Gomes Emílio, Araújo Daniela, Nogueira Teresa, Oliveira Ricardo, Silva Sónia, Oliveira Lorena V N, Azevedo Nuno F, Almeida Carina, Castro Joana
INIAV-National Institute for Agrarian and Veterinary Research, Vila do Conde, Portugal.
LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
Front Cell Infect Microbiol. 2025 Apr 28;15:1593219. doi: 10.3389/fcimb.2025.1593219. eCollection 2025.
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.
食源性疾病暴发影响着全球数百万人，是一个重大且日益严重的全球健康威胁，新出现的毒性越来越强的食源性病原体加剧了这一威胁。检测这些疾病暴发的传统方法，包括基于培养的技术、血清分型以及实时荧光定量PCR等分子方法，仍被广泛使用。然而，这些方法往往缺乏明确追踪疾病暴发源以及区分密切相关病原体菌株所需的精度和分辨率。全基因组测序（WGS）已成为疾病暴发调查中的一项革命性工具，它提供高分辨率、全面的遗传数据，能够进行准确的物种鉴定和菌株区分。WGS还便于检测毒力和抗菌药物耐药性（AMR）基因，为深入了解食源性病原体的潜在致病性、治疗/控制方案以及传播风险提供关键信息。这种能力增强了疾病暴发监测、源头追踪和风险评估，使WGS日益成为公共卫生监测系统的一个组成部分。尽管WGS具有诸多优势，但其广泛应用面临一些紧迫挑战，包括测序成本高、需要专业的生物信息学专业知识、资源有限地区的计算基础设施不足，以及监管机构和公共卫生机构之间数据共享框架的标准化问题。克服这些障碍对于最大限度地发挥WGS对食源性疾病监测的影响至关重要。即便如此，WGS正成为食品安全和公共卫生领域的一项重要工具，例如，它成为疾病暴发检测金标准的潜力已得到美国、欧盟、澳大利亚和中国等公共卫生当局的认可。本综述重点介绍了WGS在食源性疾病暴发调查中的作用、实施挑战及其对公共卫生监测的影响。
