Dynamics and prognostic value of plasma cell-free DNA PCR in patients with invasive aspergillosis and mucormycosis

Aspergillus species and Mucorales agents are the primary etiologies of invasive fungal disease (IFD). Biomarkers that predict outcomes are needed to improve care. Patients diagnosed with invasive aspergillosis and mucormycosis using plasma cell-free DNA (cfDNA) PCR were retested weekly for 4 weeks. The primary outcome included all-cause mortality at 6 weeks and 6 months based on baseline cycle threshold (CT) values and results of follow-up cfDNA PCR testing. Forty-five patients with Aspergillus and 30 with invasive Mucorales infection were retested weekly for a total of 197 tests. Using the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium (EORTC/MSG) criteria, 30.7% (23/75), 25.3% (19/75), and 38.7% (29/75) had proven, probable, and possible IFD, respectively. In addition, 97.3% (73/75) were immunocompromised. Baseline CT increased significantly starting at week 1 for Mucorales and week 2 for Aspergillus. Aspergillosis and mucormycosis patients with higher baseline CT (CT >40 and >35, respectively) had a nonsignificantly higher survival rate at 6 weeks, compared with patients with lower baseline CT. Mucormycosis patients with higher baseline CT had a significantly higher survival rate at 6 months. Mucormycosis, but not aspergillosis patients, with repeat positive cfDNA PCR results had a nonsignificantly lower survival rate at 6 weeks and 6 months compared with patients who reverted to negative. Aspergillosis patients with baseline serum Aspergillus galactomannan index <0.5 and <1.0 had significantly higher survival rates at 6 weeks when compared with those with index ≥0.5 and ≥1.0, respectively. Baseline plasma cfDNA PCR CT can potentially be used to prognosticate survival in patients with invasive Aspergillus and Mucorales infections.

IMPORTANCE

We show that Aspergillus and Mucorales plasma cell-free DNA PCR can be used not only to noninvasively diagnose patients with invasive fungal disease but also to correlate the baseline cycle threshold with survival outcomes, thus potentially allowing the identification of patients at risk for poor outcomes, who may benefit from more targeted therapies.

Utility of an in-house real-time PCR in whole blood samples as a minimally invasive method for early and accurate diagnosis of invasive mould infections

INTRODUCTION

Invasive mould infections (IMIs) are a leading cause of death in patients with compromised immune systems. Proven invasive mould infection requires detection of a fungus by histopathological analysis of a biopsied specimen, sterile culture, or fungal DNA amplification by PCR in tissue. However, the clinical performance of a PCR assay on blood samples taken from patients suspected of invasive mould disease has not been fully evaluated, particularly for the differential diagnosis of invasive aspergillosis (IA) and invasive Mucormycosis (IM).

OBJECTIVES

To assess the diagnostic utility of our previously validated in-house real-time PCR in blood samples for diagnosis of invasive aspergillosis and mucormycosis in patients with suspected invasive mould infection.

METHODS

All patients with suspected invasive mould infection were prospectively enrolled from May 2021 to July 2021. Conventional fungal diagnosis was performed using tissue and respiratory samples. In-house PCR was performed on blood samples and its diagnostic performance evaluated.

RESULTS

A total of 158 cases of suspected invasive mould infection were enrolled in the study. The sensitivity and specificity of in-house PCR performed on blood samples was found to be 92.5% and 81.4% respectively for diagnosis of probable IA, and 65% and 84.62% respectively for diagnosis of proven and probable IM. It was also able to detect 3 out of 5 cases of possible IM where no other microbiological evidence of IM was obtained.

CONCLUSIONS

This assay could be helpful in minimally invasive diagnosis of IMIs for patients in whom invasive sampling is not feasible, especially as a preliminary or screening test. It can help in early diagnosis, anticipating conventional laboratory confirmation by days or weeks. Possible correlation between fungal load and mortality can help in initiating aggressive treatment for patients with high initial fungal load.

Galactomannan testing and Aspergillus PCR in same-day bronchoalveolar lavage and blood samples for diagnosis of invasive aspergillosis

In recent years galactomannan antigen testing (GM) and also Aspergillus PCR have become increasingly important for diagnosis of invasive aspergillosis (IA). Whether or not these tests need to be performed with bronchoalveolar lavage fluid (BALF; i.e., primary site of infection), or testing of blood samples is sufficient, remains, however, a matter of debate. We evaluated the diagnostic performance of GM ELISA, and Aspergillus PCR by using BALF samples and blood samples obtained at the same day from a total of 53 immunocompromised patients (16 with probable/proven IA and 37 with no evidence of IA according to the revised EORTC/MSG criteria; 38 patients with hematological malignancies were prospectively enrolled at the Medical University of Graz, Austria, 15 patients with mixed underlying diseases at the Mannheim University Hospital). Patients with possible IA were excluded from this analysis. A total of 34/53 (64%) of all patients and 12/16 (75%) of patients with probable/proven IA received mold-active antifungal prophylaxis/therapy at the time of the BALF procedure. Sensitivities of GM and Aspergillus PCR were 38% and 44% in BALF, and 31% and 0% in blood, respectively. Best sensitivity (75%) for detecting proven/probable IA was achieved when BALF Aspergillus PCR, BALF GM (>1.0 ODI), BALF-culture and serum-GM (>0.5 ODI) were combined (specificity 95%). In conclusion, sensitivities of the evaluated diagnostic tests-when interpreted on their own-were low in BALF and even lower in blood, sensitivities increased markedly when diagnostic tests were combined.

Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease

Diagnosis of life-threatening deep-seated infections currently requires invasive sampling of the infected tissue to provide a microbiologic diagnosis. These procedures can lead to high morbidity in patients and add to healthcare costs. Here we describe a novel next-generation sequencing assay that was used to detect pathogen-derived cell-free DNA in peripheral blood of patients with biopsy-proven invasive fungal infections. The noninvasive nature of this approach could provide rapid, actionable treatment information for invasive fungal infections when a biopsy is not possible.

Comparison of Pneumocystis nucleic acid and antibody profiles and their associations with other respiratory pathogens in two Austrian pig herds

Pneumocystis carinii f. sp. suis (PCS) nucleic acid and antibody profiles on two Austrian-farrow-to-finish farms were investigated. Furthermore, associations with other respiratory pathogens were evaluated. Respiratory specimen and sera from pigs of five age classes between the 1st week and the 3rd month of life as well as samples from sows were analyzed. On Farm A, PCS infection occurred early in life. The suckling piglets were already infected in the 1st week of life and the pigs remained positive until the 3rd month of life. On Farm B, pigs were infected later, between 3 and 4 months of age. The maximum PCS nucleic acid load on Farm A was 8.3 log10 genome copies/mL BALF, whereas on Farm B the PCS burden was significantly lower, with 4.0 log10 genome copies/mL BALF. Anti-PCS antibodies were detected in sows, as maternal antibodies in suckling piglets and as an immunological reaction to infection. On both farms, PCS infection was accompanied by several co-infections. On Farm A, there were concurrent infections with PRRSV, a virulent strain of Haemophilus parasuis, and Mycoplasma hyopneumoniae. On Farm B, PCS was accompanied by infections with swine influenza virus, Mycoplasma hyopneumoniae, and a non-virulent strain of Haemophilus parasuis. The results clearly show that the PCS profiles can vary between farms. Younger pigs may be more susceptible as they had higher PCS burdens. It is possible that PCS may contribute to a respiratory disease in pigs and further investigation of its potential role is warranted.

Molecular assays for the diagnosis of sepsis in neonates

BACKGROUND

Microbial cultures for diagnosis of neonatal sepsis have low sensitivity and reporting delay. Advances in molecular microbiology have fostered new molecular assays that are rapid and may improve neonatal outcomes.

OBJECTIVES

To assess the diagnostic accuracy of various molecular methods for the diagnosis of culture-positive bacterial and fungal sepsis in neonates and to explore heterogeneity among studies by analyzing subgroups classified by gestational age and type of sepsis onset and compare molecular tests with one another.

SEARCH METHODS

We performed the systematic review as recommended by the Cochrane Diagnostic Test Accuracy Working Group. On 19 January 2016, we searched electronic bibliographic databases (the Cochrane Library, PubMed (from 1966), Embase (from 1982), and CINAHL (from 1982)), conference proceedings of the Pediatric Academic Societies annual conference (from 1990), clinical trial registries (ClinicalTrials.gov, International Standard Randomised Controlled Trial Number (ISRCTN) registry, and World Health Organization (WHO) International Clinical Trials Platform (ICTRP) Search portal), and Science Citation Index. We contacted experts in the field for studies.

