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

项目摘要/摘要 该项目的长期目标是减少由食物和其他食物引起的疾病爆发的频率。 被肠道病原体污染的环境来源。确定和清除污染物的来源 污染是实现这一目标的关键。将假定的来源与患者集群公共卫生联系起来 实验室历来使用脉冲场凝胶电泳法(PFGE)寻找匹配的遗传指纹。 然而，PFGE将被废弃，取而代之的是基于全基因组的监测 测序(WGS)。 WGS正被州和联邦公共卫生实验室采用，因为它具有更高的基因分辨率 与PFGE相比，以及它被证明有能力改善来源归因。描述了WGS 因为基因组中的每个核苷酸都可以被查询和系统发育，所以提供了最终的解决方案 可以使用建立良好的计算模型来推断关系。然而，要实现充分的 在这项技术的承诺下，需要大型的精心策划的数据库来存放序列和关联的 来自不同地点和时间收集的隔离的元数据。这样的数据库有助于来源归属， 了解生物体的自然历史，并为数据挖掘提供宝贵的资源。 一个这样的数据库是由GenomeTrakr网络管理的。这个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化的基因组草稿 在接下来的五年里。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)进行实时监测。 该项目的预期结果将是扩大高质量支架的GenomeTrakr数据库 链接到元数据的基因组。这将允许更准确的亚型将患者病原体与 在特定的食物或环境来源，并最终减少病原体传播的疾病。

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.