TY - JOUR AU - Nienhold, Ronny AU - Mensah, Nadine AU - Frank, Angela AU - Graber, Anne AU - Koike, Jacqueline AU - Schwab, Nathalie AU - Hernach, Claudia AU - Zsikla, Veronika AU - Willi, Niels AU - Cathomas, Gieri AU - Hamelin, Baptiste AU - Graf, Susanne AU - Junt, Tobias AU - Mertz, Kirsten D. PY - 2022 M3 - Methods TI - Unbiased screen for pathogens in human paraffin-embedded tissue samples by whole genome sequencing and metagenomics JO - Frontiers in Cellular and Infection Microbiology UR - https://www.frontiersin.org/articles/10.3389/fcimb.2022.968135 VL - 12 SN - 2235-2988 N2 - Identification of bacterial pathogens in formalin fixed, paraffin embedded (FFPE) tissue samples is limited to targeted and resource-intensive methods such as sequential PCR analyses. To enable unbiased screening for pathogens in FFPE tissue samples, we established a whole genome sequencing (WGS) method that combines shotgun sequencing and metagenomics for taxonomic identification of bacterial pathogens after subtraction of human genomic reads. To validate the assay, we analyzed more than 100 samples of known composition as well as FFPE lung autopsy tissues with and without histological signs of infections. Metagenomics analysis confirmed the pathogenic species that were previously identified by species-specific PCR in 62% of samples, showing that metagenomics is less sensitive than species-specific PCR. On the other hand, metagenomics analysis identified pathogens in samples, which had been tested negative for multiple common microorganisms and showed histological signs of infection. This highlights the ability of this assay to screen for unknown pathogens and detect multi-microbial infections which is not possible by histomorphology and species-specific PCR alone. ER -