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Developing tools and tests for targeted sequencing based infectious diseases diagnostics

A Global Pathogen Detection System

Project Summary  

Infectious diseases remain a major global health threat, particularly in low- and middle-income countries. According to the WHO, 3 of the top 10 causes of death globally in 2021 were infectious including lower respiratory infections (2.5 million) and TB (1.3 million). Poor diagnostics contribute significantly to these preventable deaths. Current microbiological diagnosis relies on culture, which is slow and laborious. Rapid, comprehensive and affordable tests are urgently required to reduce the global burden of infectious diseases.

This PhD project will focus on the development of targeted next generation sequencing (tNGS) based diagnostic tests that combine the speed of PCR with the comprehensiveness of sequencing technology. The PhD student will begin by developing an AI powered tool for designing high-level multiplex PCR (hundreds of PCR primers) to target pathogens and AMR markers. This tool will be designed to output functioning primer pools, removing the requirements for months of iterative manual primer design and optimisation. The tool will then be used to design test primer pools that will be validated using spiked clinical samples.  When the tool is optimised it will be used to generate primer schemes for complex clinical syndromes like sepsis and respiratory tract infections. Pools will be optimised for specificity and sensitivity, if necessary, and form the basis of tNGS diagnostics assays using nanopore sequencing technology.  

Potential Supervisors

  • Professor Justin O’Grady (Senior Director of Science Applications, Pathogen Program, EIT)
  • Dr Philip Fowler (Associate Professor, Modernising Medical Microbiology consortium in the Nuffield Department of Medicine, University of Oxford)
  • Professor David Eyre (Professor of Infectious Diseases, Nuffield Department of Medicine, University of Oxford)

Skills Recommended

  • To be confirmed

Skills Developed

  • Expertise in microbiology, molecular biology, sequencing, bioinformatics, AI and diagnostics and have access to high level talent in these areas
  • A highly transferrable and employable skillset
  • Be exposed to both industry and academia, giving them a good understanding of both and allowing them to make an informed choice about their future career path

University DPhil Course(s) 

Relevant Background Reading 

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