Despite the scientific advances observed in the recent decades and the emergence of new methodologies, the diagnosis of systemic fungal infections persists as a problematic issue. Fungal cultivation, the standard method that allows a proven diagnosis, has numerous disadvantages, as low sensitivity (only 50% of the patients present positive fungal cultures), and long growth time. These are factors that delay the patient's treatment and, consequently, lead to higher hospital costs. To improve the accuracy and quickness of fungal infections diagnosis, several new methodologies attempt to be implemented in clinical microbiology laboratories. Most of these innovative methods are independent of pathogen isolation, which means that the diagnosis goes from being considered proven to probable. In spite of the advantage of being culture-independent, the majority of the methods lack standardization. PCR-based methods are becoming more and more commonly used, which has earned them an important place in hospital laboratories. This can be perceived now, as PCR-based methodologies have proved to be an essential tool fighting against the COVID-19 pandemic. This review aims to go through the main steps of the diagnosis for systemic fungal infection, from diagnostic classifications, through methodologies considered as “gold standard”, to the molecular methods currently used, and finally mentioning some of the more futuristic approaches.
The diagnosis of a fungal infection is a lengthy process, especially due to the symptomatic similarities between a bacterial and fungal infection. Fig. 1 provides a simplified framework reviewing the steps for the diagnosis of systemic fungal infections. When a patient that presents clinical signs of infections does not respond to an antibiotic treatment (Fig. 1A), an invasive fungal infection should be included in the patient's differential diagnosis (Fig. 1B and C). The host factors and clinical signs defined by the EORTC and MSG-ERC are analysed (Fig. 1D) and methodologies available for mycological evidences should be selected accordingly. There are several methodologies available for mycological evidences but it is important to notice that the type of methodology used will dictate the diagnosis classification (Fig. 1E). Methodologies that are capable of detecting the fungal pathogen through histopathological or culture methods from sterile sites provide a proven diagnosis. However, if positive mycological evidence is achieved through molecular methodologies, such as PCR-based methods or serological tests, a probable diagnosis is attributed.
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