Modelling early warning of emerging antimicrobial resistance and comparative impact assessment of antimicrobial use-reducing interventions in livestock (1.0 FTE)

Job Description

Sustainable control of antimicrobial resistance (AMR) requires a One Health approach, as humans and animals can exchange bacteria and genetic mobile elements encoding for AMR. Early detection of newly emerging AMR in animal populations is important in case of resistance to antimicrobials of critical importance to humans. Moreover, as antimicrobial use (AMU) in animals favours AMR development in bacterial populations, the potential impact of different AMU-reducing interventions needs to be assessed. Two research consortia led by the Veterinary Medicine Faculty of Utrecht University in collaboration with Wageningen Bioveterinary Research (WBVR) and the Dutch National Institute for Public Health and Environment (RIVM) have been formed to develop a Blueprint for Early Warning of Antimicrobial Resistance Emergence in animals (BEWARE) and to perform a Comparative Impact Assessment of Options to Curtail Inessential Antimicrobials On-farm (CIAOCIAO). BEWARE will focus on carbapenemase-producing Enterobacteriaceae  in livestock (e.g. veal calves, pigs and broilers) and will include assessment of introduction risk, estimating transmission parameters, development of a metagenomics CPE assay and dynamic mathematical modelling. CIAOCIAO will quantify the impact and cost-effectiveness of biosecurity, vaccination and husbandry practices on AMU reduction in broilers, weaned piglets and veal calves using stochastic simulation modelling to show all potential outcomes of the interventions. Both BEWARE and CIAOCIAO are supported by ZonMw grants.

We are seeking 2 motivated PhD candidates willing to contribute to develop the blueprint for early warning of AMR (BEWARE) or to assess the impact of different AMU-reducing interventions (CIAOCIAO) in livestock. These projects aim to detect resistance against antimicrobials of critical importance to humans before it becomes widespread in animal populations and to provide policy makers and livestock sectors with quantitative evidence to reduce AMU on-farm and so decrease AMR at its source.

The tasks of the PhD candidate associated with the BEWARE project will include assessment of AMR introduction risk, to develop a dynamic mathematical model to simulate surveillance for early warning, to parameterize the model and apply it to test various surveillance scenarios. Furthermore, this candidate will design and analyse an in vivo experiment using broilers. The tasks of the PhD candidate associated with the CIAOCIAO project will include developing a scenario-based modelling framework to assess the impact of different biosecurity standards, vaccination schemes and husbandry practices on AMU reduction on-farm, using both existing and newly collected data, and to perform cost-effectiveness analyses. Moreover, the candidate will contribute to the development of a policy management tool to be named AMU-Lowering Estimation Tool (AMU-LET ) intended to set targets for implementing interventions with the highest AMU-reducing potential.

Most of the research will be carried out at Utrecht University, but for specific topics the PhD candidates will be temporarily stationed at the collaborating institutes of WBVR in Lelystad and at the RIVM in Bilthoven.

Interested candidates may apply to both PhD positions and express their preference for the BEWARE or CIAOCIAO project in the motivation letter.


Suitable candidates for these PhD positions have strong analytical skills, with an original and “out of the box” mindset. The candidates are required to work independently and to regularly interact with the other researchers involved in the projects, as well as technicians and their supervisors.

Suitable candidates hold a MSc degree recognized by the board of promotions of Utrecht University in one of the life sciences, with a strong quantitative component, such as theoretical biology, systems biology, physics, applied mathematics, biostatistics, chemistry or epidemiology. The candidates should be able to use at least one programming language, preferably R, and have proven experience with the use or development of computational models for the study of (biological) dynamical processes. Experience or affinity with working with experimental animals is preferred for BEWARE, while experience or affinity with farm animal practice is preferred for CIAOCIAO. The candidates should have affinity with or a strong interest in One-Health aspects of antimicrobial resistance in livestock production.

