CREATE PhD Programme

Respiratory viruses can increase bacterial colonisation, density, and secretion from the upper respiratory tract (URT), yet these interactions remain poorly understood-particularly in low- and middle-income countries (LMICs). Characterising these relationships is pivotal in formulating measures to mitigate secondary bacterial infections and bacterial transmission. To address these key knowledge gaps this study investigates the impact of respiratory viruses on the colonisation and transmission dynamics of Streptococcus pneumoniae, Staphylococcus aureus, and Streptococcus pyogenes in Gambian households. Using an existing longitudinal household dataset (TransVir), which includes over 14,000 oral/nasal swabs collected weekly from 349 participants across 52 households, I will: 1.​ Determine the impact of respiratory viruses on URT carriage and density of S. pneumoniae, S. aureus, and S. pyogenes using qPCR-based bacterial quantification. 2.​ Assess how respiratory viral infections influence household transmission of these bacteria using hidden Markov models. 3.​ Characterise virus-induced changes in the URT microbiome through metagenomic sequencing, evaluating shifts in microbial composition and strain-level dynamics. My preliminary analyses indicate that respiratory viruses such as RSV and rhinovirus increase pneumococcal colonisation risk, but SARS-CoV-2 does not. These findings will enhance understanding of viral-bacterial interactions and aims to inform viral and bacterial vaccination strategies and viral pandemic responses in LMICs.