Recognition of Diagnostic Gaps for Laboratory Diagnosis of Fungal Diseases: Expert Opinion from the Fungal Diagnostics Laboratories Consortium (FDLC)

Abstract

Fungal infections are a rising threat to our immunocompromised patient population as well as other non-immunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing, to detect and identify new, emerging or under-recognized, rare or uncommon fungal pathogens, and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory’s capability to rapidly and accurately diagnose fungal infections.

Identification of Mucormycosis by Fluorescence In Situ Hybridization Targeting Ribosomal RNA in Tissue Samples

“…Cultivation of Mucorales from clinical samples remains difficult, and identification of Mucorales by morphology of fungal elements in tissue has been shown to be error-prone. Consequently, experts identified the diagnosis of mucormycosis and the direct identification of fungal pathogens such as Mucorales in FFPE tissues as major diagnostic gaps [ 12 ].…”

Taking a Closer Look: Clinical and Histopathological Characteristics of Culture-Positive versus Culture-Negative Pulmonary Mucormycosis

“…Another limitation of these data is the reliance on the typical appearance of Mucorales in tissues as the diagnostic "gold standard" of MCR. However, there is significant interobserver variability in the accuracy of histopathology-based identification of molds [7]. Specifically, in a multicenter study using culture as the diagnostic "gold standard," 11% of culture-proven aspergillosis cases were misidentified as MCR by histopathology [8].…”

A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture

“…Current clinical diagnostic methods for invasive fungal infections require considerable expertise, infrastructure, and time. Even with the advent of mass spectrometry-based pathogen identification, delays in clinical diagnosis often result from slow subculture steps required for optimal accuracy (5, 12). We recently developed Phirst-ID, a novel approach for amplification-free, multiplexed fluorescence-based rRNA hybridization to identify bacteria directly from clinical specimens (18).…”

“…Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality, accounting for at least 1.6 million global deaths annually (1,2) and rising in incidence and severity in recent years (2)(3)(4), particularly in growing immunocompromised populations. Despite this critical threat, clinical fungal diagnostics remain slow and cumbersome (5)(6)(7)(8), leading to delayed recognition and treatment with clear mortality cost (7,9,10) and increased empiric antifungal use (11). Rapid assays for fungal biomarkers such as the cell wall components beta-D-glucan or galactomannan have emerged in recent years, but these largely lack the sensitivity or specificity to guide clinical care, aside from antigen tests for a limited number of species (5,6,8).…”