Population Genetics of M. Tuberculosis During Disease Epidemics

描述（由申请人提供）：该提案概述了一个5年的培训计划，以促进博士Pepperell的职业发展作为一个学术医生科学家。Pepperell博士最近在斯坦福大学完成了传染病的临床培训。拟议的项目利用了斯坦福大学现有的优秀技术和智力资源来研究M。结核加里斯考尼克博士和彼得·斯莫尔博士将担任该项目的共同导师。Schoolnik博士是国际公认的结核病分子生物学和发病机制的权威，而Small博士也有一个同样成功的研究项目，专注于结核病的进化遗传学。候选人建议获得细菌种群遗传学方面的培训，以便从病原体的角度研究目前无法解释的结核病流行方面。尽管宿主人口、治疗和环境条件各不相同，但结核病的流行在历史上一直以一种定型的方式下降。研究中的假设将结核菌群体内的遗传多样性程度与宿主群体中疾病流行的阶段联系起来。我们假设遗传多样性随着时间的推移而增加，生物体中的生物学重要变化导致或伴随着疾病流行的自然下降。通过与加拿大公共卫生当局的合作，候选人可以获得一个独特的数据集，使她能够检验这一假设。临床数据和存档的结核菌株可从两个明确定义的加拿大土著人口中获得，这两个人口经历了相隔70年的结核病流行。候选人建议使用结核病基因分型技术来创建来自这些社区的结核病分离株的微基因组。其目的是：1）重建这些流行病过程中发生的进化事件2）定义流行病开始与结束时占主导地位的菌株类型3）量化流行病过程中产生的多样性数量。研究社区在地理上和社会上是孤立的，有机会研究少数结核菌株的演变，而没有移民的混杂影响。最终，这项研究应该能够深入了解结核菌如何进化以避免人类免疫系统、药物和疫苗的攻击。了解这种演变将有助于开发更好的治疗方法，以治疗每年导致近300万人死亡的疾病。

DESCRIPTION (provided by applicant): The proposal outlines a 5-year training plan to facilitate Dr. Pepperell's career development as an academic Physician scientist. Dr. Pepperell recently completed clinical training in infectious diseases at Stanford University. The proposed project takes advantage of outstanding technical and intellectual resources available at Stanford for the study of M. tuberculosis. Drs. Gary Schoolnik and Peter Small will serve as co-mentors for the project. Dr. Schoolnik is an internationally recognized authority on the molecular biology and pathogenesis of TB, while Dr. Small has an equally successful research program focused on the evolutionary genetics of M.TB. The candidate proposes to acquire training in bacterial population genetics in order to examine currently unexplained aspects of TB epidemics from the perspective of the pathogen. TB epidemics have historically declined in a stereotypical manner despite variable host populations, treatment and environmental conditions. The hypothesis under study relates the degree of genetic diversity seen within a population of TB organisms to the stage of the disease epidemic in the host population. We hypothesize that genetic diversity increases over time and that biologically important changes in the organism either cause or accompany the natural decline of disease epidemics. Through collaboration with Canadian public health authorities, the candidate has access to a unique dataset which will allow her to examine this hypothesis. Clinical data and archived TB strains are available from 2 well defined populations of Native Canadians which experienced TB epidemics 70 years apart. The candidate proposes to use TB genotyping techniques to create a micro-phylogeny of TB isolates from these communities. The aims are to: 1) reconstruct the evolutionary events which occurred over the course of these epidemics 2) define the strain types which predominate at the initiation versus the conclusion of an epidemic and 3) quantify the amount of diversity generated over the course of an epidemic. The study communities are geographically and socially isolated and there is an opportunity to study the evolution of a small number of TB strains, without the confounding effect of migration. Ultimately, this study should provide insight into the ways in which TB bacteria evolve to avoid attack by the human immune system, drugs and vaccines. An understanding of this evolution would help to develop better treatments for a disease which kills almost 3 million people per year.