Implementing whole genome sequencing for foodborne pathogen surveillance: Insights and recommendations based on expert experiences

Roan Pijnacker^1*Maaike J.C. Van Den Beld¹Alexander Ullrich²Pieter-Jan Ceyssens³Dieter van Cauteren³Solveig Jore⁴Eva Møller Nielsen⁵Steen Ethelberg⁵Stefano Morabito⁶Maren Lanzl¹Eelco Franz¹

• ¹National Institute for Public Health and the Environment (Netherlands), Bilthoven, Netherlands
• ²Robert Koch-Institut, Berlin, Germany
• ³Sciensano, Brussels, Belgium
• ⁴Folkehelseinstituttet, Oslo, Norway
• ⁵Statens Serum Institut, Copenhagen, Denmark
• ⁶Istituto Superiore di Sanita, Rome, Italy

Whole-genome sequencing (WGS) is increasingly used as the primary typing method for foodborne disease surveillance. It offers high-resolution cluster analysis, interoperability, and comprehensive pathogen characterization. However, implementing WGS-based foodborne surveillance also poses challenges. This paper outlines these challenges and provides practical recommendations. It requires a business plan that details the financial, technical and human resources needed, since setting up WGS-based surveillance requires substantial initial investments. During the initial phase, the per sample costs of WGS are likely higher than with traditional typing method. However, this will align or even go below that when fully transitioned to WGS-based surveillance because WGS data can be used for multiple purposes such as (sero)typing and antimicrobial and virulence characterization. It is advisable to start with a single pathogen to establish a solid foundation, with the aim of having one institutional sequencing facility. Validating accuracy and consistency of results is crucial before expanding to other pathogens. While cross-disciplinary collaboration has always played an important role in foodborne surveillance, the complexity of WGS results now makes it essential for transforming findings into effective interventions. Despite its challenges, advancements in technology and computation capabilities have made it increasingly accessible, ultimately improving public health surveillance and response.