PhD Studentship: The Last of Us Developing a Genomic Epidemiology Toolkit for Fungal Outbreaks

Drug-resistant fungal infections—caused by species like Candida auris, Cryptococcus neoformans, and Aspergillus fumigatus—pose a growing threat in healthcare, with mortality rates exceeding 50% in immunocompromised patients. Resistance is often acquired before patient infection through environmental exposure to fungicides, highlighting the urgent need for effective outbreak tracking and control.

This PhD project offers a unique opportunity to develop a cutting-edge genomic epidemiology toolkit for real-time fungal surveillance. You’ll optimize DNA extraction protocols using advanced enzyme-based methods, overcoming the tough fungal cell wall. You’ll also design robust workflows for targeted long-read sequencing of clinical and environmental samples, enabling accurate identification and resistance genotyping fungal pathogens from the WHOs fungal priority pathogen list.

In the second part of the PhD, you will build scalable, user-friendly bioinformatics pipelines for rapid genome analysis, tested using samples from the UK Health Security Agency and real-world outbreaks. This interdisciplinary project integrates microbiology, molecular biology, bioinformatics, and public health, offering hands-on training and the chance to make a real impact on global infectious disease management. The resulting toolkit will help public health labs worldwide detect and track fungal outbreaks swiftly and accurately.

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.

Supervisors: Dr. Megan McDonald (UoB Biosciences), Dr Lucy Crouch (UoB Institute of Microbiology and Infection), Dr Johanna Rhodes (UoB Biosciences), Dr Joshua Quick (UoB Biosciences), Mycological Reference Lab Bristol (UKHSA) and Dr Charlie Reid (UKHSA).

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