PhD opportunities

...population dynamics 

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.

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Supervisory team:

• Professor Alan McNally
• Dr Meera Chand
• Professor Nick Loman

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.

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Supervisory team: 

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

...pathogenicity in clinical environments

In 2017, the WHO first identified a group of priority pathogens presenting the greatest risk to global human health. As of 2024, Acinetobacter baumannii, remains a top priority. The microbe thrives in hospitals and resists most antibiotics. Remarkably, the microbe lacks disease causing genes. Instead, it is thought the microbe constantly rearranges its genome to avoid eradication by the immune system an opportunistically attack human cells. In this respect mobile DNA elements (particularly transposons) appear key. We have developed a new genomic method to track genome rearrangements that occur at low levels within A. baumannii populations. You will use this to understand how chromosomal changes increase pathogenicity and provide an advantage in hospital settings.

You will use a combination of genomic, genetic, and molecular tools. To understand out collection of recent A. baumannii isolates from infected patients at the nearby Queen Elizabeth hospital. The ultimate goal is to understand the mechanisms by which genome rearrangements allow the bacterium to better infect the human host and persist in hospital settings.

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Supervisory team

• Professor David Grainger
• Professor Katie Hopkins
• Professor Jessica Blair
• Professor Willem van Schaik

...implications for public health in a changing climate

Climate change is increasing the frequency of extreme rainfall and flooding, placing pressure on ageing wastewater systems and leading to the release of untreated sewage into rivers and homes. These events can reshape microbial communities and elevate the risk of human exposure to harmful pathogens.

This project will use cutting-edge metagenomic, genomic and transcriptomic sequencing to investigate how microbial diversity, antimicrobial resistance, and key pathogens (e.g. E. coli, Leptospira, Norovirus and Exophiala) fluctuate in river systems and flooded residential environments. Samples will be collected regularly from sewage-impacted rivers and from properties affected by flood events. Data will be analyses using advanced bioinformatics to characterise community structure, resistance genes and mutations, and potential environmental-clinical links.

Working in partnership with the UK Health Security Agency (UKHSA) and Environment Agency (EA), the project will provide insights to support environmental modelling, risk assessment, and climate resilience planning. Students will gain hands-on experience in environmental sampling, short- and long-read sequencing, microbial genomics and bioinformatics, whilst contributing to vital public health research. This multidisciplinary project suits candidates interested in environmental microbiology, genomics, and climate-driven infectious disease.

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Supervisory team:

• Dr Johanna Rhodes
• Professor Willem van Schaik
• Dr Marie Chattaway
• Dr Claire Jenkins

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 bioinformatics 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 and potentially developing bioinformatic tools and focused on clear interpretation and communication of this data.

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Supervisory team:

• Dr Michael Cox
• Dr Meera Chand
• Dr David Cleary
• Dr Dhruv Parekh
• Dr Miruna David

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.

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Supervisory team:

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

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.

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.