Background

The global burden of fungal infections

Fungal pathogens are a major public health threat with significant global effects which, surprisingly, are not being addressed as they should. Globally, invasive fungal infections take around 1.5 million lives, and the number of people who die each year from the top 10 invasive fungal diseases is at least equal to those dying from tuberculosis or malaria. Moreover, the mortality rate of invasive fungal infections is usually greater than 50%.

In contrast, funding for medical mycology is highly underrepresented, accounting for 1.4-2.5% of the total of what the Welcome Trust, the U.K. Medical Research Council and the U.S. National Institutes of Health spent in the last 5 years. This under-representation could be just an effect of the number of applications for funding in the area, but even so, the need for an increased awareness and engagement by funding institutions and researchers is no less urgent: the development of new diagnostic and therapeutic tools is critical to improve the situation of high-risk patients.

The most common fungal infections are superficial skin, nails and mucosal infections, which are caused in most cases by fungi of the genus Candida. These infections are usually not life threatening and have such common manifestations as athlete's foot and vulvovaginal candidiasis.

Invasive fungal infections, on the other hand, have unacceptably high mortality rates. Patients with a compromised immune system -such as AIDS patients and post-transplantation patients taking immunosuppresants- are at special risk as they do not have the usual barriers that prevent invasive infections in healthy individuals.

According to Brown et al., (2012), more than 90% of the reported deaths caused by fungi are associated with species from four genera: Cryptococcus, Candida, Aspergillus and Pneumocystis, but epidemiological data for fungal infections is poor, as these infections are often misdiagnosed and there is a lack of accurate data from the developing world.

Endemic dimorphic mycoses

Endemic mycoses occur in geographically localized hotspots where even immunocompetent individuals are at risk. The following table is a reproduction of the information presented in Brown et al., (2012), where the authors make some comments regarding the quality of that information: 1) The data is extrapolated from a few and geographically localized studies and 2) accurate data is lacking from the developing world and the calculations may underestimate the true values of the presented statistics.

Disease (most common species)	Location	Estimated life-threatening infections/year at that location	Mortality rates (% in infected population)
Endemic dimorphic mycoses
Blastomycosis (Blastomyces dermatitidis)	Midwestern and Atlantic United States	~3,000	<2–68
Coccidioidomycosis (Coccidioides immitis)	Southwestern United States	~25,000	<1–70
Histoplasmosis (Histoplasma capsulatum)	Midwestern United States	~25,000	28–50
Paracoccidioidomycosis (Paracoccidioidesbrasiliensis)	Brazil	~4,000	5–27
Penicilliosis (Penicillium marneffei)	Southeast Asia	>8,000	2–75

Opportunistic invasive mycoses

Opportunistic mycoses affect those patients with a compromised immune system, such as AIDS patients and patients taking immmunosuppressants, particularly those that were received a solid transplantation. The following table is also a reproduction of the information presented in Brown et al., (2012).

Disease (most common species)	Location	Estimated life-threatening infections/year at that location	Mortality rates (% in infected population)
Opportunistic invasive mycoses
Aspergillosis (Aspergillus fumigatus)	Worldwide	>200,000	30–95
Candidiasis (Candida albicans)	Worldwide	>400,000	46–75
Cryptococcosis (Cryptococcus neoformans)	Worldwide	>1,000,000	20–70
Mucormycosis (Rhizopus oryzae)	Worldwide	>10,000	30–90
Pneumocystis (Pneumocystis jirovecii)	Worldwide	>400,000	20–80

The diagnostic tools currently employed to detect fungal pathogens:

The methods employed to diagnose fungal infections at present vary in performance as each type of pathogen has a greater proclivity for being detected by some tests than others. However, microscopy has always been the mainstay as far as diagnosis of fungal infections is concerned. We look forward to improve the diagnostic capabilities of conventional microscopy by enhancing specificity and visibility through the application of molecular biology.The following table was compiled from Fungal Infection Thrust.

Fungal infection	Diagnostic technique
	Microscopy	Agar culture	Xrays/scans	Antigen	Blood antibody	DNA detection
Thrush	+++	+++	-	-	-	-
Candida bloodstream	-	+++	+	+	+	+++
Candida abdominal	+	+++	+	-	-	-
Cryptococcal meningitis	++	+++	+	+++	-	-
Invasive aspergillosis	+	+	+++	++	-	++
Chronic aspergillosis	+	+	+++	-	+++	++
Allergic aspergillosis	+	+	++	-	+++	+
Coccidioidomycosis	+	++	++	-	+++	-
Histoplasmosis	+	++	+	++	-	-
Zygomycosis	+++	+	++	-	-	-

Detection by Polymerase Chain Reaction

The table above denotes a summary of the techniques used at present to detect the leading fungal pathogens in the world. Note that the column titled "DNA detection" is a term that mainly involves the use of the Polymerase Chain Reaction (PCR) to detect pathogens. Although it is touted as a reliable technique, it has several disadvantages such as high cost, requirement of laboratory settings of high standards and false positives due to detection of pathogenic DNA EVEN AFTER the resolution (clearance) of the disease. Finally, PCR amplifies the DNA in a sample and only gives qualitative results. While Real-Time PCR can give information on the initial amount of the sample, it requires RNA samples which are degraded by RNases in the body and even if it is not, it requires a well equipped laboratory to prevent further degradation.Therefore, this method cannot be used reliably in many parts of the world (especially in underdeveloped countries).

Another technique to detect pathogens through their DNA is DNA-hybridization, but the downside with this method is that it is labor intensive and involves the use of radio-labelled probes.

Detection by Microscopy

As mentioned before, microscopy has been the mainstay for detection of pathogenic fungi. This is primarily due to the fact that it is one of the oldest and most widely available means of detection. It only requires a microscope, a stain for contrast, the sample from a patient and a user with some experience. Furthermore, this technique requires neither the consideration of multiple parameters (such as in a PCR) nor much time (agar plate cultures need at least a day) to yield results.

Thus, we believe that improving detectability through microscopy by giving it the advantage of molecular biology (specificity and a better scope for visualization) while maintaining the advantages of conventional microscopy.

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References

1. 1. Brown et al., (2012), Hidden Killers: Human Fungal Infections, Sci Transl Med, Vol. 4, Issue 165.