Advances in Whole Genome Sequencing for Foodborne Pathogens: Implications for Clinical Infectious Disease Surveillance and Public Health

Emílio Gomes ¹ Daniela Araújo ¹ Teresa Nogueira ¹ Ricardo Oliveira ¹ Sónia Silva ² Lorena V N Oliveira ³ Nuno F Azevedo ⁴ Carina Almeida ¹ Joana Castro ^1*

• ¹ National Institute for Agricultural and Veterinary Research (INIAV), I.P., Vila do Conde, Portugal
• ² CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal, Braga, Portugal
• ³ Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States
• ⁴ Laboratory of Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Porto, Portugal

Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence of new and increasingly virulent foodborne pathogens. Traditional methods of detecting these outbreaks, including culture-based techniques, serotyping and molecular methods such as real-time PCR, are still widely used. However, these approaches often lack the precision and resolution required to definitively trace the source of an outbreak and distinguish between closely related strains of pathogens. Whole genome sequencing (WGS) has emerged as a revolutionary tool in outbreak investigations, providing high-resolution, comprehensive genetic data that allows accurate species identification and strain differentiation. WGS also facilitates the detection of virulence and antimicrobial resistance (AMR) genes, providing critical insight into the potential pathogenicity, treatment/control options and risks of spreading foodborne pathogens. This capability enhances outbreak surveillance, source tracing and risk assessment, making WGS an increasingly integrated component of public health surveillance systems. Despite its advantages, the widespread implementation of WGS faces several pressing challenges, including high sequencing costs, the need for specialized bioinformatics expertise, limited computational infrastructure in resource-constrained settings, and the standardization of data-sharing frameworks across regulatory and public health agencies. Addressing these barriers is crucial to maximizing the impact of WGS on foodborne disease surveillance. Even so, WGS is emerging as a vital tool in food safety and public health, and its potential to become the gold standard in outbreak detection has been recognized by public health authorities in the USA, the European Union, Australia and China, for example.