Detection and identification of fungal pathogens in blood by using molecular probes

Phylogeny and PCR identification of clinically important Zygomycetes based on nuclear ribosomal-DNA sequence data

A molecular database for all clinically important Zygomycetes was constructed from nucleotide sequences from the nuclear small-subunit (18S) ribosomal DNA and domains D1 and D2 of the nuclear large-subunit (28S) ribosomal DNA. Parsimony analysis of the aligned 18S and 28S DNA sequences was used to investigate phylogenetic relationships among 42 isolates representing species of Zygomycetes reported to cause infections in humans and other animals, together with commonly cultured contaminants, with emphasis on members of the Mucorales. The molecular phylogeny provided strong support for the monophyly of the Mucorales, exclusive of Echinosporangium transversale and Mortierella spp., which are currently misclassified within the Mucorales. Micromucor ramannianus, traditionally classified within Mortierella, and Syncephalastrum racemosum represent the basal divergences within the Mucorales. Based on the 18S gene tree topology, Absidia corymbifera and Rhizomucor variabilis appear to be misplaced taxonomically. A. corymbifera is strongly supported as a sister group of the Rhizomucor miehei-Rhizomucor pusillus clade, while R. variabilis is nested within Mucor. The aligned 28S sequences were used to design 13 taxon-specific PCR primer pairs for those taxa most commonly implicated in infections. All of the primers specifically amplified DNA of the size predicted based on the DNA sequence data from the target taxa; however, they did not cross-react with phylogenetically related species. These primers have the potential to be used in a PCR assay for the rapid and accurate identification of the etiological agents of mucormycoses and entomophthoromycoses.

Specific detection of Aspergillus species in blood and bronchoalveolar lavage samples of immunocompromised patients by two-step PCR

The increasing incidence of aspergillosis, a life-threatening infection in immunocompromised patients, emphasizes the need to improve the currently limited diagnostic tools. We developed a two-step PCR assay that specifically amplifies a region of the 18S rRNA gene that is highly conserved in Aspergillus species. A number of primers with the least homology to equivalent human or Candida gene sequences were screened for the pairs that gave the highest sensitivity and specificity. No cross-reaction with the wide range of fungal and bacterial pathogens so far tested was observed. This assay allows direct and rapid detection of down to 10 fg of Aspergillus DNA corresponding to 1 to 5 CFU per ml of blood. A total of 315 blood and bronchoalveolar lavage samples from 140 subjects, including 93 patients at risk for invasive fungal disease, were screened. The result was a 100% correlation between positive histology, culture, or high-resolution computed tomography findings and PCR results. The test specificity was 89%. Our data point to the considerable potential clinical value of this simple, specific, rapid, and inexpensive PCR assay for improving the means of early diagnosis of systemic aspergillosis in high-risk patients.

Approaches to fungal diagnosis in transplantation

The diagnosis of invasive fungal infection in patients undergoing solid organ or bone marrow transplantation remains a significant clinical challenge. Consideration of the epidemiology of these infections and host risk factors may be an important clue to a specific fungal diagnosis. Despite extensive investigation on methods such as serologic techniques to improve the rapid diagnosis of these infections, the diagnosis of invasive mycoses remains largely dependent on clinical presentation. For example, the signs and symptoms that result from angioinvasion of fungal organisms include pleuritic chest pain or hemoptysis. In a high-risk patient these findings can be important clues to invasive fungal infection. Cultures of opportunistic fungi in certain settings, such as Aspergillus in respiratory samples from immunosuppressed patients, may be associated with infection. Radiographic findings can also be useful to establish a diagnosis of infection. In patients with invasive aspergillosis as well as other angioinvasive moulds, chest CT scans may demonstrate lesions that are not visible on plain radiographs. Serodiagnosis of these infections remains largely investigational. Microbiological antifungal resistance has increasingly been reported, but in patients at high risk for serious fungal infection, including patients undergoing bone marrow and organ transplantation, antifungal resistance remains uncommon, particularly in Candida albicans. Higher doses of azoles should be used to treat patients with infections due to less susceptible yeasts and those with more serious infection. Prompt recognition of fungal infection combined with intensive antifungal therapy is needed for successful therapy.

