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

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 multipl

SUBMITTER: Pijnacker R 

PROVIDER: S-EPMC12756440 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature