Does genetic variability in non-typeable Haemophilus influenzae strains influence their ability to cause pneumonia in children?

external supervisor

Professor Mark Nicol, University of Western Australia

Background

With the widespread implementation of vaccines to prevent invasive disease due to Haemophilus influenzae type b, non-typeable strains of H. influenzae have emerged as a major contributor to pneumonia aetiology in children. Analysis of 16S rDNA amplicon sequences of nasopharyngeal samples from a birth cohort in South Africa identified two amplicon sequence variants (ASVs) of H. influenzae that vary in their association with pneumonia.

We completed whole genome sequencing of 1,346 H. influenzae isolates from the same cohort. We now aim to identify whether the ASVs map to different genetic lineages of H. influenzae and will explore the population structure of H. influenzae in this cohort to identify lineages with differing pathogenic potential.

RESEARCH EXPERIENCE, RESEARCH METHODS AND TRAINING

The student will work with teams in Oxford, Cape Town and Perth to analyse H. influenzae whole genome sequences, map these sequences onto a global phylogeny and to the ASVs identified by 16S rDNA sequencing, 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.

FIELD WORK, SECONDMENTS, INDUSTRY PLACEMENTS AND TRAINING

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

PROSPECTIVE STUDENT

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