- 3.5 year PhD studentship funded by UK’s Medical Research Council under its Doctoral Antimicrobial Research Training (DART) Programme at University of East Anglia (UEA)
- Position based at Quadram Institute Biosciences (QIB), on the Norwich Research Park, supervised by Dr Gemma Langridge, an expert in bacterial genomics
- QIB provides 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 Industrial partner RevoluGen Ltd, is a leader in the field of high molecular weight (HMW) DNA extraction methodologies and will host a 3-month placement
- The studentship will undertake long read metagenomic analysis of important pathogens to understand the local strains, mobile elements and antimicrobial resistance determinants to support public health
London, UK – 22 September 2021 – The UK genomic tools developer, RevoluGen Ltd. (RevoluGen or the Company), today announces that it is the Industrial partner in a grant awarded to Quadram Institute Biosciences (QIB), Norwich to use DNA sequencing as part of pathogen surveillance to identify circulating strains and antimicrobial resistance (AMR) genes in Salmonella and Campylobacter.
The 3.5 year PhD studentship is funded by UK’s Medical Research Council (MRC) under its Doctoral Antimicrobial Research Training (DART) Programme. Applications are open until 11 October.
In this project, Campylobacter and Salmonella isolates from diarrhoeal stool specimens will be investigated by applying high throughput high molecular weight (HMW) 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 PhD student will join the research group of Dr Gemma Langridge, an expert in bacterial genomics based at QIB, an interdisciplinary state-of-the-art research facility with access to advanced Oxford Nanopore sequencing facilities, expertise in research microbiology, molecular epidemiology and bioinformatics, as well as facilities across the Norwich Research Park, including the Norfolk and & Norwich University Hospital.
As the Industrial partner RevoluGen, will provide its expertise in HMW DNA extraction methodologies. Its Fire Monkey Nucleic Acid Isolation and Purification (NAIP) technology is based on a spin-column protocol to extract HMW-DNA which, despite the use of high g-forces, protects the long and fragile DNA molecules from more massive shearing. This DNA extraction has broad application across both short- and long-read DNA sequencing. These applications include population genomics, epidemiological mutation screening and antibiotic microbial resistance gene monitoring.
The project will address the challenge of processing stool samples for HMW DNA extraction prior to long read metagenomic analysis. RevoluGen will optimize its extraction methodologies 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.
“We have been working with Quadram for over two years and I am delighted that RevoluGen has been chosen as the industrial partner in this MRC DART grant. It will enable the next generation of microbiology students to gain both academic and industry experience 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,” said Dr Georgios Patsos CSO at RevoluGen.
The MRC DART programme, starting in 2021/2022 provides a full studentship award to support living costs, research costs and full University of East Anglia tuition fees.
Quadram Institute, Norwich
RevoluGen R&D facilities, Hadfield