Antifungal prophylaxis in neutropenia

Despite the widespread prophylactic use of antifungal agents in neutropenic patients, invasive fungal infections continue to emerge as major causes of morbidity and mortality. With the exception of fluconazole prophylaxis in allogeneic marrow transplant recipients, no firm conclusions can be drawn due to the lack of reliable, randomized trials. At the present time, it seems that antifungal chemoprophylaxis is more a matter of faith rather than science. Earlier diagnosis based on noninvasive diagnostic techniques and pre-emptive strategies may offer more promise than a liberal prophylactic approach.

Fungal infections of the central nervous system

This review discusses a practical approach to the patient with possible fungal infection of the central nervous system (CNS). Difficulties in establishing the diagnosis come from the nonspecific clinical syndromes (subacute meningitis, meningoencephalitis, and brain abscess) and the low isolation rate of fungi from cerebrospinal fluid (CSF). Helpful diagnostic clues often come from knowledge of the patient's geographic travels, risk factors, evidence of systemic organ infection, and fungal serologic tests. Standard and new antifungal agents are evaluated and the initial and suppressive drug management of the common fungal infections is presented.

New perspectives in the diagnosis of systemic fungal infections

Profound and prolonged neutropenia following chemotherapy is a major risk factor for systemic fungal infections. Mortality associated with disseminated fungal infection is high, and treatment with conventional amphotericin B is complicated by renal toxicity. Candida and Aspergillus are among the major pathogens in these patients. Many patients remaining neutropenic over a prolonged period of time will receive empirical antifungal therapy. The clinical and laboratory diagnoses of these infections are neither sensitive nor specific and are generally limited in the early detection of invasive fungal infection. However, several new approaches to diagnosis are being developed, which should be translated into routine practice, based on a greater understanding of the pathogenesis of systemic fungal infection and virulence determinants of fungal pathogens. These include antigen detection and polymerase chain reaction. Patients with presumed fungal infection require more intense and accurate monitoring for signs of disseminated infection. Early diagnosis may guide appropriate treatment and prevent mortality. Continued development of commercial tests should help achieve the objective of definitive diagnostic tests for systemic fungal infections.

Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species

Nucleic Acid Sequence Based Amplification (iNASBA), an isothermal amplification technique for nucleic acids, was evaluated for the identification of medically important Candida species using primers selected from 18S rRNA sequences conserved in fungi. An RNA fragment of 257 nucleotides was amplified for Candida albicans. Nineteen different fungi were tested for rRNA amplification with the NASBA. All were positive when analyzed on agarose gel, whereas human RNA was negative. For the identification of Candida species, NASBA amplification products were analyzed in an enzyme bead-based detection format, using species-specific biotinylated probes and a generic Candida HRPO probe or a membrane-based system using biotinylated probes and avidin-HPRO. Discrimination of the major human pathogenic Candida spp. was based on a panel of biotinylated probes for C. krusei, C. tropicalis, C. albicans, C. glabrata, and C. lusitaniae. Using rRNA dilutions obtained from pure cultures of C. albicans, the combination of NASBA and the enzymatic bead-based detection yielded a sensitivity equivalent to 0.01 CFU. In a model system using 1 ml of artificially contaminated blood as few as 1-10 CFU of C. albicans could be detected. Testing of 68 clinical blood samples from patients suspected of candidemia showed that eight samples were positive for C. albicans and one for C. glabrata. Testing of 13 clinical plasma samples from patients suspected of fungemia identified the presence of C. albicans in two specimens. The whole procedure of sample preparation, amplification and identification by hybridization can be performed in 1 day. This speed and the observed sensitivity of the assay make the NASBA a good alternative to PCR for the detection of candidemia.

Infections in recipients of blood and marrow transplantation

The approach to infections in blood and marrow transplant (BMT) recipients involves an understanding of clinical infection syndromes and the natural history of individual infections, taken in the context of patterns of immunosuppression after transplantation and mechanisms underlying immune system reconstitution over time. The conditioning regimen used to prepare the host is a major determinant of host tissue injury and may lead to mucositis or diarrhea, facilitating transmucosal origin of bloodstream infections. Infectious risk also differs between autologous and allogeneic grafts as a consequence of ongoing immunosuppression from graft-versus-host disease and its therapy. Post-transplant complications may mimic infectious processes, and multiple infections may occur in one patient at the same time. Thus, the BMT patient with suspected infection should be evaluated in the context of pretransplant exposure history (infectious disease serologies), conditioning regimen, available culture data from nonsterile mucosal surfaces, previous and recent infections, contemporary transplant complications, and the current degree and duration of neutropenia, cellular immunodeficiency, and hypogammaglobulinemia.

