Genomics and Metagenomics of Animal, Environmental and Human Samples to Understand Resistance Gene Transmission Amongst Enterobacteriaceae in Oxfordshire

Project Overview

Antimicrobial resistance (AMR) is a major health concern, and is exemplified by the rapid emergence of AMR in several key species of the bacterial family of Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae. These bacteria are able to colonise human, animal and environmental niches, but are also a major cause of human disease. The emergence of resistance in these organisms is largely facilitated by intra- and inter-species exchange of AMR genes on mobile genetic vectors, such as plasmids, but it remains unclear where the predominant hotspots of resistance gene emergence are; to what extent species, resistance genes and resistance gene vectors are segregated in various reservoirs versus shared between them; what the population structure of important genera of Enterobacteriaceae is (human and non-human); and how to classify and define plasmid diversity and characterise plasmid evolution. This project aims to analyse the rich resource of sequence data (metagenomes [n=180], complete bacterial assemblies [n=1000]) being generated as part of the REHAB study ( together with sequences from human bloodstream infections. The project will involve a diverse range of genome sequence processing and analytical disciplines including: evolutionary genomics, bioinformatics, biostatistics, population genetics and comparative genomics. The successful candidate will be enrolled at the University of Oxford’s Medical Sciences Doctoral Training Partnership for additional training opportunities and local student cohort activities. 

Training Opportunities

This is a highly inter-disciplinary research opportunity making use of an unprecedented sequencing resource with a view to acquiring knowledge of and skills in the following disciplines: Environmental and clinical microbiology; clinical epidemiology and biostatistics; long and short read sequencing, including metagenomics, and sequence data analysis; bioinformatics; statistical genetics


Immunology & Infectious Disease and Genetics & Genomics


Project reference number: 972

Funding and admissions information


Name Department Institution Country Email
Professor (Ann) Sarah Walker Experimental Medicine Division Oxford University, John Radcliffe Hospital GBR
Dr Hyun Soon Gweon Bioinformatics University of Reading GBR
Dr Daniel Read Centre of Ecology and Hydrology GBR
Dr Nicole Stoesser Experimental Medicine Division Oxford University, John Radcliffe Hospital GBR

There are no publications listed for this DPhil project.