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external supervisor

Professor Mark Nichol, University of Western Australia


The role of M. catarrhalis in the pathogenesis of pneumonia in children is controversial. We have recently completed a systematic review showing widely varying association (from protective to increased risk) between the presence of M. catarrhalis in the nasopharynx of children and pneumonia.

One explanation for these varying findings is that strains of M. catarrhalis may differ in their pathogenic potential, however there are very limited data on the global population structure of this species. We have completed whole genome sequencing of a large collection (n=1,429) of isolates of M.  catarrhalis from the nasopharynx of infants enrolled in a South African birth cohort. This probably represents the largest such collection worldwide.

We now aim to describe the population structure of M. catarrhalis in this cohort and identify whether there are distinct lineages that may differ in their pathogenic potential. We will also explore associations with a range of exposures associated with the development of pneumonia in childhood.


This project will involve working with teams in Oxford, Cape Town and Perth to analyse M. catarrhalis whole genome sequences, map these sequences onto a global phylogeny, identify lineages and explore associations with disease phenotype and other participant metadata, including exposures such as HIV and cigarette smoke.

It is anticipated that this work will lead to publishable findings.


Training in epidemiologic, bioinformatics and genomic analyses will be provided by the PIs and other experienced members of their research groups.


The ideal candidate would have strong computational and analytical skills and interest, preferably with some experience working with genome sequence datasets.