Rapid detection and identification of Aspergillus from lower respiratory tract specimens by use of a combined probe-high-resolution melting analysis

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.

Effectiveness of front line and emerging fungal disease prevention and control interventions and opportunities to address appropriate eco-sustainable solutions

Fungal pathogens contribute to significant disease burden globally; however, the fact that fungi are eukaryotes has greatly complicated their role in fungal-mediated infections and alleviation. Antifungal drugs are often toxic to host cells and there is increasing evidence of adaptive resistance in animals and humans. Existing fungal diagnostic and treatment regimens have limitations that has contributed to the alarming high mortality rates and prolonged morbidity seen in immunocompromised cohorts caused by opportunistic invasive infections as evidenced during HIV and COVID-19 pandemics. There is a need to develop real-time monitoring and diagnostic methods for fungal pathogens and to create a greater awareness as to the contribution of fungal pathogens in disease causation. Greater information is required on the appropriate selection and dose of antifungal drugs including factors governing resistance where there is commensurate need to discover more appropriate and effective solutions. Popular azole fungal drugs are widely detected in surface water and sediment due to incomplete removal in wastewater treatment plants where they are resistant to microbial degradation and may cause toxic effects on aquatic organisms such as algae and fish. UV has limited effectiveness in destruction of anti-fungal drugs where there is increased interest in the combination approaches such as novel use of pulsed-plasma gas-discharge technologies for environmental waste management. There is growing interest in developing alternative and complementary green eco-biocides and disinfection innovation. Fungi present challenges for cleaning, disinfection and sterilization of reusable medical devices such as endoscopes where they (example, Aspergillus and Candida species) can be protected when harboured in build-up biofilm from lethal processing. Information on the efficacy of established disinfection and sterilization technologies to address fungal pathogens including bottleneck areas that present high risk to patients is lacking. There is a need to address risk mitigation and modelling to inform efficacy of appropriate intervention technologies that must consider all contributing factors where there is potential to adopt digital technologies to enable real-time analysis of big data, such as use of artificial intelligence and machine learning. International consensus on standardised protocols for developing and reporting on appropriate alternative eco-solutions must be reached, particularly in order to address fungi with increasing drug resistance where research and innovation can be enabled using a One Health approach.

Development of a Sensitive and Specific Novel qPCR Assay for Simultaneous Detection and Differentiation of Mucormycosis and Aspergillosis by Melting Curve Analysis

Molecular diagnostic assays can expedite the diagnosis of fungal infections, and subsequently help in early interventions and appropriate management of patients. The aim of this study was to develop a single set of primers for a real-time quantitative polymerase chain reaction (qPCR) assay to detect and identify commonly reported, clinically relevant molds i.e., Aspergillus spp, Mucorales and Fusarium spp., up to genus level by melting curve analysis. This assay was evaluated in whole blood from patients with suspected invasive aspergillosis (IA), and in tissue biopsy, bronchoalveolar lavage (BAL) fluid and other site-specific samples from patients with suspected invasive mucormycosis (IM). The limit of detection (LoD) was determined as 10 copies/μl for all three molds. The mean coefficient of variation (CV) across all sets of intra- and inter-assay data was 0.63% (ranging from 0.42 to 1.56%), showing high reproducibility of the assay. Sensitivity and specificity of the assay were 93.3 and 97.1% respectively for diagnosis of IA, and 99.29 and 83.84% respectively for diagnosis of IM. Fusarium was not detected in any of the clinical samples included and the few laboratory confirmed cases of fusariosis did not meet the inclusion criteria of the study. Hence no ROC curve or cutoff value could be generated for the same. This newly developed qPCR assay therefore appears to be a promising tool in detection of IA and IM.

Rapid identification of clinical common invasive fungi via a multi-channel real-time fluorescent polymerase chain reaction melting curve analysis

The incidence of invasive fungal infections (IFIs) has recently increased, and early and accurate diagnosis of IFIs is important for the rational selection of antifungal drugs with high efficacy. We developed a method for rapid and accurate clinical diagnosis of IFIs and provide a reference for personalized drug treatment.We designed and screened fungal internal transcribed spacer regions with universal primers and designed 8 TaqMan detection probes to establish a multi-channel real-time fluorescent polymerase chain reaction (PCR) melting curve analysis (MCA) method. The sensitivity, specificity, and reproducibility of this method were investigated using standard fungal strains and clinical isolates. Candidemia was detected using the MCA method.The limit of detection and assay cut-off (melting temperature [Tm]) for Candida albicans were 0.05 pg/μL and 66.50 °C; Candida glabrata were 0.1 pg/μL and 66.25 °C; Candida tropicalis were 0.1 pg/μL and 60.15 °C; Candida krusei were 0.1 pg/μL and 72.15 °C; Candida parapsilosis were 0.2 pg/μL and 63.10 °C; Candida guilliermondii were 0.1 pg/μL and 61.84 °C; Cryptococcus neoformans were 0.1 pg/μL and 65.50 °C; Aspergillus flavus were 0.05 pg/μL and 71.50 °C; Aspergillus terreus, Aspergillus fumigatus, and Aspergillus niger were 0.05 pg/μL and 76.80 °C. Analytical specificity was evaluated using 13 clinical pathogens including Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae, etc. No false-positive results were obtained for any of these samples. The MCA method can detect and identify different candidemia simulations. The limit detection concentration of C albicans was 44 cfu/mL, C glabrata was 73 cfu/mL, C tropicalis was 29 cfu/mL, C parapsilosis was 21 cfu/mL, C krusei was 71 cfu/mL, and C guilliermondii was 53 cfu/mL.The multi-channel real-time fluorescence PCR melting curve analysis displayed high sensitivity and specificity in detecting various clinically invasive fungi. Furthermore, it simultaneously detected the genera Candida, Cryptococcus, and Aspergillus and identified Candida at the species level. Our method can facilitate early and accurate clinical diagnosis and personalized medication regimens.

High incidence of invasive fungal infection during acute myeloid leukemia treatment in a resource-limited country: clinical risk factors and treatment outcomes

BACKGROUND

Invasive fungal infection (IFI) causes high morbidity and mortality during acute myeloid leukemia (AML) treatment. Interventions to prevent fungal infection, including air filtration systems and antifungal prophylaxis, may improve outcomes in this group of patients. However, they are expensive and therefore inapplicable in resource-limited countries. The benefit of antifungal therapy is also dependent on the local epidemiology. That led us to conduct the study to evaluate the characteristics and impact of IFI in AML patients without prophylaxis in our setting.

METHODS

Clinical data from patients with AML who have been treated with chemotherapy without antifungal prophylaxis were retrieved during a 5-year period at Thailand's hematology referral center. Incidence and risk factors of IFI and outcomes of patients were evaluated.

RESULTS

Among 292 chemotherapy courses, there were 65 (22.3%) episodes of IFI. Of those, 10 (15.4%) were proven, 19 (29.2%) were probable, and 36 (55.4%) were categorized as being possible IFI. Molds were the most commonly observed causative pathogens (93.1%). The incidence of probable/proven IFI was highest during first induction (20.5%), followed by second induction (6.1%), and consolidation (2.7%). A long duration of neutropenia, old age, and low serum albumin were the strongest predictors of IFI. Compared with patients who had no IFI, patients with probable/proven IFI had a longer length of hospital stay and higher in-hospital mortality. Patients with proven IFI had a significantly worse outcome at 1 year.

CONCLUSIONS

These results suggest the change in health policy to implement IFI preventive measures to improve outcomes of AML treatment.

Rapid and accurate identification of black aspergilli from grapes using high-resolution melting (HRM) analysis

BACKGROUND

Aspergillus is a diverse genus of fungi with high economic and social impact. Various species that belong to section Nigri (black aspergilli) are common agents of grape spoilage and potent producers of ochratoxin A (OTA), a mycotoxin associated with various nephrotoxic and immunotoxic effects in humans. Black aspergilli are difficult to classify following only phenotypic criteria; thus chemotaxonomic and molecular methods are employed in parallel with phenotypic ones for species characterization. These approaches, though accurate and replicable, require more than one individual step and are to a certain extent laborious when a rapid identification of these species is required.

RESULTS

The aim of this study was to develop a high-resolution melting polymerase chain reaction (HRM-PCR) assay as a rapid method for identification of Aspergillus spp. section Nigri isolates and their detection in grape samples. Melt curve analysis of amplicons originating from the internal transcribed spacer 2 (ITS2) ribosomal region generated species-specific HRM curve profiles, enabling the accurate differentiation of the analyzed genotypes. Furthermore, the assay was able to identify A. carbonarius, A. tubingensis, A. niger, A. ibericus and A. japonicus in grape samples artificially inoculated with conidia of these fungi.

CONCLUSION

To our knowledge this is the first report on the development of an HRM-PCR assay for the identification of black Aspergillus species in grape samples. © 2018 Society of Chemical Industry.

DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction of Aspergillus species

We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions.

Evaluation of PCR-reverse line blot hybridization assay for simultaneous identification of medically important saprophytic fungi

BACKGROUND

In immunocompromised patients suffering from invasive fungal infections, rapid identification of fungal species is important since the appropriate treatment is usually related to the responsible species. We describe here, an assay based on combination of PCR and reverse line blot hybridization (PCR/RLB) for differentiation causative agent of fungal infections.

MATERIALS AND METHODS

We performed PCR/RLB assay on 10 reference strains, which include Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. clavatus), Mucor circnelloides, Rhizopus oryzae, Alternaria alternata, Cladosporium herbarum, and Fusarium solani. Besides, twenty-two clinical specimens from patients with proven fungal infections were analyzed for the identification of species. The obtained results were then compared with the results of culture and sequence analysis.

RESULTS

The fungal species-specific oligonucleotide probes were able to distinguish between all species represented in this study with the exception of cross-reactivity between A. niger and A. fumigatus species. Two specimens, which were represented as mixed fungi in culture, were identified properly by this method. Results of the RLB assay were concordant with the culture and ITS sequencing results.

CONCLUSION

Our result demonstrate that the RLB assay potentially is suitable for rapid and simultaneous identification of variety fungal pathogens directly from culture as well as from clinical specimens.

Evaluating the use of PCR for diagnosing invasive aspergillosis

INTRODUCTION

Aspergillus species, primarily Aspergillus fumigatus, are still the most emerging fungal pathogens. Within recent years, novel molecular methods have been developed to improve the diagnosis of life-threatening invasive aspergillosis in high risk patients. Especially patients with malignant hematological diseases undergoing intensive chemotherapy are at risk and mortality rates are exceptionally high, in part due to difficulties and delays in establishing a microbiologic diagnosis. Early diagnosis and treatment are crucial for an adequate therapeutical management, but, however, are hardly achieved in the clinical setting because most of the current conventional diagnostic tools either lack specificity or acceptable sensitivity at the critical early phase of the infection. Areas covered: To review the clinical value, advantages and problems as well as drawbacks of molecular approaches, especially polymerase chain reaction (PCR)-based assays to detect genomic DNA of Aspergillus species in clinical samples of immunocompromised, especially hematological patients at high risk for IA, a comprehensive review of the literature was performed and expert opinion was expressed. Expert commentary: The results of numerous attempts to diagnose invasive aspergillosis by PCR-based detection of fungal genome in clinical samples highlight the potential of the PCR technique to improve early diagnosis of invasive aspergillosis in patients with hematological malignancies during intensive antineoplastic treatment, combined with imaging surveillance and serologic diagnostic tools. Further comparative validation of reliable assays in prospective multicenter studies is mandatory and urgently needed in order to establish a harmonization and standardization, so that 'gold standard assays' may be incorporated into diagnostic and therapeutic algorithms that improve the prognosis of patients with life-threatening infections caused by Aspergillus species.

Discrimination of three genetically close Aspergillus species by using high resolution melting analysis applied to indoor air as case study

Background

Indoor air pollution caused by fungal contamination is suspected to have a public health impact. Monitoring of the composition of the indoor airborne fungal contaminants is therefore important. To avoid problems linked to culture-dependent protocols, molecular methods are increasingly being proposed as an alternative. Among these molecular methods, the polymerase chain reaction (PCR) and the real-time PCR are the most frequently used tools for indoor fungal detection. However, even if these tools have demonstrated their appropriate performance, some of them are not able to discriminate between species which are genetically close. A solution to this could be the use of a post-qPCR high resolution melting (HRM) analysis, which would allow the discrimination of these species based on the highly accurate determination of the difference in melting temperature of the obtained amplicon. In this study, we provide a proof-of-concept for this approach, using a dye adapted version of our previously developed qPCR SYBR®Green method to detect Aspergillus versicolor in indoor air, an important airborne fungus in terms of occurrence and cause of health problems. Despite the good performance observed for that qPCR method, no discrimination could previously be made between A. versicolor, Aspergillus creber and Aspergillus sydowii.

Methods

In this study, we developed and evaluated an HRM assay for the discrimination between A. versicolor, Aspergillus creber and Aspergillus sydowii.

Results

Using HRM analysis, the discrimination of the 3 Aspergillus species could be made. No false positive, nor false negatives were observed during the performance assessment including 20 strains of Aspergillus. The limit of detection was determined for each species i.e., 0.5 pg of gDNA for A. creber and A. sydowii, and 0.1 pg of gDNA for A. versicolor. The HRM analysis was also successfully tested on environmental samples.

Conclusion

We reported the development of HRM tools for the discrimination of A. versicolor, A. creber and A. sydowii. However, this study could be considered as a study case demonstrating that HRM based on existing qPCR assays, allows a more accurate identification of indoor air contaminants. This contributes to an improved insight in the diversity of indoor airborne fungi and hence, eventually in the causal link with health problems.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0996-4) contains supplementary material, which is available to authorized users.

New Panfungal Real-Time PCR Assay for Diagnosis of Invasive Fungal Infections

The diagnosis of invasive fungal infections (IFIs) is usually based on the isolation of the fungus in culture and histopathological techniques. However, these methods have many limitations often delaying the definitive diagnosis. In recent years, molecular diagnostics methods have emerged as a suitable alternative for IFI diagnosis. When there is not a clear suspicion of the fungus involved in the IFI, panfungal real-time PCR assays have been used, allowing amplification of any fungal DNA. However, this approach requires subsequent amplicon sequencing to identify the fungal species involved, increasing response time. In this work, a new panfungal real-time PCR assay using the combination of an intercalating dye and sequence-specific probes was developed. After DNA amplification, a melting curve analysis was also performed. The technique was standardized by using 11 different fungal species and validated in 60 clinical samples from patients with proven and probable IFI. A melting curve database was constructed by collecting those melting curves obtained from fungal species included in the standardization assay. Results showed high reproducibility (coefficient of variation [CV] < 5%; r > 0.95) and specificity (100%). The overall sensitivity of the technique was 83.3%, with the group of fungi involved in the infection detected in 77.8% of the positive samples with IFIs covered by molecular beacon probes. Moreover, sequencing was avoided in 67.8% of these "probe-positive" results, enabling report of a positive result in 24 h. This technique is fast, sensitive, and specific and promises to be useful for improving early diagnosis of IFIs.

Molecular Diagnostic Testing for Aspergillus

The direct detection of Aspergillus nucleic acid in clinical specimens has the potential to improve the diagnosis of aspergillosis by offering more rapid and sensitive identification of invasive infections than is possible with traditional techniques, such as culture or histopathology. Molecular tests for Aspergillus have been limited historically by lack of standardization and variable sensitivities and specificities. Recent efforts have been directed at addressing these limitations and optimizing assay performance using a variety of specimen types. This review provides a summary of standardization efforts and outlines the complexities of molecular testing for Aspergillus in clinical mycology.

Diagnosis of filamentous fungi on tissue sections by immunohistochemistry using anti-aspergillus antibody

Identification based on histology alone has limitations as Aspergillus species share morphology with other filamentous fungi. Differentiation of Aspergillus species from hyalohyphomycetes and dematiaceous fungi is important as the antifungal susceptibility varies among different species and genera. Given these problems, ancillary techniques are needed to increase specificity. Our aim was to study the utility of immunohistochemistry (IHC) with anti-Aspergillus antibody in the identification of Aspergillus species and to differentiate them from other filamentous fungi. Fifty formalin fixed, paraffin embedded tissue sections including 47 from cases of culture proven filamentous fungi, 3 from colonies of cultures of hyalohyphomycetes, and 11 smears from cultures were subjected to IHC studies using polyclonal rabbit anti-Aspergillus antibody (Abcam, UK) after antigen retrieval. The IHC on tissue sections was positive in 88% cases involving culture proven Aspergillus species. There was no cross reactivity with Mucorales species, Candida species, dematiaceous fungi and hyalohyphomycetes. Hence immunohistochemistry can be used as an ancillary technique for the diagnosis of Aspergillus species.