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ESR 2.3: Rapid direct detection of micro-organisms and resistance determinants using innovative approaches



Infections are a leading cause of morbidity and mortality globally, and are a major challenge in clinical medicine. Rapid detection and identification of micro-organisms and resistance determinants is paramount for therapy and prevention of infections. Currently culture-based methods are often indispensable but relatively slow. The PhD candidate will develop automated methods and novel technical options, such as hyperspectral imaging combined with colorigenic/fluorogenic substrates and molecular methods, including next generation sequencing (metagenomics). The project aims at boosting diagnostic quality and speed up time to result while containing costs at a reasonable level. Combining the strengths of rapid culture-based, molecular, and novel diagnostic modalities offers novel options. Ultimately, an optimized, automated, multi-modal work flow should lead to early personalized treatment of patients. A training period with the collaboration partner in Italy to gain experience with diagnostic tools and automated high quality sample processing will be part of the project.


Department of Medical Microbiology, University Medical Center Groningen, Groningen, The Netherlands, [MMB]


The projects will be performed in collaboration with Copan (Brescia, Italy), a leading innovative company in this field, featuring an R&D campus for students from the University of Brescia, School of Engineering.

Maurice Aalders, Academic Medical Center Amsterdam, an expert in hyper-spectral monitoring and imaging in the field of forensic biophysics.

Relevant publications

  1. Zhou K, Lokate M, Deurenberg RH, Tepper M, Arends JP, Raangs EGC, et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum beta-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016 Feb 11;6.
  2. Dik J-WH, Poelman R, Friedrich AW, Panday PN, Lo-Ten-Foe JR, van Assen S, et al. An integrated stewardship model. Future Microbiol. 2016 Jan;11(1):93–102.
  3. Dik J-WH, Hendrix R, Poelman R, Niesters HG, Postma MJ, Sinha B, et al. Measuring the impact of antimicrobial stewardship programs. Expert Rev Anti Infect Ther. 2016 Jun;14(6):569–75.


microbiology, diagnostics, next-generation sequencing, metagenomics, hyper-spectral imaging, anti-microbial resistance