Rapid diagnosis is critical for the effective clinical management of life-threatening infections, especially bloodstream infections (BSI). This is because every hour delay in effective antimicrobial therapy increases risk of mortality by 10%. The gold standard for the diagnosis of BSI is blood culture. However, culture has low sensitivity and a long turnaround time, with results only available 2-5 days after sample collection. Slow diagnostics lead to: 1) poor patient outcomes, 2) the overuse of broad-spectrum antibiotics, which promotes the emergence of antimicrobial resistance (AMR) and 3) increased hospital costs. Nanopore sequencing based clinical metagenomics could replace culture, as it is rapid and can detect any pathogen and AMR gene in a sample (see O’Grady group publications – https://scholar.google.co.uk/citations?user=tyLC9iEAAAAJ
PhD project aims:
1. to develop a metagenomics sequencing based BSI diagnostic pipeline combining novel pathogen enrichment and host depletion technologies with nanopore sequencing and analysis
2. to optimise, evaluate and validate the method on spiked blood samples
3. to clinically evaluate the pipeline on blood samples from patients with suspected sepsis/BSI.
4. to develop and apply bioinformatic analysis tools that utilise the diagnostic metagenomic data for public health applications, such as hospital infection control and pathogen molecular epidemiology
The PhD student will work closely with Momentum Bioscience Ltd, a diagnostics company with a focus on sepsis and will spend 3 months at the company in Oxford. The student will be trained transferable skills such as host DNA depletion (using methods developed and patented by O’Grady), qPCR, nucleic acid extraction from clinical samples, clinical protocol writing, ethical approval, nanopore sequencing, new technologies including Flongle and PromethION and bioinformatics tool development and analysis.
This project is funded by the MRC Doctoral Antimicrobial Research Training Programme (DART). Shortlisted applicants will be interviewed as part of the studentship competition. Interviews are expected to be held on either Monday 12 August, Tuesday 13 August or Wednesday 14 August 2019.
Students will benefit from collaborative training with the Norwich Research Park Doctoral Training Programme, as well as a breadth of training possibilities across UEA and Norwich Research Park partners.
Through collaboration with a non-academic partner, iCASE students will spend 3-18 months on a placement with the partner company. Through this placement, students gain access to training, facilities and expertise not available in an academic setting alone, significantly enhancing future employability.
Applicants must meet the minimum eligibility requirements as specified by MRC, as well as the entry requirements for UEA postgraduate research degrees.
For further information and to apply, please visit our website: https://www.uea.ac.uk/study/postgraduate/research-degrees/phds-and-studentships/dart-mrc-icase
For funding eligibility please visit: View Website.
The studentships are for 3.5 years and cover full tuition fees (Home/EU), a student stipend of £17,509 (2019/20 UKRI stipend £15,009pa & iCASE partner contribution of £2,500pa) and a Research Training Support Grant (£5,000pa) and are available to students who meet the UK residency requirements. Students from EU countries who do not meet the UK residency requirements may be eligible for a fees-only award.