PCR and other non-culture methods for diagnosis of invasive Candida infections in allogeneic bone marrow and solid organ transplant recipients

In this prospective study 197 serum and 152 urine samples were collected from 40 bone marrow and solid organ transplant recipients with clinically suspected invasive fungal infection before, during and after empirical treatment with lipid formulation of amphotericin B or fluconazole. Serum was analysed by Candida polymerase chain reaction (PCR) and urine by measurement of D/L-arabinitol ratio. One serum from each patient was also tested for concentration of (1-->3)-beta-glucan and two commercial Candida antigens. Invasive fungal infection was diagnosed in four candidosis and one aspergillosis patients (13%). Positive PCR, elevated D/L-arabinitol ratio, (1-->3)-beta-glucan concentration and antigens were detected in nine, 15, 17, and seven patients, respectively. The agreement between PCR and D/L-arabinitol assays was poor. However, 56% agreement was observed between positive PCR and beta-glucan and/or antigen assays, and 60% agreement between positive D/L-arabinitol and beta-glucan and/or antigen assays. Combination of several non-culture assays is needed to diagnose invasive fungal infection in high-risk transplant recipients. No single test was sufficient for diagnosis.

The evolving role of direct amplification tests in diagnosing osteoarticular infections caused by mycobacteria and fungi

Polymerase chain reaction-based direct amplification tests have been developed for many species of mycobacteria and fungi. Their applications in clinical medicine are evolving rapidly but are still not fully defined. Uncritical use of direct amplification tests for individual patients without a clear understanding of their limitations and how to integrate their results with other clinical and laboratory data may lead to incorrect patient management. Although presently available tests seem to be clinically useful when properly applied, further technical development and clinical studies are needed before these powerful diagnostic tools achieve their full value.

Interventional antimicrobial therapy in febrile neutropenic patients

In febrile neutropenic patients, prompt empiric antimicrobial intervention is mandatory. Numerous studies have demonstrated the benefit of broad-spectrum beta-lactams active against Gram-negative aerobes as well as against streptococci and Staphylococcus aureus in this setting. With this interventional strategy, a reduction of infection-related mortality to < or = 10% of patients undergoing intensive remission induction or consolidation chemotherapy could be obtained. Thereby, subgroups of patients have been identified who require an empiric modification of antimicrobial treatment, e.g., patients with catheter-related infections, with pulmonary infiltrates, or with unexplained fever (FUO) not responding to first-line antibacterials. In two consecutive, prospectively randomized trials conducted by the German Paul Ehrlich Society it could be shown that empiric antifungal therapy is beneficial for second-line treatment in patients with persistent FUO and improves first-line treatment results in patients with lung infiltrates. The addition of glycopeptides, however, should be restricted to patients with catheter-related infections due to coagulase-negative staphylococci or with infections due to multiresistant Gram-positive pathogens.

A polymerase chain reaction enzyme immunoassay for diagnosing infection caused by Aspergillus fumigatus

AIM

To develop a polymerase chain reaction enzyme immunoassay (PCR-EIA) to measure levels of circulating aspergillus DNA in invasive aspergillosis caused by Aspergillus fumigatus.

METHODS

The PCR reaction was based on primers from the 18s rRNA gene. Binding of the product to a streptavidin coated microtitration plate was mediated by a biotinylated capture probe. The product was digoxigenylated during PCR and this was the tag to which antibody was bound in the subsequent EIA.

RESULTS

The optical density (OD) endpoint was < 0.1 in 10 sera from neutropenic patients with no evidence of invasive aspergillosis, and in 10 sera from nonneutropenic patients with bacterial pneumonia (group 1). The OD from five of 12 patients with allergic bronchopulmonary aspergillosis (ABPA) (group 2), three with an aspergilloma (group 3), and five with possible invasive aspergillosis (group 4) was > or = 0.1. In 63 sera from 33 cases of proven invasive aspergillosis (group 5) an OD > or = 0.1 was achieved in 48 sera from 30 patients. The maximum OD was 0.510. The level fell in survivors and gradually rose in fatal cases.

CONCLUSIONS

This assay validated the concept of diagnosing invasive aspergillosis by measuring levels of circulating fungal DNA in serum.

