Commercial Molecular Tests for Fungal Diagnosis from a Practical Point of View

Mycobiota and Antifungal Antibodies as Emerging Targets for the Diagnosis and Prognosis of Human Diseases

The human body is colonized by diverse microorganisms, with bacteria being the most extensively studied. However, fungi, collectively known as "the mycobiota," are increasingly recognized as integral components of the microbiota, inhabiting nearly all mucosal surfaces. Commensal fungi influence host immunity similarly to bacteria and contribute to other essential functions, including metabolism. This emerging understanding positions fungi as potential biomarkers for the diagnosis and prognosis of various diseases. In this review, we explore the dual roles of fungi as both commensals and pathogens, and the potential of antifungal antibodies to serve as diagnostic and prognostic tools, especially in chronic immune-inflammatory non-communicable diseases, including inflammatory bowel disease, rheumatoid arthritis, multiple sclerosis, and neurodegenerative disorders. Finally, we address current challenges and outline future perspectives for leveraging fungal biomarkers in clinical practice.

Development and evaluation of a novel rapid fungal nucleic acid extraction kit

Fungal infections can cause different diseases, and nucleic acid extraction is a crucial step in assisting the diagnosis of fungal infections. Traditional methods and current commercial fungal nucleic acid extraction kits are often time-consuming and involve hazardous chemicals. We developed a nucleic acid extraction kit that is safe, rapid, and efficient, designated as FNA-REK (Fungal Nucleic Acid Extraction Kit), which facilitates the simultaneous extraction of DNA and RNA without the necessity for hazardous chemicals, liquid nitrogen, or glass beads. This kit is user-friendly and achieves complete extraction within a mere 10 min. The RNA from the culture of Cryptococcus neoformans, Candida albicans, Candida krusei, Aspergillus flavus, Aspergillus niger and Aspergillus fumigatus. Meanwhile, the RNA from Candida albicans, Candida glabrata and Candida tropicalis of mid-stream urine, vaginal discharge and sputum samples, respectively, Cryptococcus neoformans, genus Aspergillus and Pneumocystis jirovecii of sputum samples, genus Aspergillus of bronchoscopy rinsing fluid were extracted using both the FNA-REK and the BIO-TEK. The concentration and purity of the extracted RNA were measured by nanodrop photometer. The nucleic acid extracted from Cryptococcus neoformans and Candida albicans using FNA-REK showed higher concentration and purity compared to BIO-TEK following a 10-6 dilution. The maximum coefficients of variation for intra-run and inter-run replicates were 2.26% and 8.44%, respectively, significantly lower than 10%, indicating the high reproducibility of the FNA-REK. The FNA-REK yielded a lower cycle threshold (Ct value) than the BIO-TEK for cultured Candida krusei, Aspergillus niger and Aspergillus fumigatus obtained from clinical laboratory. Also, FNA-REK performed better than BIO-TEK for Candida albicans, Candida glabrata, Candida tropicalis, and genus Aspergillus in sputum samples from patients with severe pneumonia. The FNA-REK is a sensitive and stable nucleic acid extraction kit, offering an economical, efficient, and environmentally sustainable approach for fungal nucleic acid extraction. Its high extraction efficiency provides significant technical support for both laboratory and clinical applications, positioning it as a strong contender to become the most convenient and fastest fungal nucleic acid extraction kit currently available on the market.

Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

Development and Evaluation of a Fully Automated Molecular Assay Targeting the Mitochondrial Small Subunit rRNA Gene for the Detection of Pneumocystis jirovecii in Bronchoalveolar Lavage Fluid Specimens

The fungal pathogen Pneumocystis jirovecii causes Pneumocystis pneumonia. Although the mitochondrial large subunit rRNA gene (mtLSU) is commonly used as a PCR target, a mitochondrial small subunit rRNA gene (mtSSU)-targeted MultiCode PCR assay was developed on the fully automated ARIES platform for detection of P. jirovecii in bronchoalveolar lavage fluid specimens in 2.5 hours. The assay showed a limit of detection of 800 copies/mL (approximately equal to 22 organisms/mL), with no cross-reactivity with other respiratory pathogens. Compared with the reference Pneumocystis-specific direct fluorescent antibody assay (DFA) and mtLSU-targeted PCR assay, the new assay demonstrated sensitivity of 96.9% (31/32) and specificity of 94.6% (139/147) in detecting P. jirovecii in 180 clinical bronchoalveolar lavage fluid specimens. This assay was concordant with all DFA-positive samples and all but one mtLSU PCR-positive sample, and detected eight positive samples that were negative by DFA and mtLSU PCR. Receiver operating characteristic curve analysis revealed an area under the curve of 0.98 and a threshold cycle (C_T) cutoff of 39.1 with sensitivity of 90.9% and specificity of 99.3%. The detection of 39.1 <C_T < 40.0 indicates the presence of a low load of the organism and needs further determination of either colonization or probable/possible Pneumocystis pneumonia. Overall, the new assay demonstrates excellent analytical and clinical performance and may be more sensitive than mtLSU PCR target for the detection of P. jirovecii.

