Insights from Comparative Genomics for the Treatment of Pneumococcal Infections

描述(由申请人提供)：这项提案包括1年的指导研究，以发展与中耳炎(OM)相关的微生物发病机制的职业生涯，随后是3年的同一学科的独立研究。首席研究员在Kasturi Haldar博士的指导下，在西北大学完成了免疫学和微生物致病学博士学位。作为她论文工作的一部分，她通过生物信息学确定了一种与疟疾感染相关的新的真核分泌组，这极大地扩大了潜在的抗疟疾药物靶点的池。她继续在Garth Ehrlich博士那里接受博士后培训，在那里她将重点转向原核病原体，专注于细菌诱导的中耳炎，并开发了一套用于比较基因组学的生物信息学工具，以确定基因和表型之间的相关性。她的工作揭示了肺炎链球菌临床菌株中非常广泛的基因组多样性，并表明水平基因转移(HGT)是慢性多克隆肺炎链球菌感染过程中产生多样性的主要机制。现任提案中概述的行动计划将通过将教育机会、尖端设施和资源以及基因组科学中心(CGS)提供的科学和指导专业知识进行独特的整合，继续扩大她的科学技能。指导部分将在Garth Ehrlich博士的指导下进行。Ehrlich博士是CGS的执行董事，他负责这一重大范式转变，即培养阴性、抗药性的慢性细菌感染是由于代谢从浮游生物形式转变为生物膜形式造成的。他也是分布式基因组假说的作者，这是一种与生物膜概念类似的遗传假说，是许多比较细菌基因组学工具的先驱。他培养了大量的研究生、博士后研究员和初级教师。CGS生物膜主任J·威廉·科斯特顿博士也将提供科学和职业建议，他是皇家学会和美国微生物学会的会员。此外，科斯特顿博士是现代生物膜范式(1978年)的创始人，也是微生物生物膜、生态学和多微生物群落许多方面的先驱研究员。科斯特顿博士从世界各地的学生团体那里获得了许多硕士教师奖，他被公认为是开发和推进与他共事的初级科学家职业生涯的专家。计算课程、生物信息学讲习班和科学会议，以及最近开展的多项合作--其中一些已纳入该项目的设计--将进一步加强国际和平研究所的培训经验。与外部科学家的合作包括：1)开普敦大学的达伦·马丁博士，检测重组及其在进化中的作用；2)密歇根大学的大卫·谢尔曼博士，生化合成专家；3)马里兰大学的赫夫·泰特林博士和诺华公司的克劳迪奥·多纳蒂博士，他们开发了许多比较基因组学的数学工具，并领导创建了通用的肺炎球菌注释系统；4)洛克菲勒大学的亚历山大·托马斯博士和里斯本大学的赫米尼亚·德·伦卡斯特博士，他们是肺炎球菌发病机制和流行病学的权威，并收集了杰出的菌株图书馆；5)加州大学洛杉矶分校的施文元博士，他开发了专门针对微生物的多肽(STAMPS)。候选人致力于细菌致病学方面的研究，旨在提高细菌引起的OM的诊断和治疗水平。这项提案的重点是临床上重要的肺炎链球菌菌株亚群(SP-1)，它们是大流行和耐药的。其目的是：1)开发肺炎链球菌超基因组基因芯片，以提供高通量和低成本的手段对大量临床分离株进行比较基因组杂交(CGH)，并最终作为分子诊断来指导OM的治疗；2)研究新型SP-1特异性限制性内切酶修饰系统的分子机制，并确定使用抑制剂来阻断甲基转移酶的治疗潜力；以及3)研究SP-1新的抗生素群体感测基因座的作用机制，以及使用该基因座编码的多肽靶向抗肺炎链球菌和治疗感染的可能性。CGS结合了细菌生物膜、比较基因组学和中耳炎动物模型方面的专业知识，以及DNA测序、比较基因组杂交、计算生物学和共聚焦激光扫描显微镜等最先进的设施，为这项工作提供了理想的环境。总而言之，这个项目与CGS现有的杰出人员和设施资源相结合，将最大限度地发挥首席研究人员的潜力，建立一个科学利基，启动多项合作，在未来三年内申请NIH R01资金，并开始在OM微生物学和相关的慢性细菌感染方面的独立职业生涯。 公共卫生相关性：该提案的长期目标是诊断和治疗细菌引起的耳部感染。这些感染是婴幼儿最常见的疾病。

DESCRIPTION (provided by applicant): This proposal consists of 1 year of mentored research for the development of a career in microbial pathogenesis as it relates to otitis media (OM), followed by 3 years of independent research in the same discipline. The principal investigator completed a doctorate in Immunology and Microbial Pathogenesis at Northwestern University under the mentorship of Dr. Kasturi Haldar. As part of her dissertation work she identified bioinformatically a novel eukaryotic secretome associated with malarial infection that has vastly expanded the pool of potential anti-malarial drug targets. She continued her training as a post-doctoral fellow with Dr. Garth Ehrlich, where she switched her emphasis to prokaryotic pathogens focusing on bacterially- induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations. Her work has exposed the very extensive genomic diversity among clinical S. pneumoniae strains, and has shown that horizontal gene transfer (HGT) is the major mechanism of diversity generation during chronic polyclonal S. pneumoniae infections. The plan of action outlined in the incumbent proposal will continue to expand her scientific skills through a unique integration of educational opportunities; cutting-edge facilities and resources; and scientific and mentoring expertise available at the Center for Genomic Sciences (CGS). The mentored section will be carried out under the guidance of Dr. Garth Ehrlich. Dr. Ehrlich is the Executive Director of the CGS, and is responsible for the major paradigm shift that states that culture-negative, antibiotic-resistant chronic bacterial infections result from a metabolic change from a planktonic to a biofilm form. He is also the author of the Distributed Genome Hypothesis, a genetic parallel to the biofilm concept and is the pioneer of many of the tools of comparative bacterial genomics. He has trained numerous graduate students, postdoctoral