Funded PhD Opportunity Identification of factors regulating production of biofilm by antibiotic resistant Clostridium difficile using transcriptomics.

This opportunity is now closed.

Subject: Biomedical Sciences


Background to the project

Clostridium difficile is the most common cause of antibiotic-associated bacterial diarrhoea, with significant impact on morbidity and mortality rates of Healthcare-Associated Infection (HAI). Antibiotic associated dysbiosis of the gut microbiome leads to the development of C. difficile infection (CDI) mediated by the toxins (A and B) produced by the organism.  C. difficile is a multiply antibiotic resistant pathogen, and increased recurrences of CDI are hypothesised to be due, in part, to decreased efficacy of conventional antibiotic therapies. In recent years the formation of biofilms by C. difficile has been documented. This provides a specialised growth opportunity for the pathogen in which antibiotic resistance might be enhanced thereby contributing to treatment failures.  The ability to form biofilm has been increasingly linked to antibiotic resistance, sporulation, and recurrence of CDI.  Notably, the extent of biofilm formation by C. difficile strains reported in the literature varies considerably, suggesting that a multiplicity of factors influence biofilm in this organism.

We have recently shown that ClosTron-mediated disruption of the dnaK gene in C. difficile strain 630 erm results in a variety of physiological changes, including significantly increased biofilm formation.  More recent data from our lab indicates that a variety of other factors, including antibiotic sensitivity, cell surface structure, motility and response to gut metabolites is also significantly changed in the dnaK mutant.

The overall aim of this project is to dissect more fully, using state of the art molecular biology and bioimaging techniques, the changes in physiology and gene expression associated with growth of C. difficile in biofilms.  The dnaK mutant represents an excellent model system in which to examine such changes in an “enhanced biofilm former”, enabling comparison with the wild-type and a variety of antibiotic-resistant clinical C. difficile isolates.

Methods to be used

The project builds upon a series of successful PhD projects within our group and consequently the majority of techniques to be used (RNA extraction, analysis and sequencing, q-RT-PCR, biofilm assays, proteomics, antibiotic resistance and cell-staining assays) are well established in our laboratory.  Full training will be provided in these and other relevant techniques to enable the candidate to successfully complete the programme of research. We hypothesise that changes in the phenotype of biofilm grown cells will map to altered gene expression in the transcriptome as well as to changes in key structural proteins.

We will test this hypothesis by growing C. difficile strains planktonically and as biofilms under a range of physiologically relevant conditions.  Transcriptomes will be subject to RNAseq to determine global gene expression differences, with validation by qRT-PCR. Proteome changes will be analysed by GeLC-MS or Western blots as appropriate.  Of interest will be the effects of low levels of antibiotics, gut metabolites or novel antibacterial peptides on gene/protein expression and biofilm ultrastructure.

Overall, the project seeks to assist with the rational design of new antimicrobials through post identification of genes that are important for biofilm growth, development and survival. Impact The time-line between the increasing frequency of infections caused by multidrug-resistant bacteria and the development of new antibacterial agents is widening. Antibiotic development is no longer considered to be an economically wise investment for the pharmaceutical industry due to reduced economic incentives and challenging regulatory requirements. The effectiveness of currently available antibiotics needs to be optimised and extended. This will only be achieved by a multidisciplinary approach to the problem. Understanding the physiology of antibiotic resistant pathogens, as proposed in this project, will be essential to support initiatives in infection control and antimicrobial stewardship policies (ASP) that have been recently proposed.

This project will be based at Ulster's Nutrition Innovation Centre for Food and Health (NICHE).

Essential Criteria

  • Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC)
  • Sound understanding of subject area as evidenced by a comprehensive research proposal

Desirable Criteria

If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.

  • First Class Honours (1st) Degree
  • Masters at 65%
  • Research project completion within taught Masters degree or MRES
  • Practice-based research experience and/or dissemination
  • Experience using research methods or other approaches relevant to the subject domain
  • Work experience relevant to the proposed project
  • Publications - peer-reviewed
  • Experience of presentation of research findings
  • A comprehensive and articulate personal statement
  • Relevant professional qualification and/or a Degree in a Health or Health related area


    Vice Chancellors Research Scholarships (VCRS)

    The scholarships will cover tuition fees and a maintenance award of £15,009 per annum for three years (subject to satisfactory academic performance). Applications are invited from UK, European Union and overseas students.


    The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £15,009 per annum for three years. EU applicants will only be eligible for the fees component of the studentship (no maintenance award is provided).  For Non EU nationals the candidate must be "settled" in the UK.

Other information

The Doctoral College at Ulster University

Launch of the Doctoral College

Current PhD researchers and an alumnus shared their experiences, career development and the social impact of their work at the launch of the Doctoral College at Ulster University.

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My experience has been great and the people that I have worked with have been amazing

Kieran O'Donnell - 3D printing of biological cells for tissue engineering applications

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Completing the MRes provided me with a lot of different skills, particularly in research methods and lab skills.

Michelle Clements Clements - MRes - Life and Health Sciences

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Throughout my PhD I’ve been provided with continuous support and guidance by my supervisors and the staff at the University.I’ve also received many opportunities to further enhance my professional development in the form of teaching experience and presenting my work at conferences which will aid in my pursuit of a career in academia or industry.

William Crowe

Key Dates

Submission Deadline
Monday 18 February 2019
Interview Date
Weeks commencing 11, 18, 25 March 2019


Coleraine campus

Coleraine campus
Our coastal and riverside campus focussing on science and health

Contact Supervisor

Dr Nigel Ternan

Other Supervisors

Apply online

Visit and quote reference number #250109 when applying for this PhD opportunity