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 (http://modmedmicro.nsms.ox.ac.uk/rehab/) 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.
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
Project reference number: 972
|Professor (Ann) Sarah Walker||Experimental Medicine Division||Oxford University, John Radcliffe Hospital||GBRfirstname.lastname@example.org|
|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||GBRemail@example.com|
There are no publications listed for this DPhil project.