PCR-restriction enzyme analysis for detection of Candida DNA in blood from febrile patients with hematological malignancies

Blood samples were drawn daily from 72 patients who had hematological malignancies, neutropenia, and fever and who had failed to respond to broad-spectrum antibiotics. Each sample was used for conventional fungal blood cultures and for detection and identification of Candida DNA by a PCR method with subsequent restriction enzyme analysis (REA) recently developed in our laboratory. The PCR method was able to detect five CFU of Candida spp. per ml of blood, and subsequent REA of the amplicons allowed the identification of the Candida species most commonly implicated in cases of candidiasis. Thirty-one patients were PCR-REA positive, and four of these patients were also culture positive. The ultimate diagnosis for 13 of these patients and 1 patient who was PCR-REA negative was disseminated candidiasis (confirmed by clinical data, multiple cultures, histology, autopsy, and/or ultrasonographic evidence of hepatosplenic candidiasis). The molecular method is significantly more sensitive than conventional fungal blood cultures and has a high negative predictive value (97.5%) for the development of disseminated candidiasis in neutropenic patients.

Rapid diagnostic methods in the detection of sepsis

Any delay in the management of infection is deleterious, especially in patients whose illness is severe. It is of paramount importance to shorten this delay. This article emphasizes the different ways to reach this goal, including the use of new biologic markers, such as cytokines or procalcitonin.

Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system

Invasive fungal disease often plays an important role in the morbidity and mortality of immunocompromised patients. The poor sensitivity of current fungal blood culture and histological practices has led to the development of highly sensitive and specific molecular techniques, such as the PCR. Sequence variability of the internal transcribed spacer 2 (ITS2) region of fungi is potentially useful in rapid and accurate diagnosis of clinical fungal isolates. PCR with fungus-specific primers targeted toward conserved sequences of the 5.8S and 28S ribosomal DNA (rDNA) results in amplification of the species-specific ITS2 regions, which are variable in amplicon length. We have made use of the ABI PRISM 310 genetic analyzer and the ABI PRISM 310 GeneScan analysis software for the determination of variable size differences of the ITS2 region of clinically important fungi, including Candida and non-Candida yeasts, Aspergillus species, and a variety of dermatophytes. No cross-reaction occurred when samples were tested against human and bacterial genomic DNA. We have found that most clinically significant fungal isolates can be differentiated by this method, and it therefore serves to be a promising tool for the rapid (<7 h) diagnosis of fungemia and other invasive fungal infections.

Molecular biology for the critical care physician. Part II: where are we now?

The extraordinary technical developments in molecular biology are having a profound impact in clinical medicine. The contribution of recombinant DNA technology in defining the molecular pathology of common disorders and of diagnostic molecular techniques for detection of infectious organisms are used as examples to demonstrate the clinical relevance of these developments. Finally, the potential use of DNA as a therapeutic drug (gene therapy) is addressed.

Respiratory infections in immunocompromised patients

HIV disease has been dramatically reduced in the developed world by the introduction of highly active antiretroviral therapy, with implications that prophylactic therapy against opportunistic infections may be stopped; however, tuberculosis is an escalating problem in the HIV-infected and HIV-noninfected populations worldwide. Compliance with effective treatment regimens, especially through directly observed therapy, remains the cornerstone of tuberculosis control strategies. Although tuberculosis prophylaxis is of benefit for tuberculin skin reactors with HIV in the developed world, several reservations are voiced about this approach in resource-poor settings. Recent advances in technology, particularly in antigen-specific systems, have revolutionized the understanding of HIV immunology and helped to elucidate the mechanisms of pathogenesis in diseases such as cytomegalovirus. In bone marrow transplantation and solid-organ transplantation patients, quantitative polymerase chain reaction (PCR) to predict cytomegalovirus disease is an important advance, and patients who undergo bone marrow transplantation, CT scanning has proven useful in the diagnosis of pulmonary aspergillosis.

Contaminations occurring in fungal PCR assays

Successful in vitro amplification of fungal DNA in clinical specimens has been reported recently. In a collaboration among five European centers, the frequency and risk of contamination due to airborne spore inoculation or carryover contamination in fungal PCR were analyzed. The identities of all contaminants were specified by cycle sequencing and GenBank analysis. Twelve of 150 PCR assays that together included over 2,800 samples were found to be contaminated (3.3% of the negative controls were contaminated during the DNA extraction, and 4.7% of the PCR mixtures were contaminated during the amplification process). Contaminants were specified as Aspergillus fumigatus, Saccharomyces cerevisiae, and Acremonium spp. Further analysis showed that commercially available products like zymolyase powder or 10x PCR buffer may contain fungal DNA. In conclusion, the risk of contamination is not higher in fungal PCR assays than in other diagnostic PCR-based assays if general precautions are taken.

