Whole Genome Sequencing to support GenomeTrakr-Discipline A: Microbiology- Track 4

全基因组测序支持 GenomeTrakr-学科 A：微生物学-轨道 4

• 批准号: 10173143
• 负责人: WILLIAM J WOLFGANG
• 金额: $ 13.81万
• 依托单位: WADSWORTH CENTER
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10173143
• 关键词: Whole; Genome; Sequencing; support; GenomeTrakr

PROJECT SUMMARY / ABSTRACT 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. To link putative sources to patient clusters public health laboratories historically look for matching genetic fingerprints using Pulsed Field Gel Electrophoresis (PFGE). However, PFGE will have been 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 two thousand unique and diverse draft genomes from food and environmental bacterial pathogens to this database over the next five years. This will be accomplished by sequencing well-characterized isolates from the Wadsworth Center and other institutions 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.

项目总结/摘要 该项目的长期目标是减少由食物和其他因素引起的疾病爆发的频率。 受肠道病原体污染的环境源。查明和消除污染源 污染是实现这一目标的关键。将假定来源与患者群公共卫生联系起来 实验室历史上使用脉冲场凝胶电泳（PFGE）寻找匹配的遗传指纹。 然而，PFGE将被放弃，取而代之的是基于全基因组的监测 测序（WGS）。 WGS由于其更高的遗传分辨率而被州和联邦公共卫生实验室采用 与PFGE相比，它具有更好的来源归因能力。WGS描述 因为基因组中的每个核苷酸都可以被查询和系统发育， 可以使用建立良好的计算模型来推断关系。然而，为了实现全面 这项技术的承诺，大型精心策划的数据库需要港口序列和相关的 在不同地点和时间收集的分离株的元数据。这种数据库有助于来源归属， 了解生物体的自然历史，并为数据挖掘提供了宝贵的资源。 其中一个数据库是由GenomeTrakr网络管理的。该项目的近期目标是增加两个 从食品和环境细菌病原体到这个数据库的数千个独特和多样的基因组草案 在未来五年内。这将通过对来自 沃兹沃斯中心和其他机构，并与GenomeTrakr共享序列和元数据 网络和国家生物技术信息中心（NCBI）实时。 该项目的预期成果将是扩大高质量支架的GenomeTrakr数据库， 与元数据相关联的基因组。这将使更准确的亚型，以联系病人的病原体， 特定的食物或环境来源，并最终减少病原体传播的疾病。