Diagnostic Performance of a Novel Multiplex PCR Assay for Candidemia among ICU Patients

Candidemia poses a major threat to ICU patients and is routinely diagnosed by blood culture, which is known for its low sensitivity and long turnaround times. We compared the performance of a novel, Candida-specific multiplex real-time PCR assay (Fungiplex^® Candida IVD Real-Time PCR Kit) with blood culture and another established diagnostic real-time PCR assay (LightCycler SeptiFast Test) with respect to Candida detection from whole blood samples. Clinical samples from 58 patients were analyzed by standard blood culture (BC) and simultaneously tested with the Fungiplex Candida PCR (FP) and the SeptiFast test (SF) for molecular detection of Candida spp. Compared to BC, the FP test showed high diagnostic power, with a sensitivity of 100% and a specificity of 94.1%. Overall diagnostic accuracy reached 94.6%. Using SF, we found a sensitivity of 60%, a specificity of 96.1%, and an overall diagnostic accuracy of 92.9%. The Fungiplex Candida PCR has shown good sensitivity and specificity on clinical samples of high-risk patients for direct detection of Candida species in whole blood samples. Together with conventional diagnostics (BC and antigen testing), this new multiplex PCR assay may contribute to a rapid and accurate diagnosis of candidiasis.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present

Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.

Cryptococcal meningitis is a cause for cross-reactivity in cerebrospinal fluid assays for anti-Histoplasma, anti-Coccidioides and anti-Blastomyces antibodies

BACKGROUND/OBJECTIVES

Antibody detection is commonly used for diagnosis of histoplasmosis, and cross-reactions have been recognised due to endemic mycoses but not cryptococcosis. We observed cross-reactions in an anti-Histoplasma antibody enzyme immunoassay (EIA) in the cerebrospinal fluid (CSF) from a patient with cryptococcal meningitis and sought to assess the risk of cross-reactive anti-Histoplasma antibodies in persons with cryptococcal meningitis.

METHODS

An anti-cryptococcal antibody EIA was developed to measure CSF antibody response in HIV-infected subjects from Kampala, Uganda and previously healthy, HIV-negative subjects at the National Institutes of Health (NIH) with cryptococcal meningitis. Specimens were tested for cross-reactivity in assays for IgG anti-Histoplasma, anti-Blastomyces and anti-Coccidioides antibodies.

RESULTS

Among 61 subjects with cryptococcal meningitis (44 Kampala cohort, 17 NIH cohort), elevated CSF anti-cryptococcal antibody levels existed in 38% (23/61). Of the 23 CSF specimens containing elevated anti-cryptococcal antibodies, falsely positive results were detected in antibody EIAs for histoplasmosis (8/23, 35%), coccidioidomycosis (6/23, 26%) and blastomycosis (1/23, 4%). Overall, 2% (2/81) of control CSF specimens had elevated anti-cryptococcal antibody detected, both from Indiana.

CONCLUSIONS

Cryptococcal meningitis may cause false-positive results in the CSF for antibodies against Histoplasma, Blastomyces and Coccidioides. Fungal antigen testing should be performed to aid in differentiating true- and false-positive antibody results in the CSF.

Clinical use of fungal PCR from deep tissue samples in the diagnosis of invasive fungal diseases: a retrospective observational study

OBJECTIVES

To assess the clinical use of panfungal PCR for diagnosis of invasive fungal diseases (IFDs). We focused on the deep tissue samples.

METHODS

We first described the design of panfungal PCR, which is in clinical use at Helsinki University Hospital. Next we retrospectively evaluated the results of 307 fungal PCR tests performed from 2013 to 2015. Samples were taken from normally sterile tissues and fluids. The patient population was nonselected. We classified the likelihood of IFD according to the criteria of the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG), comparing the fungal PCR results to the likelihood of IFD along with culture and microscopy results.

RESULTS

There were 48 positive (16%) and 259 negative (84%) PCR results. The sensitivity and specificity of PCR for diagnosing IFDs were 60.5% and 91.7%, respectively, while the negative predictive value and positive predictive value were 93.4% and 54.2%, respectively. The concordance between the PCR and the culture results was 86% and 87% between PCR and microscopy, respectively. Of the 48 patients with positive PCR results, 23 had a proven or probable IFD.

CONCLUSIONS

Fungal PCR can be useful for diagnosing IFDs in deep tissue samples. It is beneficial to combine fungal PCR with culture and microscopy.

Invasive candidiasis: future directions in non-culture based diagnosis

INTRODUCTION

Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests.

Candida and invasive mould diseases in non-neutropenic critically ill patients and patients with haematological cancer

Critically ill patients and patients with haematological cancer are HIV-negative populations at high risk of invasive fungal infections. In intensive-care units, candidaemia and intra-abdominal candidiasis predominate, but aspergillosis has emerged as a lethal, under-recognised cause of pneumonia. In patients with haematological malignancies or who have undergone stem-cell transplantations, pulmonary disease due to aspergillus and other mould diseases predominate. In this Series paper, we provide an update on risk assessment, new diagnostic strategies, and therapeutic approaches. New concepts have emerged for use of risk prediction rules and an evidence base now exists for inclusion of biomarkers (eg, galactomannan, 1,3-β-D-glucan, and PCR assays for Aspergillus spp) into early diagnostic and therapeutic strategies. Imaging techniques remain helpful for early diagnosis of pulmonary mould diseases, with PET techniques offering potential improvements in diagnostic specificity and evaluation of clinical response. Echinocandins and triazoles have been validated extensively for prophylaxis, empirical therapy, and targeted therapy, but an increase in intrinsically resistant fungi and emergence of secondary resistance as a result of drug-induced selection pressure are of major concern. Echinocandins remain a major component of treatment of invasive candidiasis and new triazoles are the best alternative for prophylaxis and therapy of invasive aspergillosis.