The effect of the nasopharyngeal host microbiome on the transcriptional host response during viral infection

The current practice for the management, treatment and research of febrile diseases is to separate infections into either bacterial or viral. However, for paediatric respiratory infections, separating patients into this binary remains a diagnostic challenge. Due to limitations of current gold standard, pathogen based diagnostics, bacterial infections are often diagnosed from the finding of intense inflammation, which is noted from raised levels of the biomarkers C-reactive protein (CRP) or white blood cell count (WBC). However, a high proportion of patients with viral infections, such as influenza and respiratory syncytial virus (RSV), also display biomarker signatures indicative of intense inflammation. For my PhD, I want to explore the factors determining these unusual inflammatory immune responses to viral infections. My hypothesis is that the host response to viral infections is influenced by the bacteria present in the respiratory microbiome.