Alan McNally

The University of Birmingham is offering a PhD position focused on utilising large-scale metagenomic surveillance data sets to identify and track pathogen population dynamics. This project is at the forefront of microbiology and genomic epidemiology, leveraging metagenomic sequencing to diagnose infectious diseases directly from clinical samples. The approach removes the need for culture, often improving diagnostic accuracy and enabling mass-scale surveillance of pathogens, such as those found in respiratory infection samples. The MScape project, in collaboration with the UK Health Security Agency (UKHSA), is generating a vast dataset of metagenomic diagnostic sequencing data for population-level pathogen surveillance. The successful PhD candidate will analyze this dataset to reconstruct strain-level dynamics of pathogens circulating in the UK and compare these findings to traditional pathogen-specific surveillance programs. The goal is to determine the extent to which metagenomic surveillance can provide genomic epidemiological data for public health applications. This opportunity is ideal for candidates with a background in microbiology or computer science, as the project involves both biological and computational analysis. Full training will be provided, making it suitable for students eager to develop expertise in bioinformatics, infectious disease research, and population dynamics. The project will be supervised by Professor Alan McNally and Nick Loman from the University of Birmingham, and Dr Meera Chand from the UKHSA, all of whom are leading experts in the field. Applicants should submit a two-page CV and a covering letter detailing their experience, suitability, and motivation for the project. The application deadline is January 9th, 2026. For more information, candidates can refer to the project links provided. While the announcement does not specify funding details, the position offers a unique opportunity to contribute to cutting-edge research in metagenomics, pathogen surveillance, and public health. Keywords: metagenomics, pathogen surveillance, genomic epidemiology, microbiology, bioinformatics, infectious disease, population dynamics.