MSc in Paediatric Infectious Diseases

Overview of pregnancy management in women living with HIV and infant outcomes in at OUH between 2021 and 2026 and comparison with national data

The project will cover:

• Description of timing and setting of HIV diagnosis with focus on diagnosis at antenatal screening
• Infant outcomes and management of the post-natal prophylaxis (audit on alignment with BHIVA guidelines on choice and timing of post-natal prophylaxis)
• Focus on breastfeeding vs bottle feeding and infant outcomes with option of qualitative project on challenges/facilitators to breastfeed by interviewing women who have chosen to breastfeed in the form of satisfaction survey and/or interviewing health care staff involved in women’s support.

Overview of CMV testing on dried blood spots (D B S) after abnormal audiology tests in infants 

This project will focus on:

• proportion of CMV VL requested
• turnaround time of result that might have caused delay in treatment
• follow up management of positive results

A review of proportion of children from parents living with HIV tested for HIV in the UK after moving from abroad

‘The HIV status of all children, including adult children, of adults living with HIV in the UK should be known and confirmed as a matter of clinical urgency’. This is a 2026 CHIVA policy re-launch that is co-badged with BHIVA, BASHH and NHIVNA with a draft for review under consultation.

Audit involving HIV centres in the South of England.

This project might include qualitative research with healthcare professionals on their perspectives on barriers to implementation of this guidance and possible systems and care pathways to facilitate it.

Overview of sexual healthcare seeking behaviour in adolescents in regional setting in the South East of England

This project will cover:

• Reasons for attending sexual health service
• STI testing, test positivity rate, distribution of infections
• Focus on neurodiversity and how this affects presentation to sexual health services and prevalence of infections
• Do neurodiverse adolescents attend sexual health services for different reasons than non-neurodiverse adolescents?
• Is there a difference between STI testing, test positivity rate and distribution of infections between neurodiverse and non-neurodiverse adolescents? 

Systematic review & meta-analysis on an ID topic:

• Impact of point of care tests in ED on antimicrobial use
• Use of immunoglobulin + ribavirin for treatment of RSV in immunocompromised patients
• Long term outcomes of infants with cCMV 

Human Challenge Models for Respiratory infections

Despite available vaccines, pneumonia is still a major killer affecting particularly vulnerable populations, such as children and the elderly. Pneumococcal infections are most common in the winter with secondary pneumococcal pneumonia being the major cause of mortality following seasonal and pandemic influenza infection. Our group uses Human Challenge models in which participants are deliberately infected with live respiratory viruses and bacteria to study host-pathogen interactions, immune responses, pathogen transmission and to accelerate development of vaccines.

We have several projects in the following areas:

• Host and pathogen gene expression associate with pneumococcal shedding
• Correlates of protection to respiratory infection and vaccination
• Susceptibility to respiratory disease: why children and older people get sick
• Interaction of viral and bacterial co-infections and immune response modulation
• Computational biology and machine learning

Each project can be tailored to give the student exposure to their methods of interest including B and T cell ELISPOTs, ELISAs, Luminex, multicolour flow cytometry and cell sorting, handling of data including transcriptomic analysis and extensive data analysis (including R) and computational biology (machine learning).

Examples of desk-based projects – computational biology and systems analysis

Colonisation of the upper respiratory tract by pneumococcus is important for disease development and transmission across the population. The immunological mechanisms that contain pneumococcus during colonisation are well-studied in mice but remain poorly explored in humans.

