Pathogen detection in ancient DNA

Molecular pathogen detection in archived samples

The identification of (novel) pathogens, especially for the restrospective detection in past outbreaks, is often restrained by the absence of stored serum or cerebrospinal fluid samples. However, from such epidemics, case series, or single cases of unknown etiology, formalin-fixed paraffin-embedded samples sometimes remain in pathology archives for retrospective molecular analysis. The past decade has seen a steady increase in the appilcability of NGS for the detection and characterization of pathogens also from such archived tissue samples. Nucleic acids recovered from these clinical specimens that were not stored specifically for later DNA (and RNA) analyses may provide insights not only in the cause of a past outbreak, but also in pathogen evolution.

Formalin fixation, which allows tissue preservation and storage at room temperature, leads to cross-linking of macromolecules including nucleic acids and complicates the extraction of intact DNA and RNA. NGS might be less sensitive than PCR from FFPE samples on some sequencing platforms. This problem might be solved by using higher sequence depths.
Broken windows and crumbling walls of a derelict hospital.
Historic tissue samples by PCR and NGS
With a focus on highly pathogenic bacteria and viruses, we also analyze archived historic tissue samples by PCR and NGS.



RG Zoonoses

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Research Group Leader

Prof. Dr. Dennis Tappe

Telefon: +49 40 285380-499

Fax: +49 40 285380-252