Molecular diagnostics for invasive fungal infections: a call for refinement and implementation.

Fungal infections are a silent epidemic. In contrast to the epidemics caused by RNA viruses such as influenza A and dengue, which are the material of headline news, the epidemic of fungal infections is played out quietly with few in attendance. Fungal infection affects immunocompromised hosts, patients hospitalized with severe underlying diseases (eg, acute myelogenous leukemia), those requiring complex surgical procedures (eg, trauma patients), and individuals who require support in intensive care units. And this epidemic continues to grow. The causes of this ever-increasing immunocompromised population include congenital and infectious causes of immunosuppression (e.g., the heretofore uncontrolled AIDS pandemic), the ongoing success of stemcell and solid organ transplantations, the need for chemotherapy and immunotherapy for the treatment of patients with cancer, and the use of new monoclonal antibody therapy for conditions such as rheumatoid arthritis and Crohn’s disease, as well as a variety of other reasons. The types of fungal infection that occur in the patients described vary accordingly with the type of underlying disease of the host, as well as with their epidemiological exposure. For example, patients with profound neutropenia are at heightened risk for invasive filamentous fungal infections, whereas patients in the intensive care unit who have numerous indwelling intravascular access catheters are at increased risk for infections by yeasts, such as Candida species. Many patients, however, have multiple risk factors (eg, patients with neutropenia often also have indwelling intravascular catheters). Although Aspergillus fumigatus and Candida albicans are the most common causes of invasive filamentous fungal infections and yeast-related infections in these patients, there is such a wide variety of opportunistic fungal pathogens that it is impossible to determine which type of fungus may be the specific cause of an infection in an individual patient based on clinical findings and risk factors alone. For the laboratory detection of these organisms, we have relied on age-old techniques, which have a variety of limitations. These techniques include histopathology and other forms of direct examination, and culture. Although histopathology is useful in confirming the presence of many types of fungal infection, by the time the patient requires surgery the disease has usually progressed and has often deeply infiltrated the tissues. In addition, even the most highly skilled infectious disease pathologist has limitations in evaluating the morphological differentiation of many fungi that cause invasive disease. For example, although a surgical pathologist can differentiate the hyphae of zygomycetes from hyaline septate molds, it is not possible, in most instances, to differentiate the type of zygomycete present or to definitively differentiate the types of hyaline septate molds (eg, Aspergillus versus Fusarium versus Pseudallescheria boydii) that may be responsible for the infection. Likewise, although Cryptococcus neoformans may be definitively identified in histological sections through the demonstration of the capsule using histochemical stains, the yeast of the Candida genus, apart from Candida glabrata, cannot be differentiated from one another on a morphological basis alone. Culture, which is sometimes erroneously considered definitive evidence of infection, also has a number of limitations. Culture may be too insensitive for the detection of fungal pathogens in some instances. In a well-controlled animal model study wherein neutropenic rabbits were given histologically confirmed pulmonary aspergillosis, Francesconi et al determined that the most sensitive methods of detecting the presence of the pathogen in the bronchoalveolar lavage fluid were galactomannan and a quantitative Aspergillus-specific PCR, with sensitivities of 100 and 80%, respectively; in contrast, the sensitivity of culture was only 46%. In this study, the sensitivities of galactomannan, quantitative PCR, and culture fell to 92, 50, and 16%, respectively, after antifungal therapy. In addition to false-negative cultures, issues with falsepositive results also exist. Fungal agar plates of clinical