Aspergillus fumigatus and aspergillosis

Aspergillus fumigatus is one of the most ubiquitous of the airborne saprophytic fungi. Humans and animals constantly inhale numerous conidia of this fungus. The conidia are normally eliminated in the immunocompetent host by innate immune mechanisms, and aspergilloma and allergic bronchopulmonary aspergillosis, uncommon clinical syndromes, are the only infections observed in such hosts. Thus, A. fumigatus was considered for years to be a weak pathogen. With increases in the number of immunosuppressed patients, however, there has been a dramatic increase in severe and usually fatal invasive aspergillosis, now the most common mold infection worldwide. In this review, the focus is on the biology of A. fumigatus and the diseases it causes. Included are discussions of (i) genomic and molecular characterization of the organism, (ii) clinical and laboratory methods available for the diagnosis of aspergillosis in immunocompetent and immunocompromised hosts, (iii) identification of host and fungal factors that play a role in the establishment of the fungus in vivo, and (iv) problems associated with antifungal therapy.

Serum is more suitable than whole blood for diagnosis of systemic candidiasis by nested PCR

PCR assays for the diagnosis of systemic candidiasis can be performed either on serum or on whole blood, but results obtained with the two kinds of samples have never been formally compared. Thus we designed a nested PCR assay in which five specific inner pairs of primers were used to amplify specific targets on the rRNA genes of Candida albicans, C. tropicalis, C. parapsilosis, C. krusei, and C. glabrata. In vitro, the lower limit of detection of each nested PCR assay was 1 fg of purified DNA from the corresponding Candida species. In rabbits with candidemia of 120 minutes' duration following intravenous (i.v.) injection of 10(8) CFU of C. albicans, the sensitivities of the PCR in serum and whole blood were not significantly different (93 versus 86%). In other rabbits, injected with only 10(5) CFU of C. albicans, detection of candidemia by culture was possible for only 1 min, whereas DNA could be detected by PCR in whole blood and in serum for 15 and 150 min, respectively. PCR was more often positive in serum than in whole blood in 40 culture-negative samples (27 versus 7%; P < 0.05%). Lastly, experiments with rabbits injected i.v. with 20 or 200 microgram of purified C. albicans DNA showed that PCRs were positive in serum from 30 to at least 120 min after injection, suggesting that the clearance of free DNA is slow. These results suggest that serum is the sample of choice, which should be used preferentially over whole blood for the diagnosis of systemic candidiasis by PCR.

[Fungal nucleic acid detection for invasive aspergillosis]

A universal PCR-assay for the detection of fungal DNA was compared with microscopy and culture for the diagnosis of invasive aspergillosis using 78 samples from 42 patients. Eighteen patients were suffering from invasive aspergillosis, 5 patients were colonized with Aspergillus in the respiratory tract, 19 patients did not show any sign of aspergillosis. Samples from 6 of the 18 patients with invasive aspergillosis were microscopically positive with true mycelia, 15 of 18 grew Aspergillus in culture, 16 of 18 were PCR-positive. The combination of microscopy and culture led to the diagnosis in 17 of 18 patients, the combination of microscopy and PCR in 16 of 18 and the combination of culture and PCR in all the 18 patients. For 3 of 18 patients, PCR was the diagnostic key: in 2 biopsies the histologically detected fungal elements were identified as Aspergillus, in 3 bronchial lavages from 1 patients nothing but PCR was positive for Aspergillus. Four out of 5 culture positive patients with Aspergillus colonization were also PCR positive; one out of 19 patients without aspergillosis was culture positive, 3 out of 19 were falsely PCR positive. Candida colonization in the upper respiratory tract or Pneumocystis carinii pneumonia did not lead to false positive Aspergillus-PCR results. In conclusion, the evaluated fungal PCR-assay can supplement conventional methods for the diagnosis of invasive aspergillosis.

