Investigating the genetic basis for bacterial toxin production using functional genomics

肺炎链球菌是人类鼻咽的寄生菌，也是一种机会致病菌，可在免疫力低下的人群中引起肺炎、脑膜炎和败血症等严重呼吸道疾病。这种病原体对幼儿和老年人特别危险，已证明很难通过疫苗方案加以控制，因为它有各种各样的荚膜血清型，其中有90多种。目前的疫苗仅提供针对其中7-23种的保护，代表最常见的临床血清型。然而，23价疫苗不适合给予2岁以下的最危险年龄组，临床医生观察到血清型替代量增加，由此非疫苗血清型开始替代疫苗中包含的那些血清型作为疾病的原因。致病性方面，S.肺炎球菌具有一系列毒力因子，包括高度免疫原性的多糖荚膜、大量表面蛋白和粘附素以及毒素肺炎球菌溶血素。然而，许多毒力因子及其遗传调控的具体作用知之甚少，如果我们要努力改进肺炎球菌疾病的诊断、治疗和预防，还有很多东西有待发现。我的博士学位的目的是努力提高对这种细菌毒性的遗传基础的理解，具体目的是使用功能基因组学方法来识别与毒性表型相关的新基因。通过这种方法鉴定的基因将被表征，以进一步阐明这种性状的复杂遗传调控。虽然主要有助于提高知识和理解S。肺炎的毒性，这项研究也可能导致识别用于治疗疾病的新药靶标，并且希望将有助于提高解释基因组测序数据的能力，这将在长期的临床背景下有用。我将在第一年工作的基础上实现这些目标;到目前为止，我已经测定了一批临床S。pneumoniae分离株的PMEN 1克隆组，并使用该数据与关于每个分离株中存在遗传多态性的数据组合进行全基因组关联研究。这已经确定了许多与毒性表型显著相关的遗传位点，我们现在正在努力确定最具生物学相关性的多态性，以在实验室中进一步研究。该项目由BBSRC资助，适合世界级的基础生物科学研究领域，包括广泛领域的基础研究。我的工作符合分子生物学学科，这是BBSRC的高优先级研究领域之一，希望能有助于发现传染病背景下的药物或预防策略的新线索。

Streptococcus pneumoniae is both a commensal inhabitant of the human nasopharynx, and an opportunistic pathogen which can cause serious respiratory disease in the form of pneumoniae, meningitis and septicaemia in people with compromised immunity. Particularly dangerous to the very young and the very old, this pathogen has proved hard to control through vaccine programmes due to the wide range of capsular serotypes, of which there are over 90. Current vaccines only provide protection against 7-23 of these, representing the most common clinical serotypes. However, the 23-valent vaccine is unsuitable to give to the most at risk age group of those under two years old, and an increasing amount of serotype replacement is being observed by clinicians whereby non-vaccine serotypes are beginning to replace those included in the vaccine as the cause of disease. Regarding pathogenicity, S. pneumoniae has an array of virulence factors including a highly immunogenic polysaccharide capsule, an extensive number of surface proteins and adhesins, and the toxin pneumolysin. However, the specific role of many virulence factors and their genetic regulation is poorly understood and much remains to be discovered if we are to work towards improved diagnosis, treatment and prevention of pneumococcal disease. The aim of my PhD is to work towards improved understanding of the genetic basis for toxicity in this bacterium, with the specific aim of using a functional genomics approach to identify novel genes associated with the toxic phenotype. Genes which are identified through this approach will then be characterised to elucidate further the complex genetic regulation of this trait. Whilst primarily contributing to improved knowledge and understanding of S. pneumoniae toxicity, this research may also result in identification of novel drug targets for treatment of disease, and it is hoped will contribute to an improved ability to interpret genome sequencing data, which will be useful in a clinical context in the long term. I will achieve these aims by building on the work done in my first year; so far I have assayed the toxicity of a collection of clinical S. pneumoniae isolates of the PMEN1 clonal group and used this data in combination with data regarding the presence of genetic polymorphisms in each isolate to perform a genome wide association study. This has identified a number of genetic loci which are significantly associated with the toxic phenotype, of which we are now working towards identifying the most biologically relevant polymorphisms to investigate further in the lab. This project is BBSRC funded, and fits into the World class underpinning bioscience area of research which encompasses fundamental research in a broad range of areas. My work fits into the discipline of molecular biology, which is one of the high priority research areas of the BBSRC, and it is hoped will contribute to discovery of new leads for drugs or prevention strategies in the context of infectious disease.