fellows, and junior faculty. Scientific and career advice will also be provided by the CGS Biofilm Director, Dr. J. William Costerton who is a fellow of the Royal Society and of the American Society for Microbiology. Moreover, Dr. Costerton is the originator of the modern biofilm paradigm (1978), and a pioneer researcher in many aspects of microbial biofilms, ecology, and polymicrobial communities. Dr. Costerton has received numerous master teacher awards from student groups around the world and is recognized as an expert in developing and advancing the careers of junior scientists with whom he works. Computational coursework, a bioinformatic workshop, and scientific meetings, as well as the development of multiple recent collaborations, some of which have been incorporated into this project's design, will further enhance the PI's training experience. Collaborations with outside scientists include: 1) Dr. Darren Martin at Cape Town University, an expert in the detection of recombination and it's role in evolution; 2) Dr. David Sherman at the University of Michigan, a specialist in biochemical synthesis; 3) Drs. Herve Tettelin at the University of Maryland and Claudio Donati at Novartis who have developed many mathematical tools for comparative genomics and led the effort to create a universal pneumococcal annotation system; 4) Drs. Alexander Tomasz at the Rockefeller and Dr. Herminia de Lencastre at the Universidade Nova de Lisboa who are authorities on the pathogenesis and epidemiology of pneumococcus and who have collected an outstanding library of strains; and 5) Dr. Wenyuan Shi at University of California in Los Angeles who has developed specifically targeted anti-microbial peptides (STAMPs). The candidate is devoted to a career in bacterial pathogenesis designed to improve the diagnosis and treatment of bacterially-induced OM. The focus of this proposal is on a clinically important subset of Streptococcus pneumoniae strains (the SP-1) that are pandemic and drug resistant. The aims are to: 1) develop an S. pneumoniae supragenome gene chip to provide a high-throughput and cost-effective means to perform comparative genomic hybridizations (CGH) on large numbers of clinical isolates, and ultimately to function as a molecular diagnostic to guide treatment of OM; 2) investigate the molecular mechanism of a novel SP-1-specific restriction-modification system, and determine the treatment potential of using inhibitors to block the methyltransferase; and 3) investigate the mechanism of action of an novel SP-1 lantibiotic-quorum sensing locus, and the potential to use a peptide encoded within this locus to target anti-microbials to S. pneumoniae and treat infections. The CGS provides an ideal setting for this work by combining expertise in bacterial biofilms, comparative genomics, and otitis media animal models, with a state-of-the-art facilities for DNA sequencing, comparative genomic hybridization, computational biology, and confocal laser scanning microscopy. In summary, this project, combined with the outstanding personnel and facilities resources available at the CGS, will maximize the potential for the principal investigator to establish a scientific niche, initiate multiple collaborations, apply for NIH R01 funding within the next three years, and commence an independent career in the microbiology of OM and related chronic bacterial infections. PUBLIC HEALTH RELEVANCE: The long-term goal of this proposal is the diagnosis and treatment of bacterial-induced ear infections. These infections are the most common illnesses in infants and young children.