FYI – Fungi Yeast Identification

Yeast and mold fungi infections can cause severe illness especially in immunocompromised and intensive care patients. The rapid detection of the pathogen including a resistance spectrum is most important for the treatment to be successful. The goal of the project FYI is to develop a fully integrated lab-on-a-chip-system (LOC) to quickly detect yeast and mold fungi infections.

The Fraunhofer IGB and the IGVT of the University of Stuttgart are working together with the companies Euroimmun, Multi Channel Systems MCS, and Bosch as well as the Heart and Diabetes Center Nordrhein-Westfalen. So far, PCR-systems and DNA-probes of more than 50 relevant yeast and mold fungi (e.g. Candida spp. or Aspergillus spp.) have been established. Currently LOC-compatible cell disruption methods are being developed.

Infections by yeasts and mold fungi lead to severe illnesses, especially in immunocompromised patients. With a mortality rate of between 30 to 80 percent, the rapid detection of a pathogen, including its resistance spectrum, plays a particularly decisive role in the success of treatment.

The classical detection of pathogens using culture-based methods (Microdilution, Etest®) can take up to 14 days for yeasts and mold fungi. Furthermore, clinical studies have shown that phenotypic resistance testing is subject to an error rate of up to 15 percent. Cultivation often fails completely, even when the patient displays clear clinical symptoms. These cases require the initiation of a therapy of suspicion, which cannot be specifically matched to the pathogen.

Because of this, molecular biology methods such as sequencing, fluorescence-in-situ-hybridization (FISH), PCR or quantitative real-time PCR (qRT-PCR) are increasingly being used for the identification of pathogens. However, these methods have a limited multiplex capability. This means that only a small number of a large amount commonly occurring pathogens or resistances can be tested for (≤ 10 parameters). This makes numerous cost-intensive tests necessary, reducing the time advantage of the method.

DNA microarrays as the diagnostic tool of choice

It is possible to compensate for this diagnostic gap by the use of DNA microarrays, which enable the simultaneous examination of up to several thousand parameters. Such tests were previously rarely used in routine diagnostics due, among other things, to the high experimental and instrument costs of the processing of microarrays. These problems can be minimized by the application of microsystems that combine the entire testing process into a so-called lab-on-a-chip (LOC).

Aim: A fully integrated lab-on-a-chip system

The Fraunhofer IGB and the Institute for Interfacial Engineering IGVT of the University of Stuttgart, in combination with partners from medicine, science and industry and within the BMBF-funded research project “FYI-Chip – Fungi Yeast Identification”, are therefore developing a fully integrated lab-on-a-chip system for the rapid identification of fungal infections in respiratory secretions and primarily sterile body fluids in immunocompromised patients.

The scientists at the Fraunhofer IGB and IGVT are therefore closely working with the company Euroimmun, based in Lübeck, Germany, with doctors at the Heart and Diabetes Centre NRW, as well as with developers at the Reutlinger Multi Channel Systems MCS GmbH and Robert Bosch GmbH, Gerlingen. The aim is to combine the individual functional components such as sample preparation, microfluidics and the detection of pathogenic DNA into a single fully integrated LOC.

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Within the project, PCR systems and DNA probes for over 50 relevant fungal pathogens (including Candida or Aspergillus species) have been developed. In order to identify this amount of pathogens PCR systems have been developed for genes that show highly conserved areas, but are also variable enough to enable discrimination between the species. These are currently being tested for their suitability in LOC evaluation models. Furthermore, LOC-compatible cell disruption techniques for fungal species are developed. The use of disposable cartridges for the chip makes the system flexible and economical.

As a miniature laboratory, the LOC combines sample preparation directly on the chip with highly sensitive and rapid molecular biological diagnostics of yeasts and mold fungi and their resistances. This enables them to support clinicians in their diagnoses and facilitate the rapid and adequate initiation or adjustment of therapy. The LOC system is designed as an open system that might be used for further sample materials, such as biopsy tissues or for the detection of bacterial pathogens and their antibiotic resistance markers in the future.

• Euroimmun Medizinische Labordiagnostika AG
• Herz- und Diabeteszentrum NRW
• Institut für Grenzflächenverfahrenstechnik IGVT, Universität Stuttgart
• Multi Channel Systems MCS GmbH
• Robert Bosch GmbH