PhD position genomic epidemiology foodborne disease

Are you a researcher who is interested in combining microbial genomics and infectious disease epidemiology? Then this PhD position might be something for you! We are looking for someone who will further innovate and strengthen the utilization of genomics in order to improve the surveillance and outbreak investigation of foodborne diseases.

Department

You will be working within the Centre for Infectious Disease Control (CIb) of the RIVM which has the mission of detecting, combating and preventing infectious diseases for the benefit of public health in the Netherlands. In doing so, the CIb establishes a link between policy, implementation and science, as well as between various r disciplines in the human, animal and environmental health fields nationally and internationally. You will be collaborating with colleagues working in diagnostics, surveillance and risk assessment of foodborne diseases.. You will be appointed in the department of Gastro-Enteric infections and Zoonoses (GEZ) within the Center for Epidemiology and Surveillance (EPI) but you will work half of your time at the department of Bacterial and Parasitic Diagnostics (BPD) within the Centre for Infectious diseases Research, Diagnostics and laboratory Surveillance (IDS).

Research

The use of whole-genome-sequencing (WGS) in public health surveillance and outbreak investigation has taken a huge flight in recent years. Currently, WGS is applied routinely as the standard typing method for all  foodborne bacteria under surveillance. Among others, these include Salmonella, Campylobacter, Shiga toxin-producing Escherichia coli, Listeria, Shigella and Yersinia. Outbreak detection is performed with clustering algorithms using the WGS data. However, there is a strong need for enhanced data-driven insight in how to define clusters of patients, determine diversity of strains and types (incl. link to clinical outcomes and/or epidemiological characteristics) and the extent to which within host/farm short-term evolution occurs. This should lead to a more evidence-based framework for good practice genomic surveillance.

Tasks

• Perform in-depth genomic analyses using existing data on foodborne pathogens.
• Contribute to the development and implementation of improvements regarding genomic surveillance of foodborne pathogens.
• Publish and share research results in scientific publications and conferences.

Unique for this position

You will work in a multidisciplinary team of researchers and will profit from their knowledge and experience. You will learn and contribute to joint efforts to further innovate and improve the utilization of WGS data for public health. The integration of genomics into infectious disease surveillance, epidemiology and research is increasingly important. This PhD project is an excellent steppingstone for a career in public health in the Netherlands and internationally. Furthermore, the analytical and research skills within this project are highly transferable to other fields.