John Lees is a PhD student, primarily studying the integration of sequencing data from both host and pathogen in cases of bacterial meningitis. He is also interested in phylogenetics and methods for genotype-phenotype association in bacteria.
My main focus is the MeninGene project, a collaboration between Stephen Bentley, Jeffrey Barrett, Julian Parkhill (my three supervisors) and AMC Amsterdam (led by Prof Diederik van de Beek). At the WTSI we have genotyped host DNA, and whole genome sequenced culture-proven bacteria from the project. We aim to find both host and bacterial genetic factors associated with disease susceptibility and severity. As we have matched sequences from both human and bacteria, we will also search for interactions between genotypes which may contribute towards disease.
So far we have been able to show that bacterial adaptation does not occur in the blood in cases of meningitis, and are now moving on to look between niches where adaptation may occur. This will determine whether invasion is driven by genetic factors other than serotype, and will tie in with other studies on the effect of the pneumoccocal conjugate vaccine (PCV).
I am also interested in the emerging study of genome-wide association studies (GWAS) applied to bacterial populations, and have collaborated with Jukka Corander at the University of Helsinki to create a robust and high-throughput method to perform bacterial GWAS.