PhD fellowship in clinical microbiology and chronic wounds at Department of Immunology and Microbiology, Costerton Biofilm Center

Faculty of Health and Medical Sciences
University of Copenhagen

We are offering a PhD fellowship in the microbiology of chronic wounds commencing on 1 March 2020 or as soon as possible hereafter.

Our group and research
A research consortium ”PERFECTION” investigating persistent bacterial infections has recently been established at Rigshospitalet (National Hospital) in Copenhagen. The research will focus on bacterial infections caused by a range of bacterial species infecting lungs, skin (wounds) and stomach, which are often resilient to treatment and therefore develop into persistent infections. Host-microbe interactions will be investigated in infection models mimicking the relevant patient tissues, and access to bacterial strain libraries from infected patients will be exploited for analysis of infection stages and trajectories. PERFECTION is a research project supported by the Novo Nordisk Foundation with participation from Professor Helle Krogh Johansen (Rigshospitalet), Professor Thomas Bjarnsholt (SUND, University of Copenhagen), Associate Professor Kim Bak Jensen (BRIC, University of Copenhagen), Associate Professor Manuel Amieva (Stanford University, California) and Professor Søren Molin (Technical University of Denmark).

Project description
To investigate the wound conditions we will collect patient samples from the skin of healthy humans, acute trauma and chronic wounds and skin adjacent to these. Microbial community structure, clonal diversity and in vivo physiology will be examined by meta-genomic and (meta)transcriptomic analysis, as well as advanced 3D microscopy. The role of the Phd student wil be to collect patient material and perform microscopy to assess spatial structure of the bacterial community and host cell location, as well as estimate bacterial growth rates by PNA-FISH (fluorescence in situ hybridisation). In addition, the PhD student will perform direct patient measurements using novel high-resolution micro-sensors and micro-dialysis to monitor levels of systemic or locally administered antibiotics reaching the bacteria within the wounds.

Principal supervisor is Professor Thomas Bjarnsholt, Department of Immunology and Microbiology, Costerton Biofilm Center, E-mail:, Direct Phone: +4520659888.
Start: 1 March 2020
Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

  • Carry through an independent research project under supervision
  • Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points
  • Participate in active research environments including a stay at another research team
  • Obtain experience with teaching or other types of dissemination related to your PhD project
  • Teach and disseminate your knowledge
  • Write a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project e.g. Master of Medical Sciences (MD) preferably with clinical experience within clinical microbiology.

Other important criteria are:

  • The grade point average achieved
  • Professional qualifications relevant to the PhD project
  • Previous publications
  • Relevant work experience
  • Other professional activities
  • Curious mind-set with a strong interest in chronic infections
  • Language skills

Place of employment
The place of employment is at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories.

Terms of employment
The employment as PhD fellow is full time and for 3 years.

It is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins around 27,300 DKK /approx. 3,645 EUR (October 2019-level) plus pension.

For specific information about the PhD fellowship, please contact the principal supervisor.
General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School’s website:

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format: 

  1. Motivated letter of application (max. one page)
  2. CV incl. education, experience, language skills and other skills relevant for the position
  3. Master of Science diploma and transcript of records. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor will do
  4. Publication list (if possible)

Application deadline: Monday, 16 December 2019, 23.59pm CET.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.
The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.
Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.
You can read about the recruitment process at

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

The Faculty of Health and Medical Sciences comprises approximately 7500 students, 1500 PhD students and 3200 employees.

The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.


Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.


Thomas Bjarnsholt


Ansøgningsfrist: 16-12-2019
Ansættelsesdato: 01-03-2020
Arbejdstid: Fuldtid
Afdeling/Sted: Department of Immunology and Microbiology

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