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ESR5 – Developing new diagnostic tests for detection and identification of pathogens using adhesin-ligand interaction

Supervisor: Prof Alex van Belkum
Location: bioMerieux, Marcy L’Etoile, France

Background: BioMérieux designs, manufactures and markets systems, technologies and diagnostic tests to allow the detection and identification of pathogenic agents responsible for infectious disease. The current project’s overall aim is to use adhesion-ligand couples or other forms of bimolecular interaction toward the efficient detection of microbial pathogens with proven clinical usefulness. All these will be explored in the ViBrANT network. The PhD students in the network will work on measuring and understanding the binding modes of adhesins or other bimolecular interactions, on the structural biology and biophysics of adhesion, and on aspects of pathogen capture including microfluidics and the development of new diagnostic platforms.

Aim of project: The PhD student is expected to develop a genomic and phenotypic database showing variation in adhesion and ligand structures, e.g. penicillin binding protein and beta-lactam antibiotics. A direct mathematic procedure for the translation of genotypes into phenotypes will be pursued. A defined target will be the development of such a translational system that focusses directly onto the definition of an innovative antibiotic susceptibility testing system where also in vitro studies will be performed. The latter will target difference between adhesion and ligands in living, growth-arrested, dying and dead cells. In the end, the development of routine diagnostic systems is the key target. The research will comprise the development of genomic and phenotypic databases, assessing the effect of antibiotics on ligand binding to microbial cells and to develop routine tests for instance by using the bioMerieux VIDAS or BioFire FilmArray platforms.

Requirements: As a PhD student in the bioMerieux Data analytics Unit you will work within the microbiology team, performing research to demonstrate that comparative genomics and high density phenotypic analyses can lead to the development of innovative and clinically useful diagnostics and patient management. The unit has approximately 70 employees and has knowledge and expertise in the fields of next generation sequencing (NGS), bio-informatics and general microbiology. A combination of bioinformatics and wet lab biological techniques will be used.

A master’s degree in mathematics, (micro)biology or a similar field is required. Practical laboratory experience with NGS technology is welcome as is basic knowledge in genomic bioinformatics tools. You should be highly motivated to focus in-depth on scientific research questions to improve diagnosis and patient management. An ability to work independently is essential, you should be able to communicate well with colleagues and be comfortable to work jointly with international research groups. Candidates must comply with EU eligibility criteria. Due to the EU rules to promote mobility, you are not eligible for a position in a country where you have lived (worked, studied) for more than 12 months in the last 3 years. You are thus eligible for this position no matter what your nationality, unless you have studied or worked in France for more than 12 of the last 36 months. For applicants finishing or who have just finished their degree, this typically means that you can be graduating from any university except a French university.

Further details on this project are available from Alex van Belkum ( Further details on bioMerieux can be obtained at

A driving licence is required for this position.


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