Imanian Behzad, Donaghy John, Jackson Tim, Gummalla Sanjay, Ganesan Balasubramanian, Baker Robert C, Henderson Matthew, Butler Emily K, Hong Yingying, Ring Brendan, Thorp Clare, Khaksar Ramin, Samadpour Mansour, Lawless Kahlil A, MacLaren-Lee Iain, Carleton Heather A, Tian Renmao, Zhang Wei, Wan Jason
Illinois Institute of Technology, Chicago, IL, USA.
Société des Produits Nestlé S.A, Vevey, Vaud, Switzerland.
NPJ Sci Food. 2022 Aug 16;6(1):35. doi: 10.1038/s41538-022-00150-6.
The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.
现代测序技术的发展与应用给食品安全和公共卫生带来了诸多新的改进。凭借前所未有的分辨率和大数据，高通量测序（HTS）使食品安全专家能够几乎实时地对微生物的标记基因、全基因组和转录组进行测序。这些数据不仅揭示了食品供应中病原体或目标生物体的身份，还展现了其毒力潜力和功能特征。扩增子的高通量测序有助于更好地表征与食品和环境相关的微生物群落。新型且强大的生物信息学工具、算法以及机器学习技术使得开发新模型来预测和应对食源性疾病暴发等重要事件成为可能。尽管具有潜力，但将高通量测序整合到当前食品安全体系的工作仍远未完成。政府机构已接纳这项新技术，并将其用于疾病诊断、食品安全检查和疫情调查。然而，食品行业对高通量测序的采用和应用相对缓慢、零散且不完整。食品制造商将高通量测序纳入其食品安全计划，通过更深入了解我们食品和环境中微生物的特征、来源、关联性及进化情况，能够加强控制措施有效性的设计与验证。在此，我们探讨这项新技术、它的力量及潜力。文中介绍了公共卫生机构实施该技术的简要历史，以及食品行业面临的益处与挑战，还有其在食品安全背景下的未来发展。
