Development of metagenomics-based diagnostics of infectious diseases

Establishing the cause of infectious diseases can be difficult. Standard techniques are rapid and sensitive but require knowledge of potential infectious agents. The lack of a timely diagnosis can have a negative effect on patient prognosis and result in increased healthcare costs. Sequencing of both host and microorganism’s nucleic acids from clinical samples (clinical metagenomics) can fill this diagnostic gap. Metagenomics data analysis for pathogen detection is a complicated task, not unlike searching for a needle in a haystack.

I will develop a novel probabilistic method which has already been used to diagnose eight cases of encephalitis. I will use my knowledge of statistics and genomics to allow me to determine whether joint analysis of pathogen and host data can result in a definitive diagnostic test. I will collaborate with prominent clinician scientists who lead UK-wide patient cohort studies. I will analyse large collections of metagenomic datasets generated from patients with a variety of infectious diseases.

I aim to broaden our understanding of devastating infectious diseases, such as encephalitis and meningitis. Achieving a definitive diagnostic test would minimise the risk of medical mismanagement, such as incorrect prescription of antibiotics.