University of Dundee

Characterising Antimicrobial Resistance in Care Homes using Whole Genome Sequencing

Antimicrobial resistance (AMR) is an increasing public health threat and it is important to understand the role of different factors contributing to AMR in individuals. Older people living in care homes are at higher than average risk of AMR infections and have high rates of antibiotic prescriptions and hospital admissions, and the risk of acquiring infections from other residents. The aim is to use bacterial whole genome sequencing (WGS) of clinical isolates linked to source patients’ Electronic Health Records (EHR) to characterise Gram-negative organisms (coliforms) and their AMR profiles and associated patient characteristics, for all residents in a sample of care homes. Coliforms isolated from clinical samples (urine, sputum, swabs, blood cultures) from residents of these care homes will undergo WGS in addition to standard NHS culture and sensitivity testing. This project involves analysis of the linked WGS and EHR data to characterise resistomes of isolates, identify any potential transmissions using phylogenomic methods, epidemiological evidence of possible transmission, and associations between coliform species’, genotypic and phenotypic resistance traits and mechanisms, and resident risk factors (e.g. prior hospital admissions and antibiotic exposure).

This project will appeal to students with cross-disciplinary interests in infectious diseases, AMR, bacterial genomics, epidemiology, clinical microbiology and infection control.

The successful candidate will be enrolled in the MRC Quantitative and Interdisciplinary Biomedicine (QIBIOMED) Doctoral Training Programme at Dundee which will provide additional training opportunities and local student cohort activities.

Main supervisor: Dr Charis Marwick, Population Health Sciences, School of Medicine, University of Dundee

Co-supervisors: Prof Matthew Holden, School of Medicine, University of St. Andrews; Prof Bruce Guthrie, Population Health Sciences, School of Medicine, University of Dundee and Dr Ben Parcell, Infection Prevention and Control, NHS Tayside, Dundee

These studentships are open to overseas students if they can top up the tuition fees to the overseas rate. The PhD programme has funds for UK tuition rates -

To apply, please send a cover letter, curriculum vitae and two references to:

Please state clearly in your cover letter that you are applying for a Medical Research Foundation National PhD Training Programme in AMR Research funded project and give the project title. Eligibility criteria for postgraduate study at the University of Dundee and UCAS Postgraduate system (which the successful candidate will be required to complete after interview and offer of the studentship) are available here: