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Review | Open Access

The molecular revolution in fungal diagnostics: bridging gaps across clinical, agricultural, and environmental mycology

Youssuf A. Gherbawya,b( ), Helal Al-Harthic, Eman El-Dawya,b, Mahmoud Gaberd, Ioan Pete( ), Linqi Wangf,g, Pengjie Huf,g, Mohamed Husseina,b
Botany and Microbiology Department, Faculty of Science, South Valley University, Qena, Egypt
Applied and Environmental Microbiology Center, South Valley University, Qena, Egypt
Biology Department, Turabah University College, Taif University, Taif, Saudi Arabia
Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
Biotechnology Department, Faculty of Bioengineering and Animal Resources, University of Life Sciences “King Mihai I” from Timisoara, Timisoara, Romania
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
University of Chinese Academy of Sciences, Beijing, China
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Abstract

Fungi play essential roles in human health, agriculture, and ecosystems, yet their diversity has long been underestimated due to reliance on morphology and culture. Molecular innovations—DNA barcoding, multilocus and whole-genome sequencing, NGS, and rapid nucleic acid diagnostics (qPCR, LAMP, CRISPR/Cas)—have revolutionized fungal taxonomy and detection. The ITS region now serves as a universal barcode, often complemented by other loci or genomic data. High-throughput and portable tools enable near real-time identification, supported by AI-driven bioinformatics for species recognition and resistance prediction. Despite progress, challenges remain in database accuracy, primer design, and standardization. Integrating molecular taxonomy, AI, and global collaboration promises scalable, reliable frameworks for fungal surveillance and control across clinical, agricultural, and environmental domains.

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Keywords

Molecular diagnosticsfungal identificationDNA barcodingnext-generation sequencingcryptic species

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Mycology
Volume 17 Issue 2,
June 2026
Pages 350-377
DOI: 10.1080/21501203.2025.2569931

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Gherbawy YA, Al-Harthi H, El-Dawy E, et al. The molecular revolution in fungal diagnostics: bridging gaps across clinical, agricultural, and environmental mycology. Mycology, 2026, 17(2): 350-377. https://doi.org/10.1080/21501203.2025.2569931

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Received: 03 June 2025
Accepted: 29 September 2025
Published: 03 December 2025
© 2025 The Author(s).

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.