PCR detection of DNA specific for Trichosporon species in serum of patients with disseminated trichosporonosis

Deep-seated trichosporonosis is a lethal opportunistic infection that disseminates rapidly and widely in immunocompromised patients, and early diagnosis is crucial for the treatment of this infection. We developed a novel nested-PCR assay that detects DNA specific for clinically important strains of Trichosporon in serum samples from patients with disseminated trichosporonosis. In this assay, two sets of oligonucleotide primers were derived from the sequence of 26S rRNA genes of Trichosporon asahii. The specific fragment was amplified from T. asahii and T. mucoides, but not from other microorganisms, including some other basidiomycetous fungi (Cryptococcus, Malassezia, Rhodotorula, and Sporobolomyces). Target DNA was detected by the nested PCR with as little as 5 fg of the extracted DNA of T. asahii. In a study using 11 clinical samples, the specific fragment was detected by the nested PCR in 64% (7 of 11) of sera from patients with histologically diagnosed disseminated trichosporonosis, while glucuronoxylomannan antigen was detected in only 54% (6 of 11) of the samples. Our new nested-PCR assay using serum samples can be performed repeatedly throughout the course of the disease. In addition, not only can it be used for early diagnosis of trichosporonosis, but it may also be beneficial for monitoring its progress or response to therapy.

Identification of contaminating fungal DNA sequences in Zymolyase

When different preparations of Zymolyase were included in the pretreatment protocol of a panfungal PCR assay using a primer system for the 18S rRNA gene, an amplification product occurred in negative controls. The amplified fragment showed 100.0% sequence identity to the Saccharomyces sensu stricto complex and Kluyveromyces lodderae. Lyticase, lysing enzymes, and proteinase K appeared to be free from fungal DNA.

Unrelated donor bone marrow transplantation in adults: some current controversies

The results of unrelated donor bone marrow transplantation are continually improving. These improved results are due to a better understanding of the complications of the procedure and the devising of strategies to avoid them. Nonetheless, many problems remain. This review will address some of the major controversies of the field including the indications for UD-BMT, infection, GVHD prophylaxis and treatment and whether UD-BMT should only be performed in specialist centres. Conclusions will be supported by evidence from the limited published literature and the authors' experience in 3 major transplant centres.

Rapid identification of up to three Candida species in a single reaction tube by a 5' exonuclease assay using fluorescent DNA probes

We used fungus-specific PCR primers and species-specific DNA probes to detect up to three Candida species in a single reaction tube by exploiting the 5' to 3' exonuclease activity of Taq DNA polymerase. Probes to the internal transcribed spacer region of the rRNA gene were labeled at the 5' end with one of three fluorescent reporter dyes, 6-carboxy-fluorescein (FAM), tetrachloro-6-carboxy-fluorescein (TET), or hexachloro-6-carboxy-fluorescein (HEX), and at the 3' end with a quencher dye, 6-carboxy-tetramethyl-rhodamine. During PCR amplification, each reporter dye emits a characteristic wavelength as it is cleaved from its specific target DNA and from the quencher dye. Therefore, signals from up to three probes can be detected simultaneously during the PCR assay. Six probes were designed for use in this study: CA-FAM, CT-TET, and CP-HEX were added to one tube to simultaneously detect the typically fluconazole-sensitive species C. albicans, C. tropicalis, and C. parapsilosis, respectively. CG-FAM and CK-TET were added to a second tube to simultaneously detect the typically more innately fluconazole-resistant species C. glabrata and C. krusei, respectively. All-CAN-TET, a Candida genus probe, was added to a third tube to detect DNAs from all Candida species tested. DNAs recovered from 61 blood culture bottles, including 23 positive for C. albicans, 18 positive for C. glabrata, 6 positive for C. tropicalis, 6 positive for C. krusei, 5 positive for C. parapsilosis, and 3 positive for mixed fungemias, were tested. Control samples included those from blood culture bottles with no growth (n = 10) or from patients with confirmed bacteremia (n = 10). Probes detected and correctly identified the organisms in 58 of 61 specimens (95.1%) and gave no false-positive results. This method is simple and rapid and does not require post-PCR hybridization and incubation steps. It is sensitive and specific for the detection and identification of Candida species from blood culture bottles, including those containing mixtures of Candida species, and should facilitate an earlier specific diagnosis, leading to more appropriately targeted antifungal drug therapy.

Molecular methods for epidemiological and diagnostic studies of fungal infections

Over the past two decades there has been a remarkable increase in the incidence of invasive fungal infections. Molecular methods, such as karyotyping, restriction analysis and polymerase chain reaction (PCR), have now been applied to improve our current understanding of the epidemiology of these fungal infections. For example, investigations on nosocomial outbreaks of fungal infections have been greatly facilitated by molecular methods. In addition, the ability to diagnose and identify deep-seated mycoses may be enhanced by the use of molecular techniques. In the near future it is possible that PCR-based methods will supplement, or perhaps even replace, traditional methods for detection of Candida albicans blood stream infections, invasive aspergillosis and Pneumocystis carinii pneumonia. This review examines the progress of molecular biology into the clinical arena of fungal epidemiology, laboratory identification and diagnosis.

