Molecular Diagnostics (Head: Dr. Ludwig Sedlacek/PD Dr. Marius Vital)

The laboratory for "Molecular Microbiological Diagnostics" deals with molecular biological methods for pathogen identification and typing as well as the determination of antibiotic resistance and its applicability in the context of microbiological diagnostics. At the same time, it researches innovative methods and processes, in particular to optimize sequencing-based methods for their application in clinical microbiology.

The area of pathogen identification is currently based on real-time single-plex and multi-plex PCRs from patient material as well as targeted gene sequencing to identify specific bacteria and fungi. In addition to expanding the range of real-time PCR methods, we are also evaluating new diagnostic methods based on next-generation sequencing (Illumina) and so-called third-generation sequencing methods (Oxford Nanopore). The structural and process quality for these methods is optimized with regard to work within an accredited laboratory structure. Results are compared with established procedures and a concept for the presentation of results in terms of diagnostic findings is developed.

In the field of molecular pathogen typing, we create Core Genome Multi Locus Sequence Typing (cgMLST) schemes for clinically and microbiologically relevant bacteria (e.g. Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii) in order to quickly and reliably detect nosocomial outbreaks of pathogens. This method also allows the development of an outbreak strain-specific PCR, which can be used to generate rapid results within 24 hours in the event of an outbreak, under ideal conditions even on the same day, which can support hospital hygiene management. This is particularly useful in outbreaks with sensitive bacteria, where no selective culture media with antibiotic additives can be used.

The molecular biological identification of antibiotic resistance is another pillar of molecular biological diagnostics, which is being further developed through research projects. Particularly in the case of complex resistance patterns (e.g. multi-resistance of Gram-negative pathogens, MRGN), culture-based resistance tests sometimes provide results that are difficult to interpret. Available assays for the detection of carbapenemase genes are currently limited to the most common genes (e.g. Oxa-48, KPC or NDM), so that in negative cases it is still not possible to draw any conclusions about the resistance mechanisms. This is problematic both for treatment planning and for hospital hygiene management. Another field is the molecular detection of resistance in slow-growing bacteria, e.g. mycobacteria(M. tuberculosis and others). Conventional culture-based resistance testing can take several days to weeks for these bacteria. The main aim of the laboratory team is to gain a better understanding of resistance mechanisms, particularly in Gram-negative bacteria, through the development and application of sequence-based methods and algorithms, thereby generating a rapid and valid statement on antibiotic resistance and enabling targeted antibiotic therapy.