Genomic Comparison of Infectious Strains E. Faecalis

传染性粪肠球菌菌株的基因组比较

• 批准号: 7032244
• 负责人: GEORGE M WEINSTOCK
• 金额: $ 15.11万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-04-01 至 2008-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7032244
• 关键词: Enterococcus; bacteria infection mechanism; bacterial disease; bacterial genetics; computational biology; gene expression; gene mutation; genetic mapping; genetic strain; genome; method development; microarray technology; molecular biology information system; molecular cloning; polymerase chain reaction; single nucleotide polymorphism; virulence

DESCRIPTION (provided by applicant): Enterococcus faecalis is an important nosocomial pathogen. While a component of the normal human intestinal flora, E. faecalis is a low virulence organism. Yet a variety of infections by E. faecalis occur, including endocarditis, bacteremia, and infections of the urinary track and other tissues. The E. faecalis strains that cause these infections may differ in virulence factors from the docile strains that inhabit the healthy human intestine. Thus an important challenge is to determine the genetic differences between E. faecalis strains with different phenotypes. As a first step toward this goal, this project will determine the genomic sequences of two strains of Enterococcus faecalis, strains OG1RF and HH22, and compare them to the sequence of strain V583, the only other complete E. faecalis genomic sequence. Strain OG1RF is the major experimental strain of E. faecalis, used widely in research for many years, and on which much of the knowledge of E. faecalis biology is based. Strain HH22 is a closer relative of V583, but shows 100-fold greater infectivity in a mouse model. Comparison of these three genomes should provide information as to E. faecalis virulence as well as develop the methodology that can be applied to a wider ranger of strains. Two novel technologies will be used in this study. In the sequencing phase, high genome coverage using the pyrosequencing methodology of 454 Life Sciences will be aimed at reducing the amount of activity needed to bring the genome to a high quality finished grade. Once the sequences are complete, and comparison has been made to V583, the differences determined will be validated using microarrays produced by the oligonucleotide synthesis technology developed at NimbleGen. In addition to these novel methods, standard procedures will be use for shotgun sequencing, finishing, and validation of genomic sequence differences. The introduction of the novel methods will reduce costs and increase throughput, both of which are important for future scale-up to larger numbers of strains.

描述(申请人提供)：粪肠球菌是一种重要的医院内病原菌。虽然粪肠球菌是人类正常肠道菌群的一种成分，但它是一种低毒的有机体。然而，粪肠球菌的各种感染也会发生，包括心内膜炎、菌血症以及尿路和其他组织的感染。引起这些感染的粪肠球菌菌株在毒力因素上可能与居住在健康人体肠道中的温顺菌株不同。因此，一个重要的挑战是确定具有不同表型的粪肠球菌菌株之间的遗传差异。 作为实现这一目标的第一步，该项目将确定两株粪肠球菌OG1RF和HH22的基因组序列，并将它们与唯一的另一株完整的粪肠球菌基因组序列V583进行比较。OG1RF菌株是粪肠球菌的主要实验菌株，多年来被广泛应用于研究，粪肠球菌的许多生物学知识都基于OG1RF菌株。HH22菌株是V583的近亲，但在小鼠模型中显示出100倍的传染性。对这三种基因组的比较将提供有关粪肠球菌毒力的信息，并开发可应用于更广泛菌株的方法学。 这项研究将使用两项新技术。在测序阶段，使用454生命科学的焦磷酸测序方法进行高基因组覆盖将旨在减少将基因组带到高质量成品等级所需的活动量。一旦序列完成，并与V583进行了比较，所确定的差异将使用NimbleGen开发的寡核苷酸合成技术产生的微阵列进行验证。除了这些新方法外，还将使用标准程序进行鸟枪式测序、整理和验证基因组序列差异。新方法的引入将降低成本并提高产量，这两点对未来扩大到更多菌株都很重要。