Mycologic Forum
Molecular diagnosis of endemic and invasive mycoses: Advances and challengesDiagnóstico molecular de las micosis endémicas e invasivas: avances y retos

https://doi.org/10.1016/j.riam.2013.09.009Get rights and content

Abstract

The diagnosis of endemic and invasive fungal disease remains challenging. Molecular techniques for identification of fungi now play a significant and growing role in clinical mycology and offer distinct advantages as they are faster, more sensitive and more specific. The aim of this mini-review is to provide an overview of the state of the art of molecular diagnosis of endemic and invasive fungal diseases, and to emphasize the challenges and current need for standardization of the different methods. The European Aspergillus PCR Initiative (EAPCRI) has made significant progress in developing a standard for Aspergillus polymerase chain reaction (PCR), but recognizes that the process will not be finished until clinical utility has been established in formal and extensive clinical trials. Similar efforts should be implemented for the diagnosis of the other mycoses in order to fully validate the current methods or reinforce the need to design new ones.

This manuscript is part of the series of works presented at the “V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi” (Oaxaca, Mexico, 2012).

Resumen

El diagnóstico de las micosis endémicas e invasivas continúa siendo difícil. Hoy día, las técnicas moleculares para la identificación de los hongos desempeñan un papel importante y cada vez mayor en la micología clínica ya que ofrecen diversas ventajas, como su mayor rapidez, sensibilidad y especificidad. El objetivo de esta revisión es ofrecer una visión de conjunto de las técnicas moleculares más recientes para el diagnóstico de las micosis endémicas e invasivas, y destacar los retos y la necesidad actual de estandarizar los diferentes métodos. El grupo EAPCRI ha contribuido con avances muy significativos al desarrollo y estandarización de las técnicas de reacción en cadena de la polimerasa para el diagnóstico de aspergilosis, y reconoce que este proceso no estará terminado hasta que se establezca la utilidad clínica mediante ensayos clínicos, efectuados a gran escala y prolongados. Se precisan esfuerzos similares para implementar las técnicas moleculares de diagnóstico de otras micosis con el objetivo de validar por completo los métodos actuales o reforzar la necesidad de formular nuevos métodos.

Este artículo forma parte de una serie de estudios presentados en el «V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi» (Oaxaca, México, 2012).

Section snippets

Challenges for molecular fungal diagnostic assays

To understand the challenges associated with any molecular diagnostic assay, one needs to understand the incidence and the pathology of the mycoses and the impact on the sample selection for the procedure (blood, serum, plasma, corporal fluids, or biopsy material, either fresh or paraffin embedded), and to carefully evaluate the basic steps of the molecular assay: first, nucleic acid extraction, second, selection of the fungal target(s) and third, amplification method.33, 68 While it is

Nucleic acid based diagnostics for invasive aspergillosis

The amplification of Aspergillus DNA by PCR has been described since the early 1990s, and many studies on the topic have been published. However, as mentioned earlier, protocols vary widely with respect to the PCR assays used, sample target and DNA extraction methods, and this variability makes it very difficult to compare the different “in house” methods developed through the years.20, 22, 33, 68 There are only a few standardized assays that are commercially available. They include LightCycler

Nucleic acid based diagnostics for invasive candidiasis

To date, a variety of nucleic based approaches have been studied for the diagnosis of IC, using a wide range of DNA extraction methods, primers and amplification and measurement approaches, and varied results have been reported for sensitivity (33.3% up to 100%) and specificity (greater than 75% with the exception of some nested PCR assays); see review by Kourkoumpetis et al.,33 PPVs are also extremely variable, with most of the studies reporting PPVs of approximately 50%. Of importance, NPVs

Nucleic acid based diagnostics for endemic mycoses

Several molecular methods have been described for the diagnosis of endemic and systemic mycoses including histoplasmosis, paracoccidioidomycosis, blastomycosis, and coccidioidomycosis. However, all PCR assays have been developed as “in-house” methods and have not been yet established as regular diagnostic tools, there is so far no nucleic acid assay commercially available for use in clinical samples, and the existing assays have not yet been fully standardized and validated by multi-centric

Conclusion

Molecular diagnostics brings many challenges to laboratories and clinicians. Rapid and accurate identification to the genus and species levels of fungal pathogens is crucial for correct management of fungal infections. Better understanding of the strengths and weaknesses of currently available diagnostic tools, and further strategies devised to best implement them either individually or in combination, would greatly improve early and accurate diagnosis of endemic and invasive fungal diseases

Conflict of interest

The author declares no conflict of interest.

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