforts, enabling a more comprehensive understanding of the complex dynamics of foodborne diseases. By harnessing the power of WGS, outbreaks can be rapidly and accurately detected, facilitating prompt and targeted response measures.1 Furthermore, WGS enables the identification of foodborne illness sources, aiding in the prevention of further contamination and spread. This ultimately enhances the safety of the food chain while alleviating the economic burden associated with foodborne illness outbreaks.2
Despite the evident impact that WGS is making in the field of foodborne pathogen surveillance and outbreak response, its implementation still faces numerous challenges, particularly within the European context.1,3 The establishment of a comprehensive surveillance program that harnesses the benefits of WGS requires a coordinated approach involving multiple stakeholders at multiple levels within the framework of One Health. These stakeholders include public health agencies, food safety organizations, veterinary bodies, and regulatory authorities. However, achieving seamless coordination is hindered by disparities in organizational structures, cultural and political factors at local or national levels, as well as technical and operational challenges. Existing legislation, differing priorities, and resistance to change can impede the potential beneficial impact of WGS in enhancing public health and food safety response during crises, where timely data production and sharing are critical for early outbreak detection and effective outbreak response. Also, legal and ethical hurdles regarding data ownership and responsible data usage can lead to the reluctance to share data across sectors and between nations.