Autor(es):
Gomes, Emílio ; Araújo, Daniela ; Nogueira, Teresa ; Oliveira, Ricardo ; Silva, Sónia Carina ; Oliveira, Lorena V. N. ; Azevedo, Nuno F. ; Almeida, Carina ; Castro, Joana Isabel Reis
Data: 2025
Identificador Persistente: https://hdl.handle.net/1822/95678
Origem: RepositóriUM - Universidade do Minho
Projeto/bolsa:
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00511%2F2020/PT;
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F00511%2F2020/PT;
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F04469%2F2020/PT;
Assunto(s): outbreak investigation; foodborne pathogens; next-generation sequencing; molecular typing; public health
Descrição
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcimb.2025.1593219/full#supplementary-material
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. This review highlights the role of WGS in foodborne outbreak investigations, its implementation challenges, and its impact on public health surveillance.
The author(s) declare that financial support was received for the research and/or publication of this article. This work is financially supported by national funds through the FCT/MCTES (PIDDAC), under the project 2022.07654.PTDC. This work was also supported by national funds through FCT/MCTES (PIDDAC): LEPABE, UIDB/00511/2020 (DOI: 10.54499/UIDB/00511/2020) and UIDP/00511/2020 (DOI: 10.54499/UIDP/00511/2020) and ALiCE, LA/P/0045/2020 (DOI: 10.54499/LA/P/0045/2020). In addition, this study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. JC, DA, and SS also thank FCT for the CEEC Individual (DOI: 10.54499/2022.06886.CEECIND/CP1737/CT0001, 2023.06040.CEECIND, and 10.54499/CEECINST/00018/2021/CP2806/CT0003, respectively).
info:eu-repo/semantics/publishedVersion
