Application of microbial bioinformatics to investigate corneal infections

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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.