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Optimising the implementation of metagenomic sequencing for lower respiratory tract and bloodstream infections through integrated epidemiological, behavioural and health-economic modelling

Contribute to EIT's Pathogen Program, transforming how the world understands and responds to infectious disease, as a Graduate Ellison Scholar.

Key facts

Project description

Metagenomic sequencing (mNGS) has the potential to transform the diagnosis and management of lower respiratory tract infections (LRTIs) and bloodstream infections (BSIs), but its value depends not only on diagnostic performance, but also on which patients are tested, when testing occurs along the clinical pathway, and whether clinicians act on the results (1). This project will develop an integrated modelling framework to identify how metagenomic sequencing can deliver the greatest clinical and economic benefit while informing the development of mNGS testing procedures and associated implementation strategies (4).

The student will first develop epidemiological and decision-analytic health-economic models to identify which patient populations, and at which points in the clinical pathway, metagenomic sequencing is expected to provide the greatest health gains and be cost-effective across different healthcare settings(3). Initial analyses will focus on the UK and US healthcare systems, recognising differences in clinical pathways, reimbursement mechanisms, antimicrobial stewardship practices and health technology assessment frameworks.

A key innovation will be the integration of behavioural modelling using discrete choice experiments to quantify how clinicians respond to metagenomic sequencing results (2). These experiments will generate a quantitative dataset of approx. 1000 responses from prescribers in the UK and US. Diagnostic information alone does not necessarily lead to changes in antibiotic prescribing, and the student will estimate how test characteristics, turnaround time, diagnostic certainty and implementation strategies influence prescribing decisions. These behavioural predictions will be incorporated into the epidemiological and health-economic models to produce realistic estimates of clinical impact, antimicrobial use and resistance outcomes and cost-effectiveness(3,4).

Finally, the project will integrate these findings to develop evidence-based Target Product Profiles (TPPs) and accompanying implementation strategies for metagenomic diagnostics. The TPPs will define the technical, clinical and operational characteristics required for tests to be acceptable to clinicians, achieve meaningful changes in prescribing behaviour, and deliver value for money in different healthcare systems. The project will provide a quantitative framework for guiding diagnostic developers, healthcare providers and policy-makers on how metagenomic sequencing should be designed, implemented and evaluated to maximise patient and population health benefits.

Skills Required

  • Quantitative background (e.g. economics, statistics, mathematics, epidemiology or a related discipline)
  • Statistical programming (R and/or Python)  
  • Strong analytical skills
  • Strong communication and collaborative working skills
  • Interest in infectious diseases and antimicrobial resistance (AMR)

Skills to be Developed

  • Epidemiological and infectious disease modelling  
  • Health-economic decision modelling  
  • Discrete choice experiment design and behavioural modelling  
  • Development of diagnostic Target Product Profiles and implementation strategies  
  • Translation of modelling evidence into diagnostic policy and practice 

Relevant Background Reading

  1. Charalampous, T., Kay, G.L., Richardson, H. et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol 37, 783–792 (2019).  
  2. Qaife M, et al. How well do discrete choice experiments predict health choices? A systematic review and meta-analysis of external validity. Eur J Health Econ 2018;19:1053-1066.
  3. Jit M, et al. Quantifying the economic cost of antibiotic resistance and the impact of related interventions: rapid methodological review, conceptual framework and recommendations for future studies. BMC Med 2020;18:38.  
  4. Wagner, A.P., Enne, V.I., Gant, V. et al. Cost-effectiveness of rapid, ICU-based, syndromic PCR in hospital-acquired pneumonia: analysis of the INHALE WP3 multi-centre RCT. Crit Care 29, 352 (2025). 

How to apply

Stage 1: Apply to Ellison Institute of Technology

Submit an application to Ellison Institute of Technology (EIT) by 5pm UK time on Tuesday 1 December 2026.

We encourage you to apply early, as applications will be reviewed as they are received.

Learn more and apply

Stage 2: Apply to the University of Oxford 

If selected by EIT, you will receive conditional funding and will be invited to apply to the University of Oxford by following the instructions on the course page.

Your application will then follow the standard graduate admissions process and will be assessed against the entry requirements shown on the course page.