1. Using machine learning methods and bulk/mRNA sequencing data, this project will identify potential molecular biomarkers to discriminate between those protected vs susceptible to colonisation.
2. The human genome is estimated to encode approximately 25,000 protein-coding genes, and their expression could be determined by several factors, such as microRNA regulation, alternative splicing, RNA editing, and others, that are important to protection or susceptibility to infectious diseases such as pneumonia. This project will use systems biology and gold-standard bioinformatic methods to identify whether alterations of RNA regulators associate with protection from colonisation.
3. Community-acquired pneumonia (CAP) is leading cause of death worldwide. CAP disproportionally affects children under the age of five years and older adults. Our research group has been using the Experimental Human Pneumococcal Challenge (EHPC) to understand the older population's mucosal immunology better. In older pneumococcal challenge cohorts, we have identified an important activation of B and T cells by pathways enrichment analysis associated with colonisation. In this project, we will identify B and T receptors repertoire using our existent bulk RNA sequencing data and well-established computational biology tools.

Examples of laboratory-based projects

1. Vaccine induced nasal mucosa antibody-mediated agglutination of pneumococcus. The agglutinating effect of antibodies has shown to be an important factor in the protection against pneumococcal colonisation. There is a clear need for adequate methods to assess and quantify this antibody functionality particularly against different serotypes of pneumococcus. We will utilize a novel flow cytometric assay to quantify the agglutinating capacity of anti-pneumococcal antibodies using nasal mucosa samples from people vaccinated with Pneumococcal Conjugate Vaccine vs Polysaccharide Vaccine against a variety of serotypes of Spn. This assay will allow us to examine the role of pneumococcal surface antigens and demonstrate the importance of antibodies to its immunodominant antigen, the differential role of the capsular polysaccharide (CPS) in humoral responses in eliciting agglutinating IgG that confers protection from the acquisition of colonization.
2. Using an experimental pneumococcal challenge model, we have recently shown that older adults susceptible to pneumococcal colonisation have higher levels of transcripts associated with inflammation in the nasal mucosa compared to older adults protected from colonisation. During the project, candidates will determine whether (1) these soluble markers of inflammation can be detected in nasal mucosa samples before and after experimental challenge with pneumococcus by ELISA and (2) concentrations of soluble markers of inflammation in nasal lining fluids can predict susceptibility for colonisation before challenge. 

ChiMES study. Potential MSc projects could be:

• Conduct transcriptomic and proteomic assessment of serum and CSF to better understand the pathogenesis of meningitis and encephalitis in children. (Funding required)
• Conduct next generation sequencing of enterovirus using CSF samples in children with meningitis and encephalitis. (Funding required)
• Evaluate the quality of life of children admitted with meningitis and encephalitis. (Funding potentially required)

cCMV. Caroline Trotter to co-supervise an MSc student. Potential MSc projects could be:

• Conduct a systematic review and meta-analysis of the global DALY attributed to congenital CMV
• Conduct a seroprevalence study to assess the age specific prevalence of CMV antibodies using samples from UKHSA and the OVG biobank (this is a study that we have both submitted previously for funding but been unsuccessful). (Funding required) 

The recommendations for face mask use during the COVID-19 pandemic varied between different countries. The data on personal protective equipment (PPE) use were collected during the Oxford-AstraZeneca vaccine trial from healthcare worker participants in the UK and Brazil. This project aims to describe PPE use among healthcare workers in the trial and evaluate the associations between PPE use and the risk of SARS-cov-2 infection. The student will clean the data, conduct all the analysis and interpret the results with the support from OVG clinical and stats team. 

Assessing antibody responses to pneumococcus during co-infection with RSV

This MSc project will investigate how respiratory syncytial virus (RSV) co-infection influences antibody responses to Streptococcus pneumoniae (Spn) using a controlled human co-infection model for both pathogens. Pneumococcal colonisation is a major contributor to respiratory disease worldwide, and viral co-infections such as RSV are known to alter host immunity and increase susceptibility to severe infection. 

The study will analyse mucosal and systemic antibody responses to pneumococcus in participants experimentally challenged with Spn and RSV, with the aim of understanding how viral infection modifies protective immune mechanisms against pneumococcal carriage and disease. By integrating immunological assays with clinical data from a human challenge model, the project will provide valuable insight into host–pathogen interactions at the respiratory mucosa and may help inform immunisation policy and future immunisation strategies. 

