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

• Background
A PhD training partnership has been set up between the Universities of Edinburgh and Leiden in One Health Integrated Solutions. The partnership recruited its first cohort of students in December 2019.
The programme is hosted by the Centre for Inflammation Research in partnership with Edinburgh Infectious Diseases and the Roslin Institute, and one further PhD studentship based in Edinburgh and fully funded for four years focused on Integrated One Health Solutions is now available. This 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.
The additional studentship will complete the initial cohort and ensure each University funds four studentships. This additional studentship will commence in 2021 in areas previously identified where significant joint interest and expertise were identified with evidence of potential cross centre collaboration.
It is envisaged the student will be registered for the degree in the University of Edinburgh and be co-supervised with at least one co-supervisor coming from the University of Leiden. It is the expectation that student will spend time in each institution, with a minimum of 12 months in the University of Leiden.
Information about investigators from Leiden and Edinburgh and the specific projects available in this call, aligned with ‘One Health’, are given below.
Students should identify their first choice project plus a second choice they would consider undertaking – see link to other projects below.

The selection process will involve an interview with members from both institutions.


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

Exploiting Klebsiella pneumoniae genomics for its significance in One Health

Project: Klebsiella pneumoniae has long been recognized as an agent of human disease and remains among the world’s most common nosocomial pathogens. Moroever, the World Health Organization recognises extended-spectrum β-lactam (ESBL)-producing and carbapenem-resistant K. pneumoniae a critical public health threat. In the past decade, severe community-acquired infections caused by ‘hypervirulent’ K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. Its association with animal disease represents a major One Health threat and requires 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 (hypervirulent) 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 emerging multidrug resistant and hypervirulent Klebsiella pneumoniae, both in humans and animals.
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 and HOW TO APPLY: https://www.ed.ac.uk/edinburgh-infectious-diseases/teaching/phd-programmes/phd-integrated-one-health-solutions