This opportunity is now closed.

Funded PhD Opportunity

Harnessing the communication machinery of antibiotic resistant, gastrointestinal bacteria to develop novel pathogen detection strategies

Subject: Biomedical Sciences


Summary

Background to the project

Bacteria with resistance against multiple antibiotics have become a frequent complication in health care, often endangering successful outcomes of routine medical interventions. Enterococci were considered harmless bacterial members of the gastrointestinal microbiome.  However, multi-drug resistant enterococcal infections are now a leading cause of Healthcare Associated Infection (HAI). A significant concern is the spread of resistance to the antibiotic vancomycin which is a major driver in the generation of multiresistant strains. Enterococci utilise a pheromone-induced plasmid conjugation system for the transfer resistance genes into non-resistant cells. This Horizontal Gene Transfer (HGT) process is based around the ability of donor and recipient bacteria to communicate via a peptide pheromone system. Plasmid-free bacteria produce the pheromones and resistance gene transfer is initiated by binding of pheromones to cell surface receptors on plasmid-containing strains. Similar peptide based communication systems have also been reported in other Gram positive bacteria including pathogenic members of the genera Streptococcus and Bacillus. These peptide communication systems appear to be specific for each genus. Therefore pheromone-receptor binding has the potential to function as novel detection system and this will be investigated in this project.

Methods to be used

The Microbiology group have been studying pheromone based communication in enterococci for a number of years. Vancomycin resistant strains from both clinical and environmental sources are available their ability to transfer resistance genes under a variety of different conditions has been determined. Whole genome sequences of  selected enterococcal strains have been generated to in order to more fully characterise the pheromone communication machinery. The project builds upon a series of successful PhD projects within the Microbiology group and consequently the majority of techniques to be used (DNA and RNA extraction, analysis and sequencing; q-RT-PCR gene expression analysis; synthetic peptide chemistry; proteomics; antibiotic resistance profiling and bacterial conjugation assays) are well established.

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 peptide pheromones, whose structure will be determined by analysis of our whole genome sequence libraries, can be artificially synthesised and will function in a similar manner to natural peptides. We will test this in a series of HGT systems that are currently in operation in the laboratory.  Once a set of peptide pheromones is identified these will be tested for their specificity by attaching fluorescent dyes and screening against panels of gastrointestinal bacteria. If, as expected, the binding of these peptide pheromones is shown to be species specific these will be examined for inclusion as detection ligands in a variety of diagnostic platforms: agglutination, ELISA and Lateral Flow systems. Impact Tackling antibiotic resistance is a World Health Organisation priority that requires a multifactorial approach. One of the major contributors to resistance is inappropriate antibiotic are prescribing. This is a consequence of poor diagnostic systems. This project will provide new diagnostic targets for incorporation into a variety of platforms. This project will be based at Ulster's Innovation Centre for Food and Health (NICHE).

References:

Conwell M, Daniels V, Naughton PJ, and Dooley, JSG. Interspecies transfer of vancomycin, erythromycin and tetracycline resistance among Enterococcus species recovered from agrarian sources. BMC Microbiology. 2017. Vol 17. Article 19

Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically–relevant faecal environment, with implications for pathogenicity. Ternan NG, Moore N, Smyth D, McDougall G, Allwood JW, Verrall S, Gill CIR, Dooley JSG, and McMullan G. 2018. Scientific Reports 8: 16691.


Essential criteria

  • To hold, or expect to achieve by 15 August, an Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC) in a related or cognate field.
  • 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.

  • Completion of Masters at a level equivalent to commendation or distinction at Ulster
  • Experience using research methods or other approaches relevant to the subject domain
  • Work experience relevant to the proposed project
  • Publications - peer-reviewed
  • Publications record appropriate to career stage
  • Experience of presentation of research findings
  • A comprehensive and articulate personal statement
  • Use of personal initiative as evidenced by record of work above that normally expected at career stage.
  • Relevant professional qualification and/or a Degree in a Health or Health related area

Funding

    The University offers the following awards to support PhD study and applications are invited from UK, EU and overseas for the following levels of support:

    Vice Chancellors Research Studentship (VCRS)

    Full award (full-time PhD fees + DfE level of maintenance grant + RTSG for 3 years).

    This scholarship will cover full-time PhD tuition fees and provide the recipient with £15,000 maintenance grant per annum for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

    Vice-Chancellor’s Research Bursary (VCRB)

    Part award (full-time PhD fees + 50% DfE level of maintenance grant + RTSG for 3 years).

    This scholarship will cover full-time PhD tuition fees and provide the recipient with £7,500 maintenance grant per annum for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

    Vice-Chancellor’s Research Fees Bursary (VCRFB)

    Fees only award (PhD fees + RTSG for 3 years).

    This scholarship will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

    Department for the Economy (DFE)

    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 fee’s component of the studentship (no maintenance award is provided). For Non-EU nationals the candidate must be "settled" in the UK. This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.

    Due consideration should be given to financing your studies; for further information on cost of living etc. please refer to: www.ulster.ac.uk/doctoralcollege/postgraduate-research/fees-and-funding/financing-your-studies


Other information


The Doctoral College at Ulster University


Reviews

Profile picture of Kieran O'Donnell

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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Profile picture of Michelle Clements Clements

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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Profile picture of William Crowe

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
Friday 7 February 2020

Interview Date
9 to 20 March 2020


Applying

Apply Online  


Campus

Coleraine campus

Coleraine campus
The feeling of community at our Coleraine campus makes for a warm and welcoming student experience.


Contact supervisor

Professor James Dooley


Other supervisors

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