Differentiating infants with adverse events following immunisation (AEFIs) or invasive bacterial infection (IBI) is a significant clinical challenge. Febrile events following infant vaccinations are common and can lead to hospital admissions, invasive procedures, and antibiotic use to address the risk of coincidental cases of IBI. Moreover, blood biomarkers of IBI such as C-reactive protein and absolute neutrophil counts can also be elevated post-vaccination, further complicating the clinical assessment. This issue has been exacerbated by the introduction of the group B meningococcal vaccine — 4CMenB — into the routine UK immunisation schedule. This vaccine has been shown to be highly effective in preventing group B infection in infants but with fever being a common adverse reaction. This project will assess novel gene-based biomarkers to rapidly rule out bacterial infection in infants presenting with fever post-vaccination. 

The paediatric urinary microbiome in urinary tract infection: predicting susceptibility, recurrence, and clinical outcomes. 

Systematic review and meta-analysis examining the impact of maternal antibiotic use on infants’ risk of infection, antibiotic use, vaccine response, and infection-related hospitalisation.

Systemic and Mucosal Coronavirus Immunity Following SARS-CoV-2 Vaccination

A master’s project based around the analysis of paired systemic and mucosal immunology datasets collected across two clinical vaccine studies. The project is best suited to a student with some previous experience of data analysis using software such as R, Python, Stata, SPSS or SAS, although applicants with less formal experience but a willingness to develop analytical skills independently would also be well suited. Regular supervisory meetings and analytical guidance can be provided throughout.

The datasets derive from:

• Com-COV: homologous and heterologous SARS-CoV-2 priming vaccine schedules in older adults
• Com-COV3: homologous, heterologous and fractional-dose vaccine schedules, including third-dose vaccination, in adolescents

The dataset contains paired serum and mucosal lining fluid measuring both IgG and IgA

Responses are available against:

• SARS-CoV-2 spike
• SARS-CoV-2 nucleocapsid
• SARS-CoV spike
• MERS spike
• endemic seasonal coronaviruses (OC43, HKU1, NL63 and 229E)

Some analyses from the adult cohort have already been completed and submitted for publication, particularly around the relationship between vaccination and mucosal antibody responses. However, substantial opportunities remain for further novel analyses, particularly involving:

• adolescent versus adult comparisons
• relationships between systemic and mucosal immunity
• endemic coronavirus exposure and immune imprinting
• determinants of mucosal antibody responses

The final scope of the project can be tailored according to the student’s interests, analytical background and desired level of computational complexity but potential areas of focus could include:

Evidence for true mucosal IgA induction following vaccination in adolescents 

• Does mucosal IgA behave differently in adolescents compared with older adults?
• Are responses vaccine-driven or more consistent with mucosal viral exposure? 

Relationships between systemic and mucosal immunity

• How closely coupled are serum and mucosal antibody responses?
• Do these relationships vary by age group, vaccine schedule or prior exposure history? 

Baseline epidemiology of endemic human coronaviruses

• How do HCoV exposure patterns differ between adolescents and older adults?
• Are there distinct baseline immune phenotypes? 

Impact of pre-existing HCoV immunity on SARS-CoV-2 vaccine responses 

• Is there evidence for immune imprinting or cross-reactive boosting?
• Do baseline coronavirus responses influence subsequent vaccine immunogenicity?

Systemic and Mucosal Immunity to Salmonella Paratyphi Following Controlled Human Infection

Paratyphoid fever remains an important cause of enteric disease worldwide, yet the immune mechanisms that protect against infection remain poorly understood. Controlled Human Infection Models (CHIMs) provide a unique opportunity to investigate protective immune responses in humans under carefully controlled conditions. 
This MSc project will investigate systemic and mucosal immune responses to Salmonella Paratyphi A using samples collected from a controlled human infection study. The student will analyse paired serum and mucosal samples collected before and after challenge to characterise immune responses and determine how these relate to protection from infection, disease severity, and bacterial shedding. The project will contribute to ongoing efforts to identify immune correlates of protection against paratyphoid fever and may help inform the development of next-generation enteric fever vaccines. Potential techniques include ELISA, ELISpot, cytokine assays, Luminex, functional antibody assays, and statistical analysis.

Immune Correlates of Protection Against Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is one of the leading causes of healthcare-associated diarrhoea worldwide. Although antibody responses to C. difficile toxins have been associated with protection from disease and recurrence, the immune mechanisms underlying protection remain incompletely understood.
This MSc project will investigate antibody responses to toxin and non-toxin C. difficile antigens using clinical samples from individuals with previous CDI and healthy controls. The student will characterise antibody responses and examine their relationship with toxin-neutralising activity and clinical outcomes. The project aims to identify immune signatures associated with protection against CDI and contribute to the development of vaccines and antibody-based therapeutics. The work will provide experience in translational immunology, infectious diseases, and vaccine research. Potential techniques include ELISA, cytokine assays, toxin neutralisation assays, data analysis, and statistical analysis.

Immune Correlates of Protection Against Plague and Chikungunya Viruses: A Phase 1 Vaccine Immunogenicity Study

Emerging and neglected infectious diseases continue to pose major global health challenges, highlighting the need for effective vaccines. 

This MSc project will investigate immune responses induced by novel plague and bivalent chikungunya–Mayaro vaccines currently being evaluated in first-in-human Phase 1 clinical trials. The student will analyse clinical samples and immunogenicity datasets to characterise vaccine-induced antibody and cellular immune responses and explore potential immune correlates of protection. Particular emphasis will be placed on understanding the quality and durability of vaccine-induced immunity and investigating cross-reactive responses between chikungunya and Mayaro viruses. This project offers a unique opportunity to gain experience in translational vaccinology and the analysis of data generated from early-phase human vaccine trials. Potential techniques include ELISA, ELISpot, flow cytometry, Luminex, neutralisation assays, and statistical analysis.
 

A review using systematic approaches on a topic related to vaccine hesitancy and policy, or clinical trials. Can include all types of study methodologies – qualitative, quantitative or mixed methods. After conducting a review of the literature, apply meta-analysis techniques. Examples of previous reviews:

• ‘MMR Vaccine Attitude and Uptake Research in the United Kingdom: A Critical Review’
• ‘How can community engagement in health research be strengthened for infectious disease outbreaks in Sub-Saharan Africa? A scoping review of the literature’
• ‘The representation of ethnic and racial minority groups in European vaccine trials: a quantitative analysis of clinical trials registries’
• ‘Charting mandatory childhood vaccination policies worldwide’
• ‘A systematic scoping review on how public and patient attitudes toward the use of monitoring technologies in healthcare differ across countries’ 

Systematic review and meta-analysis of the global distribution of Group B streptococcus serotypes and genotypes colonising pregnant women

Further projects may be available under Dr Stephane Paulus and Associate Professor Dominic Kelly. Further information about research in the department can be found on the department's website. 

Official course title

Master of Science in Paediatric Infectious Diseases

Award

Course code

TM_JD9P1

This course is part-time only. You will be encouraged to attend residential sessions in Oxford during the course. You may also be required to conduct field work for your project.

The department has state-of-the-art laboratories with a number of research groups at different locations in Oxford, with most of the groups based at the John Radcliffe Hospital and WIMM, the Centre for Vaccinology and Tropical Medicine at the Churchill Hospital, and the Science Centre at South Parks Road.

Students will have access to the department’s IT support and University library services. Workspace will be related to individual circumstances. If undertaking experimental work, bench space will be provided within a laboratory. The provision of other resources specific to a project should be agreed with the supervisor as part of the planning stages of the agreed project.

The allocation of graduate supervision for this course is the responsibility of the Department of Paediatrics and it is not always possible to accommodate the preferences of incoming graduate students to work with a particular member of staff. Under exceptional circumstances a supervisor may be found outside of the Department of Paediatrics.