SELECTION CRITERIA

We included studies that were prospective or retrospective, cohort or cross-sectional design, which evaluated molecular assays (index test) in neonates with suspected sepsis (participants) in comparison with microbial cultures (reference standard).

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed the methodologic quality of the studies and extracted data. We performed meta-analyses using the bivariate and hierarchical summary receiver operating characteristic (HSROC) models and entered data into Review Manager 5.

MAIN RESULTS

Thirty-five studies were eligible for inclusion and the summary estimate of sensitivity was 0.90 (95% confidence interval (CI) 0.82 to 0.95) and of specificity was 0.93 (95% CI 0.89 to 0.96) (moderate quality evidence). We explored heterogeneity by subgroup analyses of type of test, gestational age, type of sepsis onset, and prevalence of sepsis and we did not find sufficient explanations for the heterogeneity (moderate to very low quality evidence). Sensitivity analyses by including studies that analyzed blood samples and by good methodology revealed similar results (moderate quality evidence).

AUTHORS' CONCLUSIONS

Molecular assays have the advantage of producing rapid results and may perform well as 'add-on' tests.

RYP1 gene as a target for molecular diagnosis of histoplasmosis

This study analyzed the RYP1 gene as a target for the molecular diagnosis of histoplasmosis. This assay detected fungal DNA in 13/13 blood samples from HIV/AIDS-patients with histoplasmosis. Therefore, the detection of RYP1 gene in whole blood sample is a quick and sensitive test to diagnose histoplasmosis.

Microbiological Diagnosis of Sepsis: Polymerase Chain Reaction System Versus Blood Cultures

OBJECTIVE

To compare the utility of a multiplex polymerase chain reaction system (SeptiFast) and blood cultures for detecting bacteria and fungi in blood samples from patients with severe sepsis or septic shock.

METHODS

In a prospective observational study, whole blood samples for SeptiFast testing and for culture were collected on admission from all patients with severe sepsis or septic shock admitted to the intensive care unit between July 2011 and September 2012. SeptiFast results were compared with blood and other culture results.

RESULTS

The probability of at least 1 microorganism being isolated at 6 hours was 13-fold higher with the SeptiFast test than with blood cultures (relative risk, 13.5; 95% CI, 5.05-36.06). Unlike culture results, SeptiFast test results were not associated with previous antibiotic consumption. The median time to the first positive blood culture result was 17 hours; SeptiFast results were available in 6 hours. SeptiFast detected genetic material from potentially multiresistant microorganisms in patients whose blood cultures showed no growth at all.

CONCLUSIONS

The SeptiFast test provided quicker microbiological diagnosis and identified significantly more microorganisms than blood cultures did, particularly when samples were collected after antibiotic therapy had started or infections were due to resistant bacteria and yeast.

[Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis]

Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

A MIQE-compliant real-time PCR assay for Aspergillus detection

The polymerase chain reaction (PCR) is widely used as a diagnostic tool in clinical laboratories and is particularly effective for detecting and identifying infectious agents for which routine culture and microscopy methods are inadequate. Invasive fungal disease (IFD) is a major cause of morbidity and mortality in immunosuppressed patients, and optimal diagnostic criteria are contentious. Although PCR-based methods have long been used for the diagnosis of invasive aspergillosis (IA), variable performance in clinical practice has limited their value. This shortcoming is a consequence of differing sample selection, collection and preparation protocols coupled with a lack of standardisation of the PCR itself. Furthermore, it has become clear that the performance of PCR-based assays in general is compromised by the inadequacy of experimental controls, insufficient optimisation of assay performance as well as lack of transparency in reporting experimental details. The recently published "Minimum Information for the publication of real-time Quantitative PCR Experiments" (MIQE) guidelines provide a blueprint for good PCR assay design and unambiguous reporting of experimental detail and results. We report the first real-time quantitative PCR (qPCR) assay targeting Aspergillus species that has been designed, optimised and validated in strict compliance with the MIQE guidelines. The hydrolysis probe-based assay, designed to target the 18S rRNA DNA sequence of Aspergillus species, has an efficiency of 100% (range 95-107%), a dynamic range of at least six orders of magnitude and limits of quantification and detection of 6 and 0.6 Aspergillus fumigatus genomes, respectively. It does not amplify Candida, Scedosporium, Fusarium or Rhizopus species and its clinical sensitivity is demonstrated in histological material from proven IA cases, as well as concordant PCR and galactomannan data in matched broncho-alveolar lavage and blood samples. The robustness, specificity and sensitivity of this assay make it an ideal molecular diagnostic tool for clinical use.