Detection of PCR-amplified fungal DNA by using a PCR-ELISA system

In order to speed up and standardize polymerase chain reaction (PCR)-based detection of medically important fungi in clinical samples we established a combination of commercially available kits for DNA extraction, PCR amplification and detection of the amplicons. The PCR plate assay proved to be as sensitive and specific as our previously published assay (5 cfu ml(-1) blood). Moreover, in a selected group of patients, all patients with proven and probable invasive fungal infection were found to be PCR-positive. Thus the PCR plate assay was found to be a sensitive, technically simplified and standardized method with potential for adaptation to automation.

Detection of Aspergillus fumigatus PCR products by a microtitre plate based DNA hybridisation assay

AIMS

To develop a DNA based plate hybridisation assay for the detection of polymerase chain reaction (PCR) products amplified from Aspergillus fumigatus DNA; and to determine the sensitivity of this technique and compare it with Southern blotting.

METHODS

A half-log dilution series of DNA extracted from A fumigatus was amplified with specific primers, one of which was 5' end labelled with biotin. PCR products were subsequently detected by agarose gel electrophoresis, Southern blotting, and binding of the products to a streptavidin coated microtitre well, followed by non-radioactive colorimetric detection. Amplification was carried out 10 times for each DNA dilution and a plot of initial DNA concentration against signal intensity was made.

RESULTS

A DNA concentration of 1.5 pg could be detected by agarose gel electrophoresis and Southern blotting with a non-radioactively labelled aspergillus specific probe; 1.5 pg was detectable by streptavidin binding of the PCR products to a microtitre plate. The signal from the microtitre plate detection was proportional to the amount of DNA in the PCR reaction on a log-log scale between 100 and 1 pg of DNA.

CONCLUSIONS

A DNA based plate hybridisation assay for the detection of A fumigatus PCR products is as sensitive as Southern blotting. However, results are obtained in three hours rather than the three days required for agarose gel electrophoresis, blotting, hybridisation, and detection.

Detection of antigen in sera of patients with invasive aspergillosis: intra- and interlaboratory reproducibility. The Dutch Interuniversity Working Party for Invasive Mycoses

The intra- and interlaboratory reproducibilities of a commercial sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of Aspergillus galactomannan in serum (Platelia Aspergillus; Sanofi Diagnostics Pasteur, Marnes-La-Coquette, France) were evaluated in six laboratories of university hospitals. Twenty serum samples were obtained from 12 neutropenic patients including 6 with invasive aspergillosis. These samples were blinded and sent to each center together with eight blinded ELISA-negative serum samples spiked with known concentrations of galactomannan. The centers were provided with ELISA microtiter plates from a single batch and a detailed protocol. Ten clinical samples showed ELISA reactivity, while 10 samples were ELISA negative. The mean coefficient of variation (CV) of the optical density values was 4.24% within a single assay and 25.6% between runs. The interassay CV of the ratios for the serum samples tested was 18.6%. Analysis of ordinal interpretation of the ELISA result (i.e., negative, gray zone, or positive) showed excellent reproducibility. Recalculation of the cutoff values for positive and negative samples suggested that the cutoff level recommended by the manufacturer could be lowered from 1.0 to 0.8 for negative samples and from 1.5 to 1.0 for positive samples. The intra- and interlaboratory reproducibilities were excellent when the ELISA results were interpreted as ordinal data, but considerable variation in optical density values and, to a lesser extent, in the ratios for the serum samples tested, was observed between runs. High assay variability was also found for serum samples spiked with known concentrations of galactomannan. Therefore, antigen titers in serum samples from a single patient, measured in different runs, should be compared with caution.

