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PhD programme in Integrated One Health Solutions in Edinburgh and Leiden - Exploiting Klebsiella pneumoniae genomics for One Health diagnostics

  • Full or part time
  • Application Deadline
    Thursday, November 28, 2019
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

• Background
A new PhD training partnership has been set up between the Universities of Edinburgh and Leiden in One Health Integrated Solutions.
The programme will be hosted by the Centre for Inflammation Research in partnership with Edinburgh Infectious Diseases and the Roslin Institute, and offers six PhD studentships fully funded for four years focused on Integrated One Health Solutions. These will cover stipend , tuition fee and travel funds.
The aim is to foster collaboration and to build on existing synergies in the identified themes of this call. Our universities have a long record of collaborative research and teaching, in particular in the fields of medicine and infectious diseases.
We anticipate that each University will fund three studentships to commence in the autumn of 2019 or over the next 12 months in areas where significant joint interest and expertise were identified.
It is envisaged that students will be registered for their degree at one or other host institution and co-supervised with at least one co-supervisor coming from the second instiution.
Projects will involve at least one supervisor from each organisation and it is anticipated that research exchanges between Leiden and Edinburgh will occur during the projects with the expectation that students will spend time in each institution, with a minimum of 12 months in the second host institution.
Information about investigators from Leiden and Edinburgh with interests aligned with ‘One Health’ is given below.
Students can apply for projects in Edinburgh or Leiden and should identify their first choice project plus two other projects they would consider undertaking from the list of projects available – see link to other projects below.
The selection process will involve an interview with members from both institutions.

Supervisors: Dr Thamarai Schneiders (Edinburgh) and Dr Els Wessels, Ed Kuiper and Eelco Franz (Leiden)

Exploiting Klebsiella pneumoniae genomics for One Health diagnostics

Project: Klebsiella pneumoniae (Kp) represents a major threat to human and animal health where this challenge has met significant efforts in genome analyses to elucidate the factors that contribute to its population structure, pathogenicity status and critically, its antimicrobial resistance.
Previous studies have demonstrated that the population structure of Kp encompasses specific traits that delineate human, animal and environmentally associated strains. Whilst these gene specifications are useful, there remains a critical need for greater discrimination of Kp genomic sequences for population-based analyses within complex datasets e.g. metagenomic data. As such the overarching aim of this project is to expand our ability to probe complex metagenomic or microbiome datasets to dissect the prevalence, transmission potential and the emergence of Kp; not least in developing tools for rapid diagnostics.
The key aims of this project are to (i) establish greater discrimination of Kp population structure, (ii) Validation and Identification of specific markers, identified in Aim 1, in complex datasets. The outlined proposal will extend and produce novel insights into the population structure caused by the major nosocomial pathogen Klebsiella pneumoniae.
The project will undertake both bioinformatic and microbiological validation of datasets and Kp strain collections. This approach has significant implications in reviewing Kp carriage, transmission and current diagnostics from the human, animal and environmental perspective. Ultimately, this approach will result in a prediction model applicable in routine diagnostic microbiology for risk estimation for spread and development of infection. The student will be entrenched in vibrant microbiology community within the University of Edinburgh, LUMC and RIVM.
The proposed project allows the student to build strong bioinformatic skills in probing Klebsiella population structure and applying these findings into complex datasets. Additionally, there are multiple opportunities to biologically validate these bioinformatic targets thus facilitating student training in both computational and biological approaches in studying Klebsiella pneumoniae.

Complete list of available projects:

Funding Notes

The successful applicant will be awarded a 4 year studentship, which includes stipend and tuition fees and is open to students from any country in the world. Funding covers contributions towards travel, up to 12 months living expenses at the second centre and research costs.

Applicants should hold at least an upper second-class degree or equivalent in a relevant discipline, e.g. immunology, microbiology, biology or fields related to the specific project.

Applicants should submit the following documents to :

(i) Personal statement about research interests and reasons for applying (200 words)
(ii) CV
(iii) ranking choice of top 3 projects


The studentship will be awarded competitively. Applicants should also arrange for two academic referees to submit letters of reference by email to [email protected] before the deadline.

All documents should be submitted no later than 5pm GMT on 28 November 2019.
Short-listed candidates will be notified by email.

Prospective students should make informal enquiries via email to Dr Thamarai Scheneiders [email protected]

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