Real-time automated polymerase chain reaction (PCR) to detect Candida albicans and Aspergillus fumigatus DNA in whole blood from high-risk patients

Molecular and nonmolecular diagnostic methods for invasive fungal infections

Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.

Rapid identification of medically important Candida isolates using high resolution melting analysis

An increasing trend in non albicans infections and various susceptibility patterns to antifungal agents implies a requirement for the quick and reliable identification of a number of medically important Candida species. Real-time PCR followed by high resolution melting analysis (HRMA) was developed, tested on 25 reference Candida collection strains and validated on an additional 143 clinical isolates in this study. All reference strains and clinical isolates inconclusive when using phenotypic methods and/or HRMA were analysed using ITS2 sequencing. Considering reference and clinical strains together, 23 out of 27 Candida species could be clearly distinguished by HRMA, while the remaining 4 species were grouped in 2 pairs, when applying the mean Tm ± 3 SD values, the shape of the derivative melting curve (dMelt curve) and, in some cases, the normalized and temperature—shifted difference plot against C. krusei. HRMA as a simple, rapid and inexpensive tool was shown to be useful in identifying a wide spectrum of clinically important Candida species. It may complement the current clinical diagnostic approach based on commercially available biochemical kits.

Identification of whole pathogenic cells by monoclonal antibodies generated against a specific peptide from an immunogenic cell wall protein

We selected the immunogenic cell wall ß-(1,3)-glucosyltransferase Bgl2p from Candida albicans as a target protein for the production of antibodies. We identified a unique peptide sequence in the protein and generated monoclonal anti- C. albicans Bgl2p antibodies, which bound in particular to whole C. albicans cells.

PCR in diagnosis of invasive aspergillosis: a meta-analysis of diagnostic performance

Invasive aspergillosis is a difficult-to-diagnose infection with a high mortality rate that affects high-risk groups such as patients with neutropenia and hematologic malignancies. We performed a bivariate meta-analysis of diagnostic data for an Aspergillus sp. PCR assay with blood specimens from high-risk hematology patients. We included all studies involving human subjects that assessed the performance of any PCR assay for invasive aspergillosis in whole blood or serum and that used the European Organization for the treatment of Cancer/Mycoses Study Group criteria as a reference standard. Three investigators independently searched the literature for eligible studies and extracted the data. Out of a total of 37 studies, 25 met strict quality criteria and were included in our evidence synthesis. Twenty-five studies with 2,595 patients were analyzed. The pooled diagnostic performance of whole-blood and serum PCR assays was moderate, with a sensitivity and specificity of 84% (95% confidence interval [CI], 75 to 91%) and 76% (95% CI, 65 to 84%), respectively, suggesting that a positive or negative result is unable, on its own, to confirm or exclude a suspected infection. The performance of a PCR assay of serum was not significantly different from that of whole blood. Notably, at least two positive PCR test results were found to have a specificity of 95% and a sensitivity of 64% for invasive infection, achieving a high positive likelihood ratio of 12.8. Importantly, the European Aspergillus PCR Initiative (EAPCRI) recommendations improved the performance of the PCR even further when at least two positive specimens were used to define PCR positivity. In conclusion, two positive PCR results should be considered highly indicative of an active Aspergillus sp. infection. Use of the EAPCRI recommendations by clinical laboratories can further enhance PCR performance.

Candida infections and their prevention

Infections caused by Candida species have been increased dramatically worldwide due to the increase in immunocompromised patients. For the prevention and cure of candidiasis, several strategies have been adopted at clinical level. Candida infected patients are commonly treated with a variety of antifungal drugs such as fluconazole, amphotericin B, nystatin, and flucytosine. Moreover, early detection and speciation of the fungal agents will play a crucial role for administering appropriate drugs for antifungal therapy. Many modern technologies like MALDI-TOF-MS, real-time PCR, and DNA microarray are being applied for accurate and fast detection of the strains. However, during prolonged use of these drugs, many fungal pathogens become resistant and antifungal therapy suffers. In this regard, combination of two or more antifungal drugs is thought to be an alternative to counter the rising drug resistance. Also, many inhibitors of efflux pumps have been designed and tested in different models to effectively treat candidiasis. However, most of the synthetic drugs have side effects and biomedicines like antibodies and polysaccharide-peptide conjugates could be better alternatives and safe options to prevent and cure the diseases. Furthermore, availability of genome sequences of Candida   albicans and other non-albicans strains has made it feasible to analyze the genes for their roles in adherence, penetration, and establishment of diseases. Understanding the biology of Candida species by applying different modern and advanced technology will definitely help us in preventing and curing the diseases caused by fungal pathogens.

Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva

A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.

A real-time PCR for the detection and characterisation of Aspergillus species

An early diagnosis of an invasive fungal infection is essential for the initiation of a specific antifungal therapy and to avoid unnecessary discontinuation of a baseline therapy for haematological or oncological diseases. A real-time PCR assay for the detection and strain identification of Aspergillus species from culture strains was evaluated. DNA preparation was evaluated in contaminated culture media, urine and serum. A LightCycler PCR to differentiate various Aspergillus species was established. A real-time PCR assay for the detection of Aspergillus species was improved and was able to detect and differentiate medically important Aspergillus spp. The sensitivity of the test was <10 plasmid equivalents/assay. The real-time PCR assay is a useful tool for the rapid identification of Aspergillus species and might be useful as an early diagnostic tool to detect an invasive fungal infection. A real-time PCR protocol was improved by generating plasmid standards, additional generation of melting curves for species identification and the correlation between the melting temperature and the nucleotide exchanges within the used 18S rRNA gene region.

PCR diagnosis of invasive candidiasis: systematic review and meta-analysis

Invasive candidiasis (IC) is a significant cause of morbidity and mortality. Diagnosis relies on culture-based methods, which lack sensitivity and delay diagnosis. We conducted a systematic review assessing the diagnostic accuracy of PCR-based methods to detect Candida spp. directly in blood samples. We searched electronic databases for prospective or retrospective cohort and case-control studies. Two reviewers abstracted data independently. Meta-analysis was performed using a hierarchical logistic regression model. Random-effects metaregression was performed to assess the effects of study methods and infection characteristics on sensitivity or specificity values. We included 54 studies with 4,694 patients, 963 of whom had proven/probable or possible IC. Perfect (100%) sensitivity and specificity for PCR in whole-blood samples was observed when patients with cases had candidemia and controls were healthy people. When PCR was performed to evaluate patients with suspected invasive candidiasis, the pooled sensitivity for the diagnosis of candidemia was 0.95 (confidence interval, 0.88 to 0.98) and the pooled specificity was 0.92 (0.88 to 0.95). A specificity of >90% was maintained in several analyses considering different control groups. The use of whole-blood samples, rRNA, or P450 gene targets and a PCR detection limit of ≤ 10 CFU/ml were associated with improved test performance. PCR positivity rates among patients with proven or probable IC were 85% (78 to 91%), while blood cultures were positive for 38% (29 to 46%). We conclude that direct PCR using blood samples had good sensitivity and specificity for the diagnosis of IC and offers an attractive method for early diagnosis of specific Candida spp. Its effects on clinical outcomes should be investigated.

A real-time PCR assay for the differentiation of Candida species

AIMS

We established a real-time PCR assay for the detection and strain identification of Candida species and demonstrated the ability to differentiate between Candida albicans the most common species, and also Candida parapsilosis, Candida glabrata, Candida tropicalis and Candida dubliniensis by LightCycler PCR and melting curve analysis.

METHODS AND RESULTS

The DNA isolation from cultures and serum was established using the QIAmp Tissue Kit. The sensitivity of the assay was ≥ 2 genome equivalents/assay. It was possible to differentiate all investigated Candida species by melting curve analysis, and no cross-reaction to human DNA or Aspergillus species could be observed.

CONCLUSIONS

The established real-time PCR assay is a useful tool for the rapid identification of Candida species and a base technology for more complex PCR assays.

SIGNIFICANCE AND IMPACT OF THE STUDY

We carried out initial steps in validation of a PCR assay for the detection and differentiation of medically relevant Candida species. The PCR was improved by generating PCR standards, additional generation of melting curves for species identification and the possibility to investigate different specimens simultaneously.

Candidemia and invasive candidiasis: a review of the literature for the burns surgeon

Advances in critical care, operative techniques, early fluid resuscitation, antimicrobials to control bacterial infections, nutritional support to manage the hypermetabolic response and early wound excision and coverage has improved survival rates in major burns patients. These advances in management have been associated with increased recognition of invasive infections caused by Candida species in critically ill burns patients. Candida albicans is the most common species to cause invasive Candida infections, however, non-albicans Candida species appear to becoming more frequent. These later species may be less fluconazole susceptible than Candida albicans. High crude and attributable mortality rates from invasive Candida sepsis are multi-factorial. Diagnosis of invasive candidiasis and candidemia remains difficult. Prophylactic and pre-emptive therapies appear promising strategies, but there is no specific approach which is well-studied and clearly efficacious in high-risk burns patients. Treatment options for invasive candidiasis include several amphotericin B formulations and newer less toxic antifungal agents, such as azoles and echinocandins. We review the currently available data on diagnostic and management strategies for invasive candidiasis and candidemia; whenever possible providing reference to the high-risk burn patients. We also present an algorithm for the management of candidemia and invasive candidiasis in burn patients.

