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MRC DiMeN Doctoral Training Partnership: Evolution of antimicrobial resistance in Clostridium difficile

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  • Full or part time
    Dr R Fagan
    Prof M Brockhurst
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Increasing resistance to antibiotics is one of the greatest health challenges facing humanity today. Clostridium difficile is the primary cause of antibiotic-associated infections in UK hospital and antibiotic-induced disruption of the gut microbiota is a prerequisite for infection. Vancomycin is the treatment of choice for severe or recurrent infection but this causes further damage to the microbiota and relapse is common. Worryingly, vancomycin resistance is now common in many bacterial species and reports are emerging of increasing resistance in C. difficile. As an alternative to traditional antibiotics, US biotech company Phylum Biosciences (formerly AvidBiotics) have engineered natural phage tail-like particles with bacteriophage receptor binding proteins (RBPs). These engineered ‘Avidocins’ display high efficacy and specificity against C. difficile and we have shown that the cell surface receptor is the essential surface protein SlpA. Resistant mutants that lacked SlpA, selected in a single step, had become entirely avirulent.

In this project we will analyse the evolution of resistance to the current frontline antibiotic vancomycin and the promising new Avidocins, answering two key questions:
1) How does resistance evolve and what are the molecular mechanisms?
2) How does compensatory evolution allow slpA mutants to survive without the normally essential S-layer?

In this project, supported by the Fagan ( and Brockhurst ( groups, you will be trained in evolutionary biology and microbiology. You will experimentally evolve resistance to vancomycin and an Avidocin and use whole genome sequencing and cutting edge molecular microbiology techniques to identify and confirm the responsible mutations. Resistance often comes at a cost so you will use classical microbiology approaches to monitor fitness as resistance emerges and biochemistry and advanced microscopy to understand the molecular basis. You will also analyse a panel of existing Avidocin resistant strains with slpA mutations to identify compensatory mutations that allow growth without S-layer. These experiments will reveal the mechanisms of resistance to vancomycin and Avidocin that will eventually emerge in the clinic. This will allow direct comparison of the evolutionary risks of resistance emergence against the current frontline antibiotic and a future antimicrobial therapy. As Avidocins are related to Myoviridae phage and use C. difficile phage RBPs, these analyses will also be relevant to bacteriophage therapy.

You will receive training at the interdisciplinary interface between molecular microbiology and evolutionary biology, supported by two dynamic research groups based within the wider Florey Institute ( that applies fundamental molecular biology to address clinical antibiotic resistance.

Please contact Dr Robert Fagan if you are interested in the project to find out more: [Email Address Removed]

Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here:
Further information on the programme can be found on our website:

Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 3.5yrs
Stipend at national UKRI standard rate
Tuition fees
Research training and support grant (RTSG)
Travel allowance
Studentships commence: 1st October 2019.

To qualify, you must be a UK or EU citizen who has been resident in the UK/EU for 3 years prior to commencement. Applicants must have obtained, or be about to obtain, at least a 2.1 honours degree (or equivalent) in a relevant subject. All applications are scored blindly based on merit. Please read additional guidance here:
Good luck!


Kirk JA, Gebhart G, Buckley AM, Lok S, Scholl D, Douce GR, Govoni GR, Fagan RP (2017) New class of precision antimicrobials redefines role of Clostridium difficile S-layer in virulence and viability. Science Translational Medicine 9:eaah6813

Wright RCT, Friman V-P, Smith MCM & Brockhurst MA (2018) Cross-resistance is modular in bacteria–phage interactions. PLoS Biology 16:e2006057

Bottery MJ, Wood AJ & Brockhurst MA (2017) Adaptive modulation of antibiotic resistance through intragenomic coevolution. Nature Ecology and Evolution 1:1364

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