Navigation auf


CRPP Comprehensive genomic pathogen detection


Classical viral pathogen detection will likely be replaced by a broad, rapid and inexpensive metagenomic analysis as the first line diagnostic tool in the near future. Today, routine laboratories have specific assays only available for the most frequent pathogens and oftentimes multiple tests have to be performed to finally identify the etiology of infection. Over the last decade, high throughput sequencing made enormous advances allowing nowadays performing metagenomic analyses by sequencing the whole genome content of clinical samples. Potentially any pathogen present in a sample can be identified and characterized in an unbiased, comprehensive and "one test fits all" approach.

Here, we propose to probe Comprehensive Genomic Pathogen Detection, called CGPD, as a new paradigm in infectious disease diagnostics. Our first aim is to develop a CGPD platform for viral and microbial pathogens using high-throughput metagenomic sequencing, pathogen capture and multiplex PCR technologies. We will devise sample preparation and enrichment strategies that allow for the sensitive detection of small amounts of pathogen genomes in abundant host DNA in diverse clinical specimens. A bioinformatics pipeline and user interface for sequence data analysis will be developed, including identification of unknown sequencing reads.
In a second aim, we will retrospectively assess complex or unresolved cases of infectious diseases and compare CGPD to routine diagnostic tests in terms of specificity, sensitivity, time to diagnosis and overall costs. We will apply CGPD in longitudinal studies in lung transplant recipients and kidney transplant donor/recipient pairs. Transplant recipients or other immunocompromised patients are uniquely suited to validate novel, comprehensive genomic pathogen detection approaches, as they are prone to infectious diseases.
Finally, we will test CGPD as well in immunocompetent individuals in a cross-sectional study in outpatients with respiratory infection.

The knowledge gained with CGPD will improve our understanding of the infecting virome and microbiome and therefore improve options for disease management and treatment. We are convinced that comprehensive genomic pathogen detection will be an important and essential part of diagnostics in the immediate future and required for optimized patient care. If successful, we seek rapid implementation of CGPD into the routine diagnostic services.

More information about the CRPP research projects: