Application of microbial bioinformatics to investigate corneal infections

应用微生物生物信息学研究角膜感染

• 批准号: NE/T014148/1
• 负责人: David Simpson
• 金额: $ 1.3万
• 依托单位: Queen's University Belfast
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FT014148%2F1
• 关键词: Application; microbial; bioinformatics; investigate; corneal

MRC : Michael Glenn: G90894FThe cornea is the thin, transparent layer at the front of eye which focuses light and protects against environmental irritants. If the cornea is damaged it can become susceptible to infection by microorganisms and then becomes inflamed, a condition known as 'keratitis'. This can result in the development of corneal ulcers, open sores which cause the cornea to become opaque and can lead to rapid loss of vision. The major risk factor for keratitis in western countries such as the UK and Canada is the misuse of contact lenses. Overnight wear or the improper cleaning of the lenses provides an environment for harmful bacteria to thrive. Keratitis is thus a severe, sight-threatening condition which requires rapid treatment in order to limit damage and preserve sight. Current treatment relies on aggressive use of antibiotics, an approach which is becoming less effective due to the alarming rise in antibiotic resistance. To combat this threat we need to develop improved diagnostic tools that can guide more targeted therapies. I believe that such tools can be developed by studying the DNA sequences of the bacteria which cause the infections. This genomic approach could augment or even replace the current assays which rely on growing the bacteria in the lab, a process that takes days to weeks to provide a result. My work to date has used a technique known as 'whole genome sequencing' (WGS) to obtain the complete DNA sequences or 'genomes' of the bacteria that have caused ~100 cases of keratitis in the UK. We now need to analyse these genomes in great detail and look for features inherent to keratitis pathogens. For example, genes which infer resistance to the major antibiotic drug classes. This will help to explain how the disease progresses and form the basis of new rapid diagnostic tests that will be able to detect similar bacteria that are present in new cases of keratitis.The aim of the proposed exchange visit to Canada is to facilitate this analysis of the genome sequences. This presents a considerable challenge because each genome comprises ~3 million letters or 'nucleotides'. Professor Brinkman's laboratory in Simon Fraser University (SFU), in Vancouver is a world leader in the development of software designed specifically to interrogate genome sequences. During my stay at her lab in the computational hub at SFU I will firstly compare all my keratitis genome sequences and others available in databases to identify common elements potentially involved in the disease. I will then apply tools designed specifically to investigate antimicrobial gene resistance profiles. Phylogenetic analysis will then be used to generate a 'family tree' that will reveal the relatedness between the different bacterial strains that cause keratitis. Detailed analysis of the proteins encoded by the keratitis bacteria will enable prioritization of targets for future development of therapeutic agents to treat the condition. The experience gained working with a team of bioinformaticians will greatly increase my computational skills and promote my future career in this expanding field.The anticipated outcome from the exchange visit is a better understanding of the genomic features of the bacteria which cause keratitis. This will guide my development of diagnostic tests back in my home laboratory in Queen's University Belfast. This will contribute to the long term goal of guiding treatment selection to facilitate a more personalized and effective approach for patients with keratitis.

MRC：迈克尔·格伦（Michael Glenn）：G90894f角膜是眼前的薄而透明的层，可聚焦光线并防止环境刺激物。如果角膜受损，它可能会因微生物感染而易受感染，然后发炎，这种疾病被称为“角膜炎”。这可能导致角膜溃疡的发展，开放疮，导致角膜变得不透明，并可能导致迅速失去视力。西方国家（例如英国和加拿大）角膜炎的主要危险因素是滥用隐形眼镜。隔夜磨损或镜头的清洁不当为有害细菌繁殖提供了一个环境。因此，角膜炎是一种严重的，威胁性的疾病，需要快速治疗才能限制损害并保护视力。当前的治疗方法依赖于积极使用抗生素，这种方法由于抗生素耐药性的惊人升高而变得越来越有效。为了应对这种威胁，我们需要开发改进的诊断工具，以指导更多的有针对性的疗法。我认为可以通过研究引起感染的细菌的DNA序列来开发此类工具。这种基因组方法可能会增加甚至取代依赖于实验室中细菌的当前测定法，该过程需要数天到几周才能提供结果。迄今为止，我的工作使用了一种称为“整个基因组测序”（WGS）的技术，以获取在英国引起约100例角膜炎的细菌的完整DNA序列或“基因组”。现在，我们需要详细分析这些基因组，并寻找角膜炎病原体固有的特征。例如，推断对主要抗生素药物类别的抗性的基因。这将有助于解释疾病如何进展并构成新的快速诊断测试的基础，这些诊断测试将能够检测到新的角膜炎病例中存在的类似细菌。拟议的交换访问的目的是促进对基因组序列的分析。这提出了一个巨大的挑战，因为每个基因组都包含约300万个字母或“核苷酸”。温哥华西蒙·弗雷泽大学（Simon Fraser University）的Brinkman's Laboratory教授是专门针对审问基因组序列的软件开发的世界领导者。在她在SFU的计算中心的实验室逗留期间，我将首先比较我的所有角膜炎基因组序列和数据库中其他可用的序列，以识别潜在涉及该疾病的常见元素。然后，我将应用专门设计的工具来研究抗菌基因抗性谱。然后，系统发育分析将用于产生“家谱”，该分析将揭示导致角膜炎的不同细菌菌株之间的相关性。对角膜炎细菌编码的蛋白质的详细分析将优先考虑靶标，以未来开发治疗剂以治疗这种疾病。与一群生物信息学家合作的经验将大大提高我的计算能力，并促进我在这个不断扩展的领域的未来职业。交换访问的预期结果是对引起角膜炎的细菌的基因组特征有了更好的了解。这将指导我在贝尔法斯特皇后大学的家庭实验室进行诊断测试的发展。这将有助于指导治疗选择的长期目标，以促进对角膜炎患者的更个性化和有效的方法。