Current status and future perspectives on molecular and serological methods in diagnostic mycology

Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex® xMAP™) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum β-D-glucan test have value for diagnosing infection and monitoring therapeutic response.

Effect of different sample volumes on the DNA extraction of Aspergillus fumigatus from whole blood

Five methods were compared, using conventional PCR, for the isolation of DNA from Aspergillus fumigatus conidia from 1-3-mL samples of whole blood. A lower detection threshold of Aspergillus conidia was achieved using 3-mL rather than 1-mL samples with three of five methods tested.

Large scale multiplex PCR improves pathogen detection by DNA microarrays

Background

Medium density DNA microchips that carry a collection of probes for a broad spectrum of pathogens, have the potential to be powerful tools for simultaneous species identification, detection of virulence factors and antimicrobial resistance determinants. However, their widespread use in microbiological diagnostics is limited by the problem of low pathogen numbers in clinical specimens revealing relatively low amounts of pathogen DNA.

Results

To increase the detection power of a fluorescence-based prototype-microarray designed to identify pathogenic microorganisms involved in sepsis, we propose a large scale multiplex PCR (LSplex PCR) for amplification of several dozens of gene-segments of 9 pathogenic species. This protocol employs a large set of primer pairs, potentially able to amplify 800 different gene segments that correspond to the capture probes spotted on the microarray. The LSplex protocol is shown to selectively amplify only the gene segments corresponding to the specific pathogen present in the analyte. Application of LSplex increases the microarray detection of target templates by a factor of 100 to 1000.

Conclusion

Our data provide a proof of principle for the improvement of detection of pathogen DNA by microarray hybridization by using LSplex PCR.

Simple method to accurately differentiate Candida albicans isolates concurrently using polymorphic patterns of PCR-amplified, species-specific nuclear and mitochondrial targets

We describe a simple method to accurately differentiate Candida albicans isolates by concurrent use of the restriction enzyme digestion patterns for PCR products, targeting two species-specific DNA regions originating from genetically different sources, the nuclear and mitochondrial genomes. The target sequence we used as the nuclear gene was derived from the PHO85 gene, a negative regulator of the PHO system, in which we found a restriction size polymorphism within the two alleles of PHO85 in the diploid genome of this fungus. The mitochondrial target was derived from EO3, a species-specific DNA fragment possessing a small size polymorphism among various clinical isolates. Our results should provide a new tool for molecular epidemiological surveys of patients suffering from candidiasis caused by C. albicans.

Improving molecular detection of Candida DNA in whole blood: comparison of seven fungal DNA extraction protocols using real-time PCR

The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.

Detection and identification of Candida spp. in human serum by LightCycler real-time polymerase chain reaction

The aim of this work was to develop LightCycler real-time polymerase chain reaction method to allow rapid detection and identification of Candida spp. in human serum with panfungal primers (internal transcribed spacer [ITS] and L18). Melting-curve analysis of the ITS sequences showed that each amplicon presented a specific melting point and enabled identification of 5 Candida spp. After parameters optimization, 58 sera were preliminary analyzed from 23 patients. For L18 primers, the LightCycler system enabled detection of DNA in 92% of patients with positive blood culture. These primers were not able to differentiate between species of Candida. By using ITS primers, the LightCycler system enabled detection of DNA in sera from 76.9% of patients with positive blood culture. With ITS primers, the species responsible for the infection was identified for 11 patients. These data revealed the LightCycler as a potential tool for early detection and identification of Candida.

Internal amplification controls have not been employed in fungal PCR hence potential false negative results

Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.

Evolution of antibody response and fungal antigens in the serum of a patient infected with Candida famata

The presence of fungal antibodies and antigens in the serum of a patient diagnosed in 1996 with acute zonal occult outer retinopathy caused by Candida famata infection was examined. Antibodies against C. famata increased until 1999–2000 when antifungal treatment was initiated. The antibodies were detected by ELISA and immunofluorescence analysis using C. famata. These antibodies were not immunoreactive against several Candida species tested. Positive immunofluorescence was obtained with IgM, but not IgA, IgG or IgE. Moreover, the IgM response disappeared several months after treatment with antifungal compounds, despite the fact that C. famata antigens were present in the blood. Finally, a sensitive test was developed to assay for the presence of C. famata antigens in serum based on the immunodetection of fungal antigens transferred to a nitrocellulose membrane and incubated with rabbit antibodies raised against C. famata. According to this method, the infection diminished with antifungal treatment.

Diagnosis of invasive candidiasis by enzyme-linked immunosorbent assay using the N-terminal fragment of Candida albicans hyphal wall protein 1

BACKGROUND

The diagnosis of invasive candidiasis is difficult because there are no specific clinical manifestations of the disease and colonization and infection are difficult to distinguish. In the last decade, much effort has been made to develop reliable tests for rapid diagnosis of invasive candidiasis, but none of them have found widespread clinical use.

RESULTS

Antibodies against a recombinant N-terminal fragment of the Candida albicans germ tube-specific antigen hyphal wall protein 1 (Hwp1) generated in Escherichia coli were detected by both immunoblotting and ELISA tests in a group of 36 hematological or Intensive Care Unit patients with invasive candidiasis and in a group of 45 control patients at high risk for the mycosis who did not have clinical or microbiological data to document invasive candidiasis. Results were compared with an immunofluorescence test to detect antibodies to C. albicans germ tubes (CAGT). The sensitivity, specificity, positive and negative predictive values of a diagnostic test based on the detection of antibodies against the N-terminal fragment of Hwp1 by immunoblotting were 27.8 %, 95.6 %, 83.3 % and 62.3 %, respectively. Detection of antibodies to the N-terminal fragment of Hwp1 by ELISA increased the sensitivity (88.9 %) and the negative predictive value (90.2 %) but slightly decreased the specificity (82.6 %) and positive predictive values (80 %). The kinetics of antibody response to the N-terminal fragment of Hwp1 by ELISA was very similar to that observed by detecting antibodies to CAGT.

CONCLUSION

An ELISA test to detect antibodies against a recombinant N-terminal fragment of the C. albicans germ tube cell wall antigen Hwp1 allows the diagnosis of invasive candidiasis with similar results to those obtained by detecting antibodies to CAGT but without the need of treating the sera to adsorb the antibodies against the cell wall surface of the blastospore.

Multiplex real-time PCR targeting the RNase P RNA gene for detection and identification of Candida species in blood

We have developed a single-tube multiplex real-time PCR method for the detection of the eight most common Candida species causing septicemia: Candida albicans, C. dubliniensis, C. famata, C. glabrata, C. guilliermondii, C. krusei, C. parapsilosis, and C. tropicalis. The method developed targets the RNase P RNA gene RPR1. Sequences of this gene were determined for seven of the Candida species and showed surprisingly large sequence variation. C. glabrata was found to have a gene that was five times longer gene than those of the other species, and the nucleotide sequence similarity between C. krusei and C. albicans was as low as 55%. The multiplex PCR contained three probes that enabled the specific detection of C. albicans, C. glabrata, and C. krusei and a fourth probe that allowed the general detection of the remaining species. The method was able to detect 1 to 10 genome copies when the detection limit was tested repeatedly for the four species C. albicans, C. glabrata, C. krusei, and C. guilliermondii. No significant difference in the detection limit was seen when the multiplex format was compared with single-species PCR, i.e., two primers and one probe. The method detected eight clinically relevant Candida species and did not react with other tested non-Candida species or human DNA. The assay was applied to 20 blood samples from nine patients and showed a sensitivity similar to that of culture.

Development of novel real-time PCR assays for detection and differentiation of eleven medically important Aspergillus and Candida species in clinical specimens

In the present study, novel real-time PCR assays targeting the fungal ITS2 region were developed for the detection and differentiation of medically important Aspergillus species (Aspergillus fumigatus, Aspergillus flavus, Aspergillus nidulans, Aspergillus niger, and Aspergillus terreus) and Candida species (Candida albicans, Candida dubliniensis, Candida glabrata, Candida krusei, Candida parapsilosis, and Candida tropicalis) using a LightCycler instrument. The combination of a group-specific and a universal primer with five Aspergillus or six Candida species-specific biprobes in one reaction mixture facilitated rapid screening and species differentiation by the characteristic peak melting temperatures of the biprobes. Both assays can be performed either as single assays or simultaneously in the same LightCycler run. The analytical sensitivity using pure cultures and EDTA-anticoagulated blood, cerebrospinal fluid (CSF), and tissue samples spiked with A. fumigatus and C. albicans cell suspensions was shown to be at least 1 CFU per PCR, corresponding to 5 to 10 CFU/ml blood and 10 CFU/200 microl CSF or 0.02 g tissue. To assess the clinical applicability, 26 respiratory samples, 4 tissue samples from the maxillary sinus, and 1 blood sample were retrospectively tested and real-time PCR results were compared with results from culture, histology, or a galactomannan enzyme-linked immunosorbent assay (ELISA). Twenty samples (64.5%) were both culture positive and positive by real-time PCR. Six samples (19.4%) showed no growth of fungi but were positive by real-time PCR. However, all of the tissue samples were positive by both PCR and histology. The blood sample showed no growth of Aspergillus, but aspergillosis was confirmed by positive galactomannan ELISA, histology, and PCR results. The remaining samples (16.1%) were culture and PCR negative; also, no other signs indicating fungal infection were observed. Our data suggest that the Aspergillus and Candida assays may be appropriate for use in clinical laboratories as simple and rapid screening tests for the most frequently encountered Aspergillus and Candida species and might become an important tool in the early diagnosis of fungal infections in the future.

DNA and the classical way: Identification of medically important molds in the 21st century

The advent of the 21st century has seen significant advances in the methods and practices used for identification of medically important molds in the clinical microbiology laboratory. Historically, molds have been identified by using observations of colonial and microscopic morphology, along with tables, keys and textbook descriptions. This approach still has value for the identification of many fungal organisms, but requires expertise and can be problematic in determining a species identification that is timely and useful in the management of high-risk patients. For the increasing number of isolates that are uncommon, atypical, or unusual, DNA-based identification methods are being increasingly employed in many clinical laboratories. These methods include the commercially available GenProbe assay, methods based on the polymerase chain reaction such as single-step PCR, RAPD-PCR, rep-PCR, nested PCR, PCR-RFLP, PCR-EIA, and more recent microarray-based, Luminex technology-based, and real-time PCR-based methods. Great variation in assay complexity, targets, and detection methods can be found, and many of these methods have not been widely used or rigorously validated. The increasing availability of DNA sequencing chemistry has made comparative DNA sequence analysis an attractive alternative tool for fungal identification. DNA sequencing methodology can be purchased commercially or developed in-house; such methods display varying degrees of usefulness depending on the breadth and reliability of the databases used for comparison. The future success of sequencing-based approaches will depend on the choice of DNA target, the reliability of the result, and the availability of a validated sequence database for query and comparison. Future studies will be required to determine sequence homology breakpoints and to assess the accuracy of molecular-based species identification in various groups of medically important filamentous fungi. At this time, a polyphasic approach to identification that combines morphologic and molecular methods will ensure the greatest success in the management of patients with fungal infections.

Development of a new real-time TaqMan PCR assay for quantitative analyses of Candida albicans resistance genes expression

Candida albicans is an important opportunistic pathogen that can cause serious fungal diseases in immunocompromised patients including cancer patients, transplant patients, and patients receiving immunosuppressive therapy in general, those with human immunodeficiency virus infections and undergoing major surgery. Its emergence spectrum varies from mucosal to systemic infections and the first line treatment is still based on fluconazole, a triazole derivate with a potent antifungal activity against most of C. albicans strains. Nevertheless the emergence of fluconazole-resistant C. albicans strains can lead to treatment failures and thus become a clinical problem in the management of such infections. For that reason we consider it important to study mechanisms inducing azole resistance and the possibilities to influence this process. In this work we give a short report on a real-time PCR (TaqMan) assay, which can be used for quantitative analyses of gene expression levels of MDR1, CDR1 and ERG11, genes supposed to contribute to development of the resistance mechanisms. We show some results achieved with that assay in fluconazole susceptible and resistant strains that confirm results seen earlier in experiments using Northern blot hybridisation and prove that the comparative DeltaCt method is valid for our system.

Molecular diagnosis of invasive aspergillosis: the long and winding road

Invasive aspergillosis is a major cause of morbidity and mortality in patients with hematological malignancies and stem cell transplant recipients. Early diagnosis and therapy are important to improve prognosis in these patients. Difficulties in establishing an early diagnosis have prompted investigations towards new and alternative diagnostic methods. During the last decade, PCR-based assays have emerged as valuable experimental tools to improve diagnostic workup and clinical management of patients with suspected or proven invasive aspergillosis. However, implementation of these molecular tools in the routine diagnostic laboratory is hampered by a lack of standardization.

MOLECULAR-GENETIC APPROACHES TO IDENTIFICATION AND TYPING OF PATHOGENIC CANDIDA YEASTS

Currently, invasive candidal infections represent an increasing cause of morbidity and mortality in seriously ill hospitalised patients. Because the accurate diagnosis of candidiasis remains difficult, a fast and reliable assay for characterization of fungal pathogens is critical for the early initiation of adequate antifungal therapy and/or for introduction of preventive measures. As novel molecular genetic techniques are continuously introduced, their role in the management of infectious diseases has also been growing. Today, molecular strategies complement conventional methods and provide more accurate and detailed insight. It can be expected that future technical development will improve their potential furthermore. In this article, we provide a critical review on the value and limitations of molecular tools in pathogenic Candida species identification and strain typing regarding their sensitivity, discriminatory power, reproducibility, cost and ease of performance.

Evaluation of the role of real-time PCR in the diagnosis of invasive aspergillosis

Recently, two developments relating to the diagnosis of invasive aspergillosis (IA) have occurred. First, the standardisation of criteria for determining the category of this disease according to the European Organisation for Research and Treatment of Cancer/Mycosis (EORTC) Study Group consensus definitions has allowed comparison of results from different studies to be undertaken. The second development is the generation of PCR assays based on real-time technologies that are able to quantify Aspergillus DNA. In this review the benefits and limitations of these new published assays are compared with nested-PCR assays and enzyme immuno assays. Results from studies where these real-time assays have been used and patient's infections were classified according the EORTC definitions are examined. The effect of anti-fungal treatment is noted. The requirement for both international standards and a consensus protocol that is sensitive enough for IA diagnosis, particularly in blood, is discussed.

Role of prospective screening of blood for invasive aspergillosis by polymerase chain reaction in febrile neutropenic recipients of haematopoietic stem cell transplants and patients with acute leukaemia

Guidelines for the use of polymerase chain reaction (PCR)-based assays to aid the diagnosis of invasive aspergillosis (IA) in high-risk haematology patients have not been formulated. We prospectively evaluated a nested PCR assay to detect Aspergillus in blood during 95 febrile neutropenic episodes, in patients with haematological malignancy and haematopoietic stem cell transplant (HSCT) recipients. PCR results were correlated with the diagnostic classification of the 2002 European Organisation for Research and Treatment of Cancer/Mycosis Study Group. When two-positive results were used to define an episode as 'PCR positive', the sensitivity, specificity, positive-predictive value and negative predictive value for 'proven'/'probable' IA (n = 13) were 100%, 75.4%, 46.4% and 100%, respectively. Consecutive positive results occurred in 61.5% of these 13 episodes. Overall, PCR positivity preceded standard diagnosis by a mean of 14 d and the median time between positive results was shorter than that in other categories of IA. All 13 episodes occurred in the setting of allogeneic HSCT recipients and acute leukaemia. If 'eligibility' for antifungal therapy were based on two-positive-PCR tests, use of empiric treatment could have been reduced by up to 37%. The nested PCR assay is a practical screening test for excluding IA. Patients with consecutive positive results or intermittent-positive results (within 14 d) warrant immediate investigations for IA and the initiation of antifungal therapy.

Rapid, specific, and sensitive detection of spoilage molds in orange juice using a real-time Taqman PCR assay

The outgrowth of spoilage organisms, including molds and yeasts, results in significant financial loss to the food industry and wastes natural resources. The objective of this study was to develop a rapid, specific, and sensitive real-time PCR method for detecting spoilage molds during screening of raw materials and final product quality control analysis. The 18S rRNA gene was used to develop PCR primers and probe. With this set of primers and probe, less than 1,000 mold cells per milliliter of orange juice (10 cells per reaction) were detected with the real-time PCR system within 6 to 7 h. No cross-reactivity was found with other common foodborne bacteria, yeasts, or food ingredients. This technique is significantly faster than current detection and identification procedures, which take from days to weeks.

Towards a nucleic acid-based diagnosis in clinical parasitology and mycology

BACKGROUND

Multiple in-house polymerase chain reaction (PCR) assays for the diagnosis of parasitic and fungal diseases have been reported. Encouraging results have been published to anticipate or improve the diagnosis. However, the absence of standardized methods has led to discrepant results. As a consequence, these tests are not recognized as consensual diagnostic criteria.

METHODS

The major breakthrough for improving the results of these methods is the emergence of real-time technologies. This markedly improves the reliability of the PCR results by dramatically decreasing the risk of false positive results due to PCR products carryover. Moreover, the quantitative results provided by these techniques allow to compare rapidly the efficiency of primers, probes, and DNA extraction. Therefore, one can expect a more consensual method to implement comparisons between laboratories. Automated DNA extraction should also be useful to achieve this goal. Whatever sophisticated technology is used, the meaning of detecting nucleic acids in a given clinical sample still needs to be defined. This requires well-designed studies with clinical consensual criteria and PCR techniques that are as similar as possible.

CONCLUSIONS

The development of real-time technology should improve our knowledge in order to give the clinicians informative clues for decision-making.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Rapid identification and enumeration of Saccharomyces cerevisiae cells in wine by real-time PCR

Despite the beneficial role of Saccharomyces cerevisiae in the food industry for food and beverage production, it is able to cause spoilage in wines. We have developed a real-time PCR method to directly detect and quantify this yeast species in wine samples to provide winemakers with a rapid and sensitive method to detect and prevent wine spoilage. Specific primers were designed for S. cerevisiae using the sequence information obtained from a cloned random amplified polymorphic DNA band that differentiated S. cerevisiae from its sibling species Saccharomyces bayanus, Saccharomyces pastorianus, and Saccharomyces paradoxus. The specificity of the primers was demonstrated for typical wine spoilage yeast species. The method was useful for estimating the level of S. cerevisiae directly in sweet wines and red wines without preenrichment when yeast is present in concentrations as low as 3.8 and 5 CFU per ml. This detection limit is in the same order as that obtained from glucose-peptone-yeast growth medium (GPY). Moreover, it was possible to quantify S. cerevisiae in artificially contaminated samples accurately. Limits for accurate quantification in wine were established, from 3.8 x 10(5) to 3.8 CFU/ml in sweet wine and from 5 x 10(6) to 50 CFU/ml in red wine.

Use of green fluorescent protein-expressing Aspergillus fumigatus conidia to validate quantitative PCR analysis of air samples collected on filters

This study used green fluorescent protein (GFP)-expressing Aspergillus fumigatus conidia to compare quantitative PCR (qPCR) enumeration with direct epifluorescent microscopic filter counts of conidia collected on filters in a test chamber. In separate experiments this study initially compared white versus fluorescent light microscopy for counting A. fumigatus conidia, then compared fluorescent microscopy counting of corresponding filter halves, and finally compared qPCR enumeration to counting by fluorescent light microscopy. The use of GFP-expressing conidia with epifluorescent microscopy yielded significantly higher conidia counts (p = 0.026, n = 41, mean of 4.1 conidia per counting field) and 40% faster counting times when compared to conventional counting using white light microscopy. GFP-expressing conidia were aerosolized in a test chamber and collected onto filters. Filters were divided in half and GFP-expressing conidia enumerated. There was no significant difference in the average conidia count per field between corresponding filter halves (p = 0.3, n = 9 filters, mean of 7.8 conidia per counting field). Thus, one filter half could be counted optically and would provide a reliable estimate of filter loading of the corresponding half, which could then be analyzed by qPCR. Filters (n = 38) loaded with GFP conidia in the aerosol chamber were divided in half and analyzed by either fluorescent microscopy or qPCR. The estimated filter loadings ranged from 15-30,000 conidia per filter. There was a linear relationship with a nearly 1:1 ratio between qPCR and direct microscopic estimates of filter loading (y = 1.06x + 404; R(2) = 0.91) showing that the outlined qPCR analysis method is in agreement with an external reference method and is reliable for enumerating A. fumigatus conidia collected on filters. The comparative data derived using GFP-expressing conidia confirmed that qPCR provides sensitive and accurate quantification of DNA from airborne conidia collected on filters.

Development of a nested qualitative real-time PCR assay to detect Aspergillus species DNA in clinical specimens

We adapted a nested Aspergillus PCR to a nested qualitative real-time format on a Light Cycler system. An evaluation using 134 clinical specimens showed that the real-time PCR assay significantly reduced the time for results to be made available without compromising sensitivity and was less labor-intensive. Its use will aid in the rapid diagnosis of invasive aspergillosis.

Towards a molecular diagnosis of invasive aspergillosis and disseminated candidosis

A lot of in-house polymerase chain reaction assays have been reported for diagnosis of invasive aspergillosis and disseminated candidosis. Encouraging results have been published to anticipate the diagnosis over the conventional microbiological methods. However, the absence of standardized methods has led to diverging results. As a consequence, these tests are not recognized as consensual diagnostic criteria, in contrast with some antigenemia detection kits. The major breakthrough for improving the results of these methods is the emergence of real-time technologies. This markedly improves the reliability of the PCR results by dramatically decreasing the risk of false positive results due to PCR products carryover. Moreover, using the quantitative results provided by this technique, this allows to rapidly compare the efficiency of primers, probes, and DNA extraction methods. Therefore, the hope is to identify the more specific and sensitive parameters to implement comparative studies. Automated DNA extraction should also be useful to achieve this goal. Whatever sophisticated technology is used, we still have to define the meaning of detecting nucleic acids in a given clinical sample. This seems simple in normally sterile anatomical sites but less obvious for example in respiratory specimens for invasive aspergillosis or in blood for candidosis in heavily colonized patients. Additional studies of the kinetics of fungal DNA are needed. The development of real-time technology should improve our knowledge in order to give the clinicians informative clues for making a decision.

Monochrome LightCycler PCR assay for detection and quantification of five common species of Candida and Aspergillus

Invasive fungal pathogens, especially in immunocompromised hosts, can result in life-threatening infections. Current laboratory/radiological methods for fungal identification are time-consuming and lack sensitivity and specificity. A monochrome, multiplex, real-time PCR assay for the identification and quantification of Candida albicans, Candida krusei, Candida tropicalis, Aspergillus flavus and Aspergillus fumigatus is described here. Detection of each of these fungi was specific and demonstrated 100 % concordance with biochemical/culture identification in all 60 isolates tested. Samples from 16 febrile neutropenic patients with haematological malignancies were also analysed and the utility of the assay in clinical samples was reconfirmed without false-negative results. The sensitivity of this assay was 0.1 pg fungal genomic DNA, corresponding to three cells, for C. albicans, C. krusei, C. tropicalis and A. flavus, and 0.01 pg fungal genomic DNA, i.e. less than one cell, for A. fumigatus. The analysis allows a low-cost, simple, rapid and sensitive alternative for clinical identification and quantification of these five common fungal species.

Aspergilluspolymerase chain reaction (PCR) diagnosis

In recent years novel molecular methods, notably polymerase chain reaction (PCR) assays, have been developed to improve the diagnosis of life-threatening invasive aspergillosis in patients at high risk, especially patients with malignant hematological disease. Early diagnosis and treatment are essential for adequate therapeutic management. Management, however, often remains difficult since most of the diagnostic tools used clinically at present either lack specificity or acceptable sensitivity. The clinical value, advantages and remaining problems of PCR approaches to detect the emerging fungal pathogen are reviewed.

Clinical significance of non-Candida fungal blood isolation in patients undergoing high-risk allogeneic hematopoietic stem cell transplantation (1993-2001)

BACKGROUND

The clinical relevance of mold isolated from blood cultures, even in severely immunosuppressed allogeneic hematopoietic stem cell transplantation (HSCT) recipients, remains uncertain. The authors hypothesized that isolation of non-Candida fungi from blood cultures in patients undergoing high-risk HSCT would have clinical significance.

METHODS

The authors reviewed the records of 73 allogeneic HSCT recipients between January 1, 1993 and January 1, 2001 in whom fungal species were isolated from blood cultures.

RESULTS

Fifty-two episodes of non-Candida fungemia occurred in 48 patients (66%) after a median of 10 days (range, 2-341) after transplantation. All 48 patients had indwelling intravascular catheters, and 23 patients (48%) had profound neutropenia. Thirty-five of 48 patients had received partially matched, related donor stem cell grafts (19 patients had 3-antigen-mismatched grafts); 35 patients had undergone T-cell depleted transplantation and 9 patients were receiving treatment for acute graft-versus-host disease. In 5 of 48 patients (10%), death was attributed to fungemia that occurred 8-11 days after the initial fungal blood culture was obtained; all 5 patients were age > 30 years. No deaths occurred in the younger age group (n = 22 patients; P = 0.05). In the 24 patients who did not receive systemic antifungal therapy, 4 deaths (17%) were attributed to infections with Penicillium (n = 2 patients), Epicoccum (n = 1 patient), or Penicillium plus Cladosporium species (n = 1 patient). Of the 24 patients who received amphotericin B, only 1 patient (4%) died as a result of a probable hematogenous Aspergillus species infection; this difference in outcome, however, was not significant (P = 0.2).

CONCLUSIONS

Most of the non-Candida fungal blood culture isolates in recipients of high-risk, mismatched donor transplantation were clinically nonsignificant. However, because these low-virulence saprophytes occasionally may cause life-threatening disease, a reevaluation of the existing diagnostic paradigm is needed so that clinically significant fungemia may be differentiated from pseudofungemia.