DNAemia detection by multiplex PCR and biomarkers for infection in systemic inflammatory response syndrome patients

Fast and reliable assays to precisely define the nature of the infectious agents causing sepsis are eagerly anticipated. New molecular biology techniques are now available to define the presence of bacterial or fungal DNA within the bloodstream of sepsis patients. We have used a new technique (VYOO®) that allows the enrichment of microbial DNA before a multiplex polymerase chain reaction (PCR) for pathogen detection provided by SIRS-Lab (Jena, Germany). We analyzed 72 sepsis patients and 14 non-infectious systemic inflammatory response syndrome (SIRS) patients. Among the sepsis patients, 20 had a positive blood culture and 35 had a positive microbiology in other biological samples. Of these, 51.4% were positive using the VYOO® test. Among the sepsis patients with a negative microbiology and the non-infectious SIRS, 29.4% and 14.2% were positive with the VYOO® test, respectively. The concordance in bacterial identification between microbiology and the VYOO® test was 46.2%. This study demonstrates that these new technologies offer great hopes, but improvements are still needed.

Determining the incidence of aspergillosis after liver transplant

OBJECTIVES

Aspergillus has become an increasingly frequent cause of life-threatening opportunistic infections in liver transplant recipients. This study seeks to determine the incidence of invasive aspergillosis in liver transplant recipients using routine and molecular methods in a teaching hospital in Shiraz, the unique center for liver transplant in Iran.

MATERIALS AND METHODS

Four hundred eight recipients who underwent liver transplant were followed for Aspergillus infections by microscopic examination, culture, and nested polymerase chain reaction. Blood samples were cultured by bedside inoculation to BACTEC medium.

RESULTS

The female-to-male ratio was 151:257 (mean age, 29.6 years; mean hospitalization, 26 days). Sensitivity and specificity of the nested polymerase chain reaction was 92.8% and 94%. Aspergillosis was detected in 19 recipients (4.6%) by routine and molecular method (4 proven, 10 probable, and 5 possible) of whom 12 recipients died (63.2%).

CONCLUSIONS

This study found the incidence rate of invasive aspergillosis as an uncommon complication of liver transplant recipient cases but associated with poor outcomes. The rate is consistent with those reported in previous studies, but molecular assay that is more-sensitive and specific was used in the present study.

Early diagnosis of systemic candidiasis in bone marrow transplant recipients

OBJECTIVES

Systemic candidiasis, are common infections during the neutropenic phase. The aim of this study was to identify quantitative Candida species ribosomal DNA using TaqMan technology for diagnosing candidiasis and monitoring them during hospitalization.

MATERIALS AND METHODS

During the prospective, cross-sectional study, from September 2006 to September 2007, a total of 375 clinical blood specimens were collected from 35 patients with hematologic disorders once a week pretransplant and posttransplant. Patients were evaluated for systemic candidiasis during hospitalization. Cultures from the throat, urine, feces, and sputum, along with sonography and computerized tomographic scans, were done when patients were febrile and not having a response to antibiotics. All samples were cultured on Sabouraud dextrose agar with chloramphenicol, and direct, microscopic examination was performed. Blood samples were cultured by bedside inoculation into BACTEC medium at 35 degrees C for 7 days. Clinical blood specimens were evaluated for Candida infections using the TaqMan-based PCR assay.

RESULTS

Of the 35 recipients, 6 had multiple samples that were TaqMan-positive with Candida species probe, 3 had 1 PCR positive-result in their blood samples, and the 26 recipients showed negative results. Fungal rDNA was found in 2 patients before and after transplant. All 6 patients with systemic candidiasis had microbiologic and/or radiologic evidence of Candida infections.

