PhD opportunities

Streptococcus pneumoniae, the pneumococcus, is a common bacterial pathobiont of the upper respiratory tract and continues to cause significant global burden of both invasive and non-invasive diseases. These include meningitis, sepsis and pneumonia. The most recent estimates suggest that ~300,000 deaths of children under the age of five occur each year globally.

The use of vaccines that target one of the main virulence factors of the pneumococcus, the polysaccharide capsule, has resulted in a significant reduction of disease. These pneumococcal conjugate vaccines (PCVs) however only target a subset of serotypes.

Consequently, through a process called ‘serotype replacement’ previously infrequent serotypes have expanded in prevalence to become those most observed. Consequently, even in countries with long-standing vaccine programmes, disease remains a challenge.

In this project the student will use genomic and novel computational approaches to examine the S. pneumoniae causing severe infections in the UK. This project aims to develop better definitions of invasiveness (how likely it is to cause disease) and identify the underlying loci that can be used to characterise pneumococci which are found in the context of airway-derived metagenomic data.

Supervisory team:

• Prof Alan McNally
• Dr Meera Chand
• Dr David Cleary

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Metagenomics (the sequencing of all genetic material within a sample) offers the promise of being a single test to diagnose all clinical infections. By directly sequencing all nucleic acid from a clinical or environmental sample we can rapidly identify all organisms present including novel strains and newly emerged pathogens. Currently such methods are only available in specialist laboratories, each performing their own techniques that vary, due to differences in the types of samples (respiratory, blood, waste water, etc) or pathogens (bacterial, viral, fungal) of specific interest.

This project aims to optimize metagenomic workflows across sample types, developing integrated, sample-specific methodologies.

Collaborating with leading academic developers and front line metagenomics users, including the UKHSA’s Imported Fever Metagenomic Service, we will evaluate diverse approaches to establish best practices.

This studentship provides a molecular biologist with exceptional training in clinical and public health genomics, combining academic research with front-line public health intervention experience.

Supervisory team: 

• Dr Joshua Quick
• Dr Steve Pullen 

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This exciting PhD project will investigate how microbial pathogens contribute to maternal and neonatal health outcomes in diverse populations. Collaborating with Birmingham Hospitals and the UK Health Security Agency (UKHSA), you will work on cutting-edge technologies, including single-cell genomics and shotgun metagenomics, to explore microbial diversity and mobile genetic elements (MGEs) that drive antimicrobial resistance and virulence.

You will gain advanced training in microbiome research, bioinformatics, and public health applications while working on clinically relevant samples from underserved populations. By integrating genomic data with clinical metadata, this project aims to uncover links between pathogen diversity, infection risks, and health inequalities, informing the development of novel diagnostics and interventions.

Join us to advance our understanding of pathogen dynamics and contribute to improving maternal and neonatal healthcare!

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.

Supervisory team:

• Prof Lindsay Hall 
• Dr Marie Chatterway
• Dr Jo Rhodes
• Dr Josh Quick

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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.

Supervisory team:

• Dr Mike Cox
• Dr Meera Chand
• Dr Dhruv Parekh
• Dr Miruna David

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This project will utilise the internationally unique pathogen genomic and associated meta data for all TB cases in the UK, numbering in the tens of thousands over more than a decade. This data set will be used to perform a comprehensive pathogen population analysis of TB in the UK, including routes of entry to the UK, onward transmission, geographic specific lineages and adaptations, including specific drug resistance and pathogenesis mutations. The project will combine classical microbial genomics with machine learning and AI analysis approaches to create the most in depth population analysis of TB this country.

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.

Supervisory team:

• Prof Alan McNally
• Dr Esther Robinson

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Wastewater is an important source of microbial (viral, fungal and bacterial) pathogens and the treatment of wastewater is regarded as a key intervention to reduce the spread of infectious agents. However, wastewater is sometimes released untreated in the UK’s streams and rivers, but the public health risks associated with these events are currently poorly characterised. In this project we will first implement a combination of metagenomic sequencing techniques to comprehensively characterise baseline levels of microbial pathogens in wastewater and surface water and compare our findings with data on currently circulating clones of gut-associated pathogens. Subsequently, we will perform an observational, longitudinal study on the river Teme to profile the abundance of microbial pathogens. This river is impacted by sewage release and is associated with significant flooding events. The student will combine experimental methods with metagenomics and bioinformatics to profile the threats associated with flooding events and recreation in freshwater.

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.

Supervisory team:

• Prof Willem van Schaik
• Dr Marie Chatterway

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The bacterium Clostridioides difficile is an important cause of diarrhoeal illness, particularly in the elderly and those undergoing antibiotic therapy. C. difficile infections (CDI) are difficult to treat and prevent due to the ability of C. difficile to produce robust spores that can survive most cleaning regimens. Since the COVID-19 pandemic, rates of CDI have increased in the United Kingdom, but the drivers behind this public health issue have not been identified. In this project, we will use a dataset of C. difficile genome sequences to generate a nationwide

population snapshot of this pathogen. This will allow the identification of clones that have recently emerged and spread in both healthcare institutions and the wider community, and will provide insights into the extent by which C. difficile can spread between these different settings. We will also determine antibiotic susceptibilities and identify known antibiotic resistance determinants in C. difficile and, through the implementation of genome-wide association methodologies, discover novel resistance genes or mutations, primarily those that contribute to resistance against antibiotics that are currently used for the treatment of CDI. The project will thus reveal whether bacterial factors are driving the recent increase in CDI rates. This information can be used to develop novel prevention and treatment strategies.

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.

Supervisory team:

• Prof Willem van Schaik
• Dr David Williams 
• Prof Alan McNally

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Global elimination of measles is a WHO target and at risk in the current climate of a reduced vaccine uptake and deteriorating global health disease surveillance infrastructure. It is therefore necessary to use all epidemiological tools, including microbial genomics, to support this endeavour. This exciting project seeks to using whole genome sequencing measles data to advance the understanding of measles evolution and naming systems (nomenclature) to support public health identification of measles outbreaks/importation and ultimately, elimination. In this project you will learn to perform genomic epidemiology, microbial genomics bioinformatics (coding skills) to assess measles evolution and diversity and implement your findings directly into WHO public health infrastructure (MEaNS database) to be used by public health specialists globally. Your outputs will directly contribute to public health at local, regional and international level, and as such you develop collaborative and multidisciplinary skills needed for public health genomic epidemiology. You will work between world leading scientists and epidemiologists across University of Birmingham and UKHSA.

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. 

Supervisory team:

• Dr Charlene Rodrigues
• Dr Ana Penedos
• Dr Vanessa Saliba
• Dr Kevin Brown
• Prof Nick Loman

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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.

Supervisory team:

• Dr Megan McDonald
• Dr Lucy Crouch 
• Dr Jo Rhodes
• Dr Josh Quick
• Mycological Reference Lab
• Dr Charlie Reid

Find out more and register your interest

1. Can international students apply?

No. We are only able to accept students who are eligible to pay Home/UK fees.  Eligibility details can be found on the Gov.uk website   

2. Can clinicians apply?

Yes, as long as they are eligible for home fees. However, the available stipend will be paid at the standard UKRI rate (£20,780) and we are not able to support clinical salary rates.

3. Can I apply for more than one project?

Yes. If there is more than one project that you are interested in you can apply to more than one. You must make this clear in your application.

4. Can I undertake this programme part time?

Part time study is possible but there are restrictions on the total length of the funding so we encourage you to discuss this with the potential supervisor.

5. Are these projects suitable for distance learning?

No. These projects require in person study.