You will receive support and guidance from your dedicated Oxford supervisor during the preparation of your dissertation. If you are completing your research project outside of Oxford you will also be required to find a local supervisor to be approved by the Course Director. It is your responsibility to agree the frequency of meetings with your supervisor(s).

You will undertake a research dissertation based on your research project

MSc projects will be developed with a supervisor and might involve, for example, a laboratory project, a clinical study, a systematic review or an analysis project using existing data. Projects are usually based in Oxford (but may exceptionally be conducted elsewhere with a supervisor from the University of Oxford) and consist of data collection and analysis followed by writing up.

Examples of recent projects include:

• Persistence of immunity against Salmonella Typhi after vaccination;
• A review of CMV detection and management in neonates in a hospital setting;
• Neonatal anti-microbial resistance in a low income setting;
• Epidemiology, resistance and sequencing of bacteria causing UTI in a LMIC setting.

Most part-time students commencing this course are already in full-time employment. The MSc aims to broaden a trainee's knowledge about paediatric infection for continued work in the subspecialty.
 

This course is offered by the Department of Paediatrics

• Course page on the department's website
• Academic staff and research in Paediatrics
• Contact details

*Three-year average (applications for entry in 2024-25 to 2026-27) 

• a first-class or strong upper second-class undergraduate degree with honours in an appropriate subject;
• an appropriate medical qualification equivalent to MBBS (Bachelor of Medicine/Bachelor of Surgery); and
• successful completion and strong performance at a first-class or strong upper second-class level of the PGDip in Paediatric Infectious Diseases.

Students who have been awarded the PGDip in Paediatric Infectious Diseases will normally be eligible for admission to the MSc up to two years after completion.

For applicants with a bachelor's degree from the USA, the minimum overall GPA that is normally required to meet the undergraduate-level requirement is 3.6 out of 4.0.

GRE General Test scores

No Graduate Record Examination (GRE) or GMAT scores are sought.

Other qualifications, evidence of excellence and relevant experience

• Publications are not expected.
• Applicants will need to provide evidence of their ability to commit time to research and an employer's commitment to make time available to undertake a research project and write up a dissertation.

Further guidance

• Students in their second year of the Postgraduate Diploma in Paediatric Infectious Diseases can apply for the MSc, but will be required to successfully complete the Postgraduate Diploma before commencing the MSc.

Interviews are normally held as part of the admissions process.  

A 15-minute telephone or online interview will be arranged for all those who appear to fulfil the basic requirements for entry to the course. Performance at interview will play a significant role in the assessment of the selection criteria. Telephone or online interviews will be held following the application deadline. They will be conducted by a minimum of two interviewers.

The purpose of the interview is to:

• establish the candidate’s level of interest, motivation and potential to benefit from the course of study;
• clarify any uncertainties about course requirements; and
• ensure that candidates are fully informed of the standard of achievement and level of commitment required by the course of study.

The following colleges accept students on this course:

• Green Templeton College
• Kellogg College
• St Cross College
• Wycliffe Hall

 In order to apply for the MSc, you must have successfully and recently completed the PGDip in Paediatric Infectious Diseases (see Entry requirements for further details).

Students currently in their second year of the PGDip should contact the course team, via the contact details provided on this page, for further details about how to apply for the MSc. If you have already successfully completed the PGDip, you should apply for the MSc via the standard graduate application process.

You are encouraged to contact the Paediatric Infectious Diseases (PID) Programme team before you apply to discuss research opportunities and supervision arrangements.

You should submit an outlined proposal for a research study that is appropriate to the aims of the course, well-designed and feasible.

If you have any queries about the length of your proposal, please contact the department directly. 

Your proposal should address your reasons for applying to this course in particular and your relevant skills and experience.

This will be assessed for your motivation for applying to this particular course; your relevant academic, research, or practical experience; and the areas of study within the subject that interest you.

Email: [email protected]