Development of a Duplex Real-Time PCR Assay for the Differentiation of Blastomyces dermatitidis and Blastomyces gilchristii and a Retrospective Analysis of Culture and Primary Specimens from Blastomycosis Cases from New York (2005 to 2019)

Blastomycosis

Blastomycosis is caused primarily by Blastomyces dermatitidis. The fungus is a mold in the environment, causing infection when conidia are dispersed and inhaled. In the lungs, the organism transforms into the yeast phase. Pneumonia is most common, but dissemination to skin, bones, and other organs also occurs. Diagnosis is established by growth in culture, identifying large thick-walled yeast with a single broad-based bud in tissue, and testing for cell wall antigens in urine and serum. Antifungal treatment and duration depend on severity. Mild-to-moderate disease is treated with itraconazole; severe blastomycosis is initially treated with amphotericin B, followed by itraconazole.

Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii

Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25-75.4 Mb) were ∼8 Mb larger than the B. dermatitidis genomes (64.88-66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04-39.26 Mb) than in B. dermatitidis (30.85-32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution.

Diagnosis of Human Endemic Mycoses Caused by Thermally Dimorphic Fungi: From Classical to Molecular Methods

Human endemic mycoses are potentially fatal diseases caused by a diverse group of fungi that can alter their morphology in response to an increase in temperature. These thermally dimorphic fungi affect both healthy and immunocompromised hosts, causing a substantial health and economic burden. Despite this, the diagnosis of endemic mycoses is still a formidable challenge for several reasons, including similar symptomatology, limited utility of classical diagnostic methods, inaccessibility to reliable molecular approaches in most endemic areas, and a lack of clinical suspicion out of these regions. This review summarizes essential knowledge on thermally dimorphic fungi and the life-threatening diseases they cause. The principle, advantages and limitations of the methods traditionally used for their diagnosis are also described, along with the application status and future directions for the development of alternative diagnostic strategies, which could help to reduce the disease burden in endemic areas.

An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections

BACKGROUND

Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens.

AREAS COVERED

We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS).

EXPERT OPINION

PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.

Blastomycosis: A Review of Mycological and Clinical Aspects

Blastomycosis is caused by a thermally dimorphic fungus that thrives in moist acidic soil. Blastomyces dermatitidis is the species responsible for most infections in North America and is especially common in areas around the Great Lakes, the St. Lawrence Seaway, and in several south-central and southeastern United States. Other Blastomyces species have more recently been discovered to cause disease in distinct geographic regions around the world. Infection almost always occurs following inhalation of conidia produced in the mold phase. Acute pulmonary infection ranges from asymptomatic to typical community-acquired pneumonia; more chronic forms of pulmonary infection can present as mass-like lesions or cavitary pneumonia. Infrequently, pulmonary infection can progress to acute respiratory distress syndrome that is associated with a high mortality rate. After initial pulmonary infection, hematogenous dissemination of the yeast form of Blastomyces is common. Most often this is manifested by cutaneous lesions, but osteoarticular, genitourinary, and central nervous system (CNS) involvement also occurs. The diagnosis of blastomycosis can be made by growth of the mold phase of Blastomyces spp. in culture or by histopathological identification of the distinctive features of the yeast form in tissues. Detection of cell wall antigens of Blastomyces in urine or serum provides a rapid method for a probable diagnosis of blastomycosis, but cross-reactivity with other endemic mycoses commonly occurs. Treatment of severe pulmonary or disseminated blastomycosis and CNS blastomycosis initially is with a lipid formulation of amphotericin B. After improvement, therapy can be changed to an oral azole, almost always itraconazole. With mild to moderate pulmonary or disseminated blastomycosis, oral itraconazole treatment is recommended.

Molecular Diagnosis of Endemic Mycoses

Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.