One Health (meta)genomics of E. coli-associated urinary tract infections in pregnancy (MATHER_Q27DTP)

Urinary tract infections (UTIs) affect up to 35% of pregnant women and are associated with maternal sepsis, pre‑term birth and markedly higher health‑care costs. Uropathogenic Escherichia coli (UPEC) accounts for 82–85% of these infections, and 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 and cytokine quantification to evaluate disease severity. Whole genome sequence data will be used to obtain an understanding of where the infections might be coming from: the genotypes of UTI-causing E. coli will be compared with 1) those in the patients’ own guts, 2) publicly available genomes obtained from non-pregnant individuals, 3) E. coli genomes from food and other environmental sources, as it’s been suggested some infections might come through the food chain.

The outcomes from this One Health and microbiome project will help combat infectious disease and antimicrobial resistance, and will provide the student with a valuable skillset in interdisciplinary research, encompassing bioinformatics, (meta)genomics and statistics with public health relevance.