PhD Studentship: Leveraging Genomics for Improved Metagenomic Surveillance of Streptococcus Pneumoniae

Streptococcus pneumoniae, the pneumococcus, is a common bacterial pathobiont of the upper respiratory tract and continues to cause significant global burden of both invasive and non-invasive diseases. These include meningitis, sepsis and pneumonia. The most recent estimates suggest that ~300,000 deaths of children under the age of five occur each year globally.

The use of vaccines that target one of the main virulence factors of the pneumococcus, the polysaccharide capsule, has resulted in a significant reduction of disease. These pneumococcal conjugate vaccines (PCVs) however only target a subset of serotypes. Consequently, through a process called ‘serotype replacement’ previously infrequent serotypes have expanded in prevalence to become those most observed. Consequently, even in countries with long-standing vaccine programmes, disease remains a challenge.

In this project the student will use genomic and novel computational approaches to examine the S. pneumoniae causing severe infections in the UK. This project aims to develop better definitions of invasiveness (how likely it is to cause disease) and identify the underlying loci that can be used to characterise pneumococci which are found in the context of airway-derived metagenomic data.

The project will be supervised by Dr David Cleary (UoB), Prof. Alan McNally (UoB) and Dr Meera Chand (UKHSA).

Applications of a two page CV and covering letter including your experience, suitability and motivation should be sent to hpru-phgenomics@contacts.bham.ac.uk via the above 'Apply' link by 9th January 2026.

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