Dissemination of the results will consist of writing a PhD thesis and peer-reviewed articles in scientific journals, as well as presentations at international conferences and stake-holder meetings. Therefore, suitable candidates have a high level of written and spoken English according to CEFR proficiency level C.

We offer

We offer two 1.0 FTE positions for an initial period of one year, with the possibility of extension to a total of four 1.0 FTE years. Salary starts at €2,222 and increases to €2,840 (scale P of the Collective Labour Agreement of the Dutch Universities) gross per month for a full-time employment in the fourth year of the appointment (according to NWO standards). Salaries are supplemented with a holiday allowance of 8% and a year-end bonus of 8,3%.

Utrecht University offers excellent secondary benefits including collective insurance schemes, an excellent pension scheme and flexible employment conditions. For more information: Working at Utrecht University.

About the organisation

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University (UU) the various disciplines collaborate intensively towards major societal themes. Our focus is on Dynamics of Youth, Institutions, Life Sciences and Sustainability.

The Faculty of Veterinary Medicine (FVM) has a unique position in the Netherlands. Not only is this the only institution where veterinarians are trained, researchers are also working together on innovative scientific research. In addition, the faculty provides specialist clinical care in the largest academic veterinary hospital in Europe. Thanks to this position, the Faculty of Veterinary Medicine is a point of contact for all veterinary matters, both nationally and increasingly internationally. The faculty employs approximately 900 veterinarians, scientists and support staff and counts 1,500 students.

The Department of Farm Animal Health (FAH) of FVM-UU focuses on the three core tasks of education, research and clinical services. However the clinic of the Department of Farm Animal Health facilitates education and research. In our research and education, we aim to optimize health and welfare of farm animals in a One Health approach, taking the (patho)fysiology in individual animals as starting point. The veterinary services provided by the department focus on preventive population medicine of farm animals.

The Department of Infectious Diseases and Immunology (I&I) of FVM-UU is renowned for its expertise in the field of infectiology and immunology, including zoonoses and antimicrobial resistance. The Department of I&I provides education and conducts research mainly in the field of clinical and molecular infectiology. To conduct its core activities, the department has a laboratory for clinical microbiological diagnostics.

Wageningen Bioveterinary Research (WBVR) is a leading international research organization in life sciences. The institute’s mission is to safeguard animal and public health through prevention, eradication and control of animal diseases. WBVR is involved in a large variety of national and international research projects commissioned by both public and private clients. WBVR is the national reference laboratory for infectious animal diseases and antimicrobial resistance in the Netherlands and is part of Wageningen University & Research. The institute is located in Lelystad and employs approximately 250 people.

The National Institute for Public Health and the Environment (RIVM) is the main governmental institution working on the prevention and control of communicable and non-communicable diseases, public health, nutrition, consumer safety and environmental protection in the Netherlands. The RIVM conducts research and collates knowledge to place information at the disposal of policy makers, researchers, regulatory authorities and the general public as to identify opportunities for interventions. The RIVM has a total of approximately 1,500 staff. The Centre for Infectious Disease Control at the RIVM coordinates the national infectious disease surveillance and response system, working with other national and international institutions to monitor the occurrence and trends in infectious diseases in the Netherlands and to carry out studies on the epidemiology and (cost-)effectiveness of measures to control such diseases. These activities are supported by high-level methodological expertise and experience in surveillance, biostatistics and mathematical modelling.

More information

For more information, please contact Prof. Arjan Stegeman by j.a.stegeman@uu.nl or by phone on +31 30 253 10 91 or Dr. Lapo Mughini-Gras, lapo.mughini.gras@rivm.nl or by phone on +31 30 274 25 19.

Please do not send your application letter to this e-mail address.

The interviews will be held on 12 April 2018.

To apply

Please send your curriculum vitae, including a letter of motivation via this link.

Closingdate: March 28th 2018

No agencies.

Keywords: Vacancy, Research, MSc, life sciences, Biology, Systems biology, Physics, Applied mathematics, Biostatistics, Chemistry, Epidemiology, Utrecht