Whole Genome Sequencing for State Food Testing Laboratories competition B

国家食品检测实验室全基因组测序竞赛B

• 批准号: 9929365
• 负责人: WILLIAM J WOLFGANG
• 金额: $ 16.5万
• 依托单位: WADSWORTH CENTER
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-05 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9929365
• 关键词: Whole; Genome; Sequencing; State; Food

The long-term goal of this project is to reduce the frequency of disease outbreaks caused by food and other environmental sources contaminated with enteric pathogens. Identification and removal of sources of contamination is key to achieving this goal. Historically, public health laboratories look for matching genetic fingerprints using Pulsed Field Gel Electrophoresis (PFGE). However, by the time this grant starts, PFGE will have been largely abandoned and replaced by surveillance based on Whole Genome Sequencing (WGS). WGS is being adopted by state and federal public health laboratories because of its greater genetic resolution when compared to PFGE, as well as its demonstrated ability to improve source attribution. WGS is described as offering the ultimate resolution since each nucleotide in the genome can be queried and phylogenetic relationships can be inferred using well-established computational models. However, to achieve the full promise of this technology, large well-curated databases are required that harbor sequence and associated metadata from isolates collected at diverse locations and times. Such databases aid in source attribution, understanding the natural history of the organisms, and provide a valuable resource for data mining. One such database is curated by the GenomeTrakr Network. The immediate goal of this project is to add four hundred unique and diverse draft genomes from food and environmental bacterial pathogens to this database. This will be accomplished by sequencing well-characterized isolates at the Wadsworth Center and sharing the sequence and metadata with the GenomeTrakr network and the National Center for Biotechnology Information (NCBI) in real-time. The expected outcome of this project will be to expand the GenomeTrakr database of high-quality scaffold genomes that are linked to metadata. This will allow more accurate subtyping to link patient pathogens to specific foods or environmental sources and ultimately reduce pathogen-borne illness.

该项目的长期目标是减少疾病爆发的频率。 由被肠道病原体污染的食物和其他环境来源引起。 确定和消除污染源是实现这一目标的关键。 从历史上看，公共卫生实验室使用 脉冲场凝胶电泳(PFGE)。然而，到这笔赠款开始时，PFGE 将在很大程度上被抛弃，取而代之的是基于 基因组测序(WGS)。 WGS正在被州和联邦公共卫生实验室采用，因为它 与PFGE相比，遗传分辨率更高，而且其已证明的能力 以提高来源归因。WGS被描述为提供终极解决方案，因为 基因组中的每个核苷酸都可以被查询，并且系统发育关系可以 使用完善的计算模型进行推断。然而，要实现充分的 这项技术的承诺，需要大型的精心策划的数据库 从不同地点和地区收集的分离物的序列和关联元数据 泰晤士报。这样的数据库有助于来源归属，了解 并为数据挖掘提供了宝贵的资源。 一个这样的数据库是由GenomeTrakr网络管理的。这样做的直接目标是 该项目是从食品和食品中添加400个独特和多样化的基因组草案 环境细菌病原体到这个数据库。这将通过以下方式实现 在沃兹沃斯中心对特征良好的分离株进行测序并分享 与GenomeTrakr网络和国家研究中心的序列和元数据 实时的生物技术信息(NCBI)。 该项目的预期结果将是扩大GenomeTrakr数据库 链接到元数据的高质量支架基因组。这将允许更准确地 将患者病原体与特定食物或环境来源联系起来的亚型 最终减少病原体传播的疾病。