CONCLUSIONS

It seems that TaqMan-based PCR assay can serve as an accurate method for diagnosing and monitoring Candida infections. This is the first report of its kind that shows Candida infections can be present in the blood of the bone marrow transplant candidates, so closer observation of the recipients who are neutropenic and receive immunosuppressive drugs seems warranted to improve their chances for survival.

Seminested PCR for detection and identification of Candida species directly from blood culture bottles

We investigated the performance of a seminested PCR (snPCR) assay carried out directly from overnight incubated blood culture bottles of 50 newborn intensive care unit (NICU) patients with suspected candidemia and compared these, for sensitivity, specificity and reliability with results from blood cultures. All positive blood cultures (n = 17) yielded positive results for snPCR, which detected the same Candida species, as did the yeast isolates of which 13 were C. parapsilosis and 4 were C. albicans. With both assays showing 32 negative samples and one sample positive with snPCR but negative with blood culture, sensitivity and specificity of snPCR were 100% and 97%, respectively. The patient with contradictory results exhibited a positive blood culture one week later yielding the same species as identified by snPCR. These are the first data demonstrating that snPCR from overnight blood culture bottles can be a potential tool for rapid detection and identification of Candida species, allowing follow-up of the "gold standard" blood culturing, as well.

Use of PCR for diagnosis of invasive aspergillosis: systematic review and meta-analysis

A systematic review and meta-analysis was done on the use of PCR tests for the diagnosis of invasive aspergillosis. Data from more than 10000 blood, serum, or plasma samples obtained from 1618 patients at risk for invasive aspergillosis were retrieved from 16 studies. Overall, the mean diagnostic odds ratios (DORs) of PCR for proven and probable cases were similar whether two consecutive positive samples were required to define positivity (DOR 15.97 [95% CI 6.83-37.34]) or a single positive PCR test was required (DOR 16.41 [95% CI 6.43-41.88]). Sensitivity and specificity of PCR for two consecutive positive samples were 0.75 (95% CI 0.54-0.88) and 0.87 (95% CI 0.78-0.93), respectively, and if only a single positive sample was required, these values were 0.88 (95% CI 0.75-0.94) and 0.75 (95% CI 0.63-0.84), respectively. Whereas specificity based on a single positive test was significantly lower (p=0.027) than two positive tests, the sensitivity and DOR did not differ significantly. A single PCR-negative result is thus sufficient to exclude a diagnosis of proven or probable invasive aspergillosis. However, two positive tests are required to confirm the diagnosis because the specificity is higher than that attained from a single positive test. Populations at risk varied and there was a lack of homogeneity of the PCR methods used. Efforts are underway to devise a standard for Aspergillus sp PCR for screening, which will help enable formal validation of PCR and estimate its use in patients most likely to benefit.

Early detection of systemic candidiasis in the whole blood of patients with hematologic malignancies

Systemic candidiasis is a significant cause of morbidity and mortality in patients with hematologic disorders. The aim of this study was to determine the prevalence of systemic candidiasis and the efficiency of the polymerase chain reaction-enzyme-linked immunosorbent assay (PCR-ELIZA) method for the early detection of Candida spp. in patients with hematologic malignancies. From 2004 to 2006, 194 patients with hematologic malignancies were evaluated for systemic candidiasis. Collected blood samples were assayed using the PCR-ELISA method for the presence of the bands on ethidium bromide stained gel, and for hybridization with Candida spp. as well. The female-to-male ratio was 61:133, the mean age was 33.7 years, and the mean hospitalization period was 21.2 days. Twenty-five patients (12.9%) had positive PCR-ELISA results for systemic candidiasis. The etiologic agents were Candida albicans (21 cases), C. tropicalis (3 cases), and C. krusei (1 case). The mean interval of PCR-ELISA positivity in blood samples before the manifestation of clinical signs was 12.6 days. Fungal PCR-ELISA assay became negative after 14 days when patients were treated successfully with amphotericin B, and the assay remained positive until death when the treatment failed. The PCR-ELISA method can potentially serve as a useful tool for the management of patients suffering from hematologic malignancies and at risk for systemic candidiasis.

[Comparison of four methods for efficient isolation of Aspergillus DNA from peripheral blood samples]

AIM OF THE STUDY

The main goal of this study was to find the best method for Aspergillus DNA isolation from peripheral blood samples. The method should be very effective but not expensive or time consuming to be suitable for routine diagnostics use.

MATERIAