(Meta)genomics of E. coli-associated urinary tract infections in pregnancy (MATHER_Q26MMB)
Key Details
- Application deadline
- 6 January 2026 (midnight UK time)
- Location
- Quadram Institute Bioscience
- Funding type
- Competition Funded (Home and International)
- Start date
- 1 October 2026
- Mode of study
- Full-time
- Programme type
- PhD
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Project description
Primary supervisor - Prof Alison Mather
Urinary tract infections (UTIs) are common in pregnancy and can cause significant maternal and neonatal morbidity and mortality. Recurrent UTIs (RUTIs) affect 4-5% of all pregnancies, and up to 35% of the pregnant cohort can develop pyelonephritis compared to 2% of non-pregnant counterparts. Uropathogenic E. coli (UPEC) is found in over 40% of cases and is the most important cause of RUTIs. There are various bacterial factors that predispose to higher infection morbidity including certain phylogenetic groups, sequence types and virulence factors.
In this project, the student will investigate the hypothesis that the increased risk of UTIs observed in pregnancy may be in part due to differences in the types of E. coli causing the infections, including variations in phylogenetic group, virulence genes and antimicrobial resistance (AMR) determinants. Working with clinicians at the Norfolk and Norwich University Hospital, the student will collect urine and faecal samples from pregnant women, and use long-read genome and metagenome sequencing to characterise urine microbial compositions in these groups and 18S qPCR to examine human DNA load, a proxy for disease severity. Whole genome sequence data will be used to compare the genotypes of UTI-causing E. coli with those in the patients’ own guts, as well as compare these against publicly available genomes obtained from non-pregnant individuals.
The outcomes will inform better patient care, and the project will provide the student with a valuable skillset in interdisciplinary research, encompassing bioinformatics, (meta)genomics and statistics with clinical relevance.
The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK and international candidates with relevant undergraduate degrees for entry in October 2026 and offers the opportunity to undertake a fully-funded 4-year PhD research project supported by the UKRI Medical Research Council in microbiology and microbial bioinformatics.
Our unique and comprehensive training programme empowers students to feel comfortable running sophisticated computer analyses alongside laboratory work and emphasises problem-based learning in microbial bioinformatics, professional development and research skills. All MMB DTP students undertake a Professional Placement.
Interviews for shortlisted candidates will take place on Tuesday 10 February 2026.
The MMB DTP is committed to equality, diversity and inclusion. Students are selected without regard to age, disability, gender identity, marriage or civil partnership, pregnancy or maternity, ethnicity, religion or belief, sex or sexual orientation or social background. We value curiosity, independence of thought, plus an aptitude for research that combines laboratory work and bioinformatics.
For information on eligibility and how to apply: http://www.uea.ac.uk/phd/mmbdtp
Entry requirements
At least UK equivalence Bachelors (Honours) 2:1. English Language requirement (MED/SCI equivalent: IELTS 6.5 overall, 6 in each category).
Funding
This project is awarded with a 4-year fully-funded studentship including direct payment of tuition fees to the University, stipend for living expenses (2025/26 rate: £20,780) and a Research Training Support Grant for each year of the studentship.
References
Carter, C. et al. Uropathogenic Escherichia coli population structure and antimicrobial susceptibility in Norfolk, UK. J Antimicrob Chemother 78, 2028-2036, doi:10.1093/jac/dkad201 (2023).
Bloomfield, S. J. et al. Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiol 110, 104162, doi:10.1016/j.fm.2022.104162 (2023).
Schmidt, K. et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother 72, 104-114, doi:10.1093/jac/dkw397 (2017).
Zamudio, R., et al. Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids. eBioMedicine. doi: 10.1016/j.ebiom.2024.105097 (2024).