Using metagenomic sequencing to diagnose the causative agent of an infectious disease is becoming one of the most hotly pursued research topics in microbiology. This method allows sequencing to be performed directly on a clinical sample, removing the need for culture and often improving accuracy of diagnosis of the causative pathogen. Their use is also now becoming widespread for mass scale surveillance of pathogens through samples such as respiratory infection samples. One such UKHSA project is MScape, which is using deposition of metagenomic diagnostic sequencing data to perform surveillance of pathogens in the wider population. This enormous data set represents a treasure trove of ID data, and this project will aim to utilise this data set to recreate strain level dynamics of pathogens circulating in the UK, and compare this to pathogen specific surveillance programs to determine the full extent to which metagenomic surveillance programs can give us genomic epidemiological level data of pathogens in the UK.

We are seeking a PhD student to perform a project analysing the MScape metagenomic surveillance of infectious disease data set. We aim to recreate strain level information of pathogens within these data sets and determine if such surveillance programs can provide genomic epidemiological data. This project will suit anyone with a microbiology or computer science background and full training will be provided to support the student with their studies.

The project will be supervised Alan McNally (UoB), Nick Loman (UoB) and 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 by 9th January 2026.