ArticleFrontiers in cellular and infection microbiology2022
Unbiased screen for pathogens in human paraffin-embedded tissue samples by whole genome sequencing and metagenomics.
Article in Frontiers in cellular and infection microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Systemic and local lymph node inflammation at disease onset in sarcoidosis patients.ERJ open research · 2026Article
- A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.Microbiology spectrum · 2026Article
- Molecular diagnosis of suspected intestinal schistosomiasis in a non-endemic area of Yunnan Province, China.Infectious diseases of poverty · 2025Article
- Cervical Actinomycosis Diagnosed via Metagenomic Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tissue: A Case Report and Literature Review.Microorganisms · 2025Article
- Human mastadenovirus pneumonia in two immunocompetent patients.Virology journal · 2025Article
- Circovirus Hepatitis in Immunocompromised Patient, Switzerland.Emerging infectious diseases · 2024Article
- Two cases demonstrate an association between Tropheryma whipplei and pulmonary marginal zone lymphoma.Infectious agents and cancer · 2024Article
- A Narrative Review of Molecular, Immunohistochemical and In-Situ Techniques in Dermatopathology.British journal of biomedical science · 2024Review
Corrections and comments
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
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