Pathogen detection in FFPE samples by metagenomics. undefined

In this study, we established and validated a whole genome sequencing (WGS) method to enable unbiased screening for unknown pathogens in human FFPE tissue samples. This assay may serve to appreciate (1) unidentified bacterial and viral (DNA) infections in FFPE tissues; (2) species of bacteria and DNA viruses in polymicrobial infections; (3) the tissue microbiome. We combined shotgun sequencing and metagenomics for taxonomic identification of bacterial and viral pathogens after subtraction of human genomic reads. To validate the assay for diagnostic use, we analyzed more than 100 samples of known composition as well as FFPE lung autopsy tissues with and without histological signs of infections. Our method detects down to 1‰ of bacterial reads in a background of human genomes. Since our approach relies on FFPE material, it complements histological readouts of infected samples. This makes it ideal for diagnostic routine applications where an infection is suspected based on clinical or histological observations, yet species-specific PCRs are negative. This method adds to the diagnostic armamentarium of pathologists for an integrated view on infections in tissues, and therefore underlines the clinical relevance of our findings.