Application of microbial bioinformatics to investigate corneal infections

MRC：Michael Glenn：G90894F角膜是位于眼睛前面的一层薄而透明的层，它聚焦光线，保护眼睛免受环境刺激。如果角膜受损，它就容易受到微生物的感染，然后发炎，这就是所谓的角膜炎。这可能会导致角膜溃疡的发展，这是一种开放性溃疡，会导致角膜变得不透明，并可能导致迅速丧失视力。在英国和加拿大等西方国家，角膜炎的主要风险因素是滥用隐形眼镜。通宵佩戴或镜片清洗不当为有害细菌提供了滋生的环境。因此，角膜炎是一种严重的、威胁视力的疾病，需要迅速治疗，以限制损害和保护视力。目前的治疗方法依赖于积极使用抗生素，由于抗生素耐药性的惊人上升，这种方法正在变得不那么有效。为了对抗这一威胁，我们需要开发改进的诊断工具，以指导更有针对性的治疗。我相信，通过研究引起感染的细菌的DNA序列，可以开发出这样的工具。这种基因组方法可能会扩大甚至取代目前依赖于实验室培养细菌的检测方法，这一过程需要几天到几周的时间才能得出结果。到目前为止，我的工作是使用一种名为“全基因组测序”(WGS)的技术来获得完整的DNA序列或细菌的“基因组”，这些细菌在英国已经导致了大约100例角膜炎。我们现在需要非常详细地分析这些基因组，并寻找角膜炎病原体的固有特征。例如，推断对主要抗生素类药物产生耐药性的基因。这将有助于解释疾病是如何发展的，并形成新的快速诊断测试的基础，该测试将能够检测出新的角膜炎病例中存在的类似细菌。建议对加拿大进行交流访问的目的是促进对基因组序列的分析。这是一个相当大的挑战，因为每个基因组由大约300万个字母或‘核苷酸’组成。布林克曼教授在温哥华西蒙·弗雷泽大学(SFU)的实验室在开发专门用于询问基因组序列的软件方面处于世界领先地位。在她在SFU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的其他可用序列，以确定可能与疾病有关的共同因素。然后，我将应用专门设计的工具来研究抗菌素基因耐药性图谱。然后，系统发育分析将被用来产生一棵‘家谱’，它将揭示引起角膜炎的不同细菌菌株之间的关系。对角膜炎细菌编码的蛋白质的详细分析将使人们能够优先考虑未来开发治疗这种疾病的治疗剂的目标。与生物信息学家团队合作的经验将极大地提高我的计算技能，并促进我未来在这个不断扩大的领域的职业生涯。交流访问的预期结果是更好地了解导致角膜炎的细菌的基因组特征。这将指导我回到贝尔法斯特女王大学的家中实验室进行诊断测试。这将有助于指导治疗选择的长期目标，以促进角膜炎患者更个性化和有效的方法。

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.