PhD Studentship: Integrating Metagenomics into Respiratory Clinical Healthcare Pathways - Forest, Trees, Needles and Haystacks in Metagenomic Data

There have been 281 million cases of COVID-19 since the start of the pandemic in Europe alone. Even before this the global burden of disease included respiratory infectious diseases amongst the top ten world-wide sources of mortality.

Diagnosis of respiratory tract infections is challenging despite them being one of the most common reasons for seeking healthcare, and one of the most common reasons for antibiotic prescription. Novel, rapid, point-of-care, precise and easily interpreted diagnostic tools are required to tackle this challenge. Direct sequencing of nucleic acids from patient samples can be rapid, precise and is pathogen agnostic, you don’t need prior knowledge of which pathogen is causing the infection to use it as a diagnostic.

Challenges remain however in standardisation, application and interpretation of the data generated and that’s where this project comes in. You’ll be applying metagenomic techniques to respiratory samples and developing analysis and interpretation approaches that facilitate decisive clinical and public health decision making.

You’ll be using metagenomic techniques gaining practical experience of their laboratory use, but much of this project will be analytical applying bioinformatic tools and focused on clear interpretation and communication of this data.

This project is part of an exciting new Doctoral Training Programme in Microbial Genomics for Health Protection in collaboration with the UK Health Security Agency (UKHSA). This is funded by NIHR as part of a Health Protection Unit in Public Health Genomics between the University of Birmingham and UKHSA. In addition to the extensive training offered to all PhD students at UoB, the cohort of students on this DTP will receive training and opportunities at both UoB and UKHSA in the area of public health genomics.

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 by 31st July 2025 via the above 'Apply' button. 

Supervisors:

Dr Michael Cox (m.j.cox@bham.ac.uk)  – Assistant Professor - Department of Microbes, Infection and Microbiomes, Dr Meera Chand – Deputy Director – UKHSA and HPRU theme lead, Dr Dhruv Parekh – Associate Professor – Department of Inflammation and Ageing, Dr Miruna David – Consultant Microbiologist and Clinical Service Lead, Queen Elizabeth Hospital Birmingham

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