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J Fungi (Basel). 2019 Sep 29;5(4). pii: E90. doi: 10.3390/jof5040090.

Identification of Mycoses in Developing Countries.

Author information

1
Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands. a.arastehfar@wi.knaw.nl.
2
The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA. wickes@uthscsa.edu.
3
Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana 01330, Turkey. macitilkit@gmail.com.
4
bioMĂ©rieux, Inc., Hazelwood, MO 63042, USA. dave.pincus@biomerieux.com.
5
Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands. f.daneshnia@wi.knaw.nl.
6
Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China. panweihua@smmu.edu.cn.
7
Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China. fangwenjie1990@126.com.
8
Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands. t.boekhout@wi.knaw.nl.
9
Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai 200003, China. t.boekhout@wi.knaw.nl.
10
Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX Amsterdam, The Netherlands. t.boekhout@wi.knaw.nl.

Abstract

Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.

KEYWORDS:

Nanopore sequencing; molecular tools; phenotypic assays; serology

PMID:
31569472
DOI:
10.3390/jof5040090
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