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Rapid and precise detection of gastrointestinal infections using metagenome sequencing

  • Full or part time

    Prof A Darby
  • Application Deadline
    Sunday, April 26, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Whole genome sequencing is now established as the gold standard for monitoring bacterial pathogens allowing both epidemics to be reconstructed and phenotype to be characterized. However, this still relies on time consuming culturing and isolation. This project will explore the viability of direct identification of gastroenteric pathogens through metagenome sequencing of faecal samples. An existing data set of short read metagenomes from a large-scale NHS study conducted in collaboration with the University of Liverpool will be used to test the extent to which different pathogens are present at detectable levels in faecal DNA. Short read sequences are still time consuming to generate and have limitations in terms of the precision with which organisms can be identified. Therefore, we will generate additional trial data from samples provided through Public Health England using rapid long read platforms such as the Oxford Nanopore Minion. This will require substantial development of both novel laboratory protocols and bioinformatics pipelines for analysis. If successful though it could transform the routine monitoring of gut pathogens both in the UK and in developing countries where distributed detection methods are urgently needed.

The project will involve a mixture of laboratory and bioinformatics research with the exact proportion dependent on the applicant. This project will be supervised by Dr Christopher Quince (University of Warwick), Dr Alistair Darby (University of Liverpool) and Dr Tim Dallman (Public Health England).

We invite applications from candidates who have a 2.1 or 1st class degree in a relevant biological science or quantitative science discipline. A Masters degree in a relevant discipline would be an advantage.
Applicants should send a full CV (including the names and email addresses of at least two academic referees), and personal statement at . This should state:
• An outline of how this programme of research and training will benefit from their past experience and impact upon their career aspirations.

The position may be based at either, The University of Liverpool, The University of Warwick or PHE (Colindale/ Porton Down), depending on the project. For some projects, students will be required to work at one of the partner Universities’ and spend time at PHE.

Funding Notes

Thesis studentships cover research costs and tuition fees at the UK/EU rate for students who meet the residency requirements only.

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