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Review
. 2024 Dec 12:1-14.
doi: 10.1080/14737159.2024.2436396. Online ahead of print.

Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?

N Esther Babady  1   2 , Charles Y Chiu  3   4 , Arryn Craney  5 , David C Gaston  6 , Rachel S Hicklen  7 , Catherine A Hogan  8   9 , Teny M John  10 , Adam G Stewart  11   12
Affiliations
Review

Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?

N Esther Babady et al. Expert Rev Mol Diagn. .

Abstract

Introduction: Invasive fungal diseases (IFDs) are a serious threat to immunocompromised patients. Routine diagnostic methods have limited performance in identifying IFDs. Next-generation sequencing (NGS), including metagenomic NGS (mNGS) and whole-genome sequencing (WGS), recently emerged as diagnostic methods that could provide more accurate and timely diagnoses and management of IFDs.

Areas covered: This article describes the emergence of NGS as a diagnostic tool to address the limitations of current tests. The literature regarding its application and clinical utility in the diagnosis of IFDs is reviewed. Practical considerations, challenges, and opportunities as they relate to the development and implementation of mNGS and WGS for fungal pathogens are discussed.

Expert opinion: NGS emerged over a decade ago with the potential to solve many of the challenges in diagnosing infectious diseases, including IFDs. However, published literature has yielded conflicting data about its clinical utility. The increased clinical adoption of NGS is improving our understanding of how to interpret and use its results to guide actionable decisions. Still, several gaps remain. As the cost, effort, and expertise involved in performing NGS decrease and the reporting of its results becomes standardized, NGS is poised to fill current gaps in the diagnosis of IFDs.

Keywords: Fungal infections; cancer; immunocompromised patients; invasive fungal disease; metagenomic; molecular diagnostics; next-generation sequencing; transplant patients.

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Conflict of interest statement

Declaration of Interests: CY Chiu is a founder of Delve Bio and on the scientific advisory board for Delve Bio, Flightpath Biosciences, Biomeme, Mammoth Biosciences, BiomeSense and Poppy Health. He is also an inventor on US patent 11380421, “Pathogen detection using next generation sequencing”, under which algorithms for taxonomic classification, filtering and pathogen detection are used by SURPI+ software for pathogen detection from mNGS data. CY Chiu receives research support from Delve Bio and Abbott Laboratories, Inc.; CAH: Inflammatrix funding; TMJ; Illumina funding. All other authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

References

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      **This reference provide important information on how invasive fungal diseases are defined.

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