Culture-independent, sequence-based pathogen diagnostics: in the field and by the bedside

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  5. Culture-independent, sequence-based pathogen diagnostics: in the field and by the bedside
Milestone n:0%
What does each milestone mean?

    1 = Clinical need
    2 = Idea
    3 = Proof of concept
    4 = Proof of feasibility
    5 = Proof of value
    6 = Initial clinical trials
    7 = Validation of solution
    8 = Approval and launch
    9 = Clinical use
    10 = Standard of care


This project aims to improve the care of patients with meningitis and encephalitis by applying cutting-edge genome sequencing technology to diagnose infections much more quickly than traditional methods.

Lay Summary

When patients are admitted to hospital with an unknown illness doctors perform tests to try to work out what is making them ill so they can treat them. We are developing a fast and accurate test to identify what is causing brain infections such as meningitis. This will allow doctors to provide better care to patients and speed up their recovery.


Existing practice for managing infections, such as meningitis and encephalitis, relies on either a nucleic-acid amplification test or microbial culture to provide a positive identification. Both these methods are too slow to inform treatment in the early stages. This project aims to replace these methods with an accurate, real-time test that can be performed near the patient. This will allow doctors to prescribe the most suitable drugs e.g. antiviral, antibiotic or antifungal drugs early in the illness improving patient outcomes and reducing recovery time.


This project will enable the real-time diagnosis of infections by detecting pathogen DNA or RNA directly from clinical samples. This relies on an advanced technology known as nanopore sequencing which can analyse single-molecules of DNA or RNA and determine their sequence. This allows us to identify what is causing the infection which may be as virus, bacteria or a fungal pathogen. It also provides information on the type, identification of virulence and antibiotic resistance which will improve the management and treatment of the infection.

Research Team

Dr Ghaniah Hassan-Smith
Dr ZakiHassan-Smith

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