Rapid extraction of genomic DNA from medically important yeasts and filamentous fungi by high-speed cell disruption

Current methods of DNA extraction from different fungal pathogens are often time-consuming and require the use of toxic chemicals. DNA isolation from some fungal organisms is difficult due to cell walls or capsules that are not readily susceptible to lysis. We therefore investigated a new and rapid DNA isolation method using high-speed cell disruption (HSCD) incorporating chaotropic reagents and lysing matrices in comparison to standard phenol-chloroform (PC) extraction protocols for isolation of DNA from three medically important yeasts (Candida albicans, Cryptococcus neoformans, and Trichosporon beigelii) and two filamentous fungi (Aspergillus fumigatus and Fusarium solani). Additional extractions by HSCD were performed on Saccharomyces cerevisiae, Pseudallescheria boydii, and Rhizopus arrhizus. Two different inocula (10(8) and 10(7) CFU) were compared for optimization of obtained yields. The entire extraction procedure was performed on as many as 12 samples within 1 h compared to 6 h for PC extraction. In comparison to the PC procedure, HSCD DNA extraction demonstrated significantly greater yields for 10(8) CFU of C. albicans, T. beigelii, A. fumigatus, and F. solani (P < or = 0.005), 10(7) CFU of C. neoformans (P < or = 0.05), and 10(7) CFU of A. fumigatus (P < or = 0.01). Yields were within the same range for 10(8) CFU of C. neoformans and l0(7) CFU of C. albicans for both HSCD extraction and PC extraction. For 10(7) CFU of T. beigelii, PC extraction resulted in a greater yield than did HSCD (P < or = 0.05). Yields obtained from 10(8) and 10(7) CFU were significantly greater for filamentous fungi than for yeasts by the HSCD extraction procedure (P < 0.0001). By the PC extraction procedure, differences were not significant. For all eight organisms, the rapid extraction procedure resulted in good yield, integrity, and quality of DNA as demonstrated by restriction fragment length polymorphism, PCR, and random amplified polymorphic DNA. We conclude that mechanical disruption of fungal cells by HSCD is a safe, rapid, and efficient procedure for extracting genomic DNA from medically important yeasts and especially from filamentous fungi.

Panfungal PCR assay for detection of fungal infection in human blood specimens

A novel panfungal PCR assay which detects the small-subunit rRNA gene sequence of the two major fungal organism groups was used to test whole-blood specimens obtained from a series of blood or bone marrow transplant recipients. The 580-bp PCR product was identified after amplification by panfungal primers and hybridization to a 245-bp digoxigenin-labeled probe. The lower limit of detection of the assay was approximately four organisms per milliliter of blood. Multiple whole-blood specimens from five patients without fungal infection or colonization had negative PCR results. Specimens from 11 infected patients had positive PCR results. Blood from three patients with pulmonary aspergillosis had positive PCR results: one patient's blood specimen obtained in the week prior to the diagnosis of infection by a positive bronchoalveolar lavage fluid culture result was positive by PCR, and blood specimens obtained from two patients 1 to 2 days after lung biopsy and which were sterile by culture were positive by PCR. The blood of four patients with candidemia, three patients with mixed fungal infections, and one patient with fusariosis also had positive PCR signals. The panfungal PCR assay can detect multiple fungal genera and may be used as an adjunct to conventional methods for the detection of fungal infection or for describing the natural history of fungal infection. Further studies are needed to define the sensitivity and specificity of this assay for the diagnosis of fungal infection prior to the existence of other clinical or laboratory indications of invasive fungal infection.

Fungal infection in the intensive care unit

Fungal infection in critically ill patients is an increasingly prevalent problem. Candida spp. cause the majority of these infections in ICU. They occur most commonly in patients with severe underlying illness, multiple courses of antibiotics and intravascular catheters. Clinical diagnosis is difficult due to nonspecific signs and the frequent occurrence of widespread superficial colonization with Candida spp. in ventilated patients. Most patients are diagnosed using inferential evidence of infection, such as persistent pyrexia despite antibiotics, raised serum C-reactive protein and the presence of individual risk factors. Amphotericin B and fluconazole are the most commonly used anti-fungals dependent on the identity of the fungus. Most of these infections are endogenous; however, a proportion may be caused via the hands of healthcare staff or contaminated medical equipment.

Comparison of different methods for extraction of DNA of fungal pathogens from cultures and blood

Five commercially available extraction kits and an in-house DNA extraction method for the release of DNA from Candida albicans and Aspergillus niger cells were assessed for sensitivity, purity, duration, and cost. All commercially available kits helped to shorten the duration of DNA extraction. However, the sensitivity varied from 1 to 1,000 fungal cells/ml and costs varied from $0.10 to 2.30. The QIAmp Tissue kit was the commercially available assay that yielded the same sensitivity and purity of fungal DNA release as the in-house protocol but was the most expensive method. In comparing these two extraction protocols, a 99% concordance of PCR results for 125 blood samples analyzed could be demonstrated.