Project Description

In this project, Campylobacter and Salmonella isolates from diarrhoeal stool specimens will be investigated by applying high throughput HMW DNA extraction and long read sequencing technologies. Sequence data will be analysed with informatic methods and interpreted by comparison with publicly available data at national and global levels to understand the local strains, mobile elements and antimicrobial resistance determinants in circulation.

The candidate will also address the challenge of processing stool for HMW DNA extraction prior to long read metagenomic analysis. The industrial partner, RevoluGen Ltd, is a leader in the field of high molecular weight (HMW) DNA extraction methodologies which will be optimised for downstream metagenomic sequencing. The aim is to significantly improve the number and quality of metagenomic assembled genomes (MAGs) from Campylobacter and Salmonella positive stools over what would be achieved with short read sequences. The MAGs will provide insight into 1) the presence and genomic location of antimicrobial resistance (AMR) determinants, 2) characterisation of virulence factors and 3) population level comparisons through strain level typing, which will indicate method viability as an option for outbreak detection.

The candidate will join the research group of Dr Gemma Langridge, an expert in bacterial genomics based at [Employer hidden], an interdisciplinary state-of-the-art research facility with access to advanced Oxford Nanopore sequencing facilities, expertise in research microbiology, molecular epidemiology and bioinformatics. The wider supportive group interlinks with facilities across the Norwich Research Park, including the Norfolk and Norwich University Hospital.

The 33-month studentship program at [Employer hidden] and 3-month industry placement at RevoluGen are ideal for a student seeking both an academic and an industry opportunity in genome level characterisation of pathogens with great public health importance, product development and using the latest genomic and metagenomic long read sequencing technologies to expand into emerging research fields.

Requirements

• At least an upper second class honours degree, or equivalent
• Meet UEA minimum English language requirements

Funding Notes

This PhD project is funded for 3.5 years. Successful students starting in 2021/22 will be eligible for a full studentship award: a stipend to support living costs (2021/22 UKRI rate: £15,609pa plus iCASE stipend enhancement of £2,500pa), research costs and full University of East Anglia tuition fees. Please note that all international awards have been made for the MRC DART programme for 2021 and we will not be accepting applications from international candidates.

Contact and Application

Informal enquiries: [contact hidden]

Apply via: UEA PhD Application