AUTHOR=Pijnacker Roan , van den Beld Maaike , Ullrich Alexander , Ceyssens Pieter-Jan , van Cauteren Dieter , Jore Solveig , Nielsen Eva Møller , Ethelberg Steen , Morabito Stefano , Lanzl Maren , Franz Eelco 
  
TITLE=Implementing whole genome sequencing for foodborne pathogen surveillance: insights and recommendations based on expert experiences
  
JOURNAL=Frontiers in Microbiology
  
VOLUME=Volume 16 - 2025
  
YEAR=2025
  
URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1707621
  
DOI=10.3389/fmicb.2025.1707621
  
ISSN=1664-302X
  
ABSTRACT=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.