With the exception of cryptococcal disease which can be diagnosed reliably by antigen testing, diagnosis of other deep fungal infections is not straightforward. Conventional culture on Sabouraud dextrose agar is the gold standard diagnosis for each of the deep fungal infections and also allows antifungal susceptibility testing; however they display low sensitivities and take days to weeks to yield positive results. Molecular-based techniques are becoming increasingly important in the species-level identification of invasive fungal disease, however, they currently costly, lack methodological standardization and validation, and unclear interpretation of the results thus not widely used routinely in resource-limited settings. Serology and biomarkers also play an important role in the diagnosis of invasive fungal diseases owing to their speed and specificity.
Many challenges exist in the management of serious fungal infections in resource-limited countries, such as; high disease burden, lack of diagnostics, limited awareness, low resource allocation, rare public health response, lack of a recognised international authority on public health mycology, lack of epidemiological data and antifungal drugs. Management of fungal infections is also still a challenge since clinicians do not know which patient to be treated due to lack of diagnosis and epidemiological data. Prophylaxis is not being used since they do not know the magnitude of the problem in the at-risk populations. Data are lacking on when to stop empiric antifungal therapy. In addition, antifungal drugs are not available in most developing countries. Besides, patients cannot afford the antifungal drugs. Therapeutic drug monitoring is not available in most centers. The role of radiology and histology in diagnosis of invasive fungal disease is not well exploited.