Amplicon-Based Next-Generation Sequencing for Detection of Fungi in Formalin-Fixed, Paraffin-Embedded Tissues: Correlation with Histopathology and Clinical Applications

Paige M.K. Larkin, Katy L. Lawson, Deisy A. Contreras, Catherine Q. Le, Marisol Trejo, Susan Realegeno, Evann E. Hilt, Sukantha Chandrasekaran, Omai B. Garner, Gregory A. Fishbein, Shangxin Yang

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Invasive fungal infections are increasing in prevalence because of an expanding population of immunocompromised individuals. To reduce morbidity and mortality, it is critical to accurately identify fungal pathogens to guide treatment. Current methods rely on histopathology, fungal culture, and serology, which are often insufficient for diagnosis. Herein, we describe the use of a laboratory-developed internal transcribed spacer–targeted amplicon-based next-generation sequencing (NGS) assay for the identification of fungal etiology in fungal stain–positive formalin-fixed, paraffin-embedded tissues by using Illumina MiSeq. A total of 44 specimens from 35 patients were included in this study, with varying degrees of fungal burden from multiple anatomic sites. NGS identified 20 unique species across the 54 total organisms detected, including 40 molds, 10 yeasts, and 4 dimorphic fungi. The histopathologic morphology and the organisms suspected by surgical pathologist were compared with the organisms identified by NGS, with 100% (44/44) and 93.2% (41/44) concordance, respectively. In contrast, fungal culture only provided an identification in 27.3% (12/44) of specimens. We demonstrated that NGS is a powerful method for accurate and unbiased fungal identification in formalin-fixed, paraffin-embedded tissues. A retrospective evaluation of the clinical utility of the NGS results also suggests this technology can potentially improve both the speed and the accuracy of diagnosis for invasive fungal infections.

Original languageEnglish (US)
Pages (from-to)1287-1293
Number of pages7
JournalJournal of Molecular Diagnostics
Volume22
Issue number10
DOIs
StatePublished - Oct 2020
Externally publishedYes

Bibliographical note

Funding Information:
Supported by the University of California, Los Angeles , Department of Pathology and Laboratory Medicine.

Publisher Copyright:
© 2020 Association for Molecular Pathology and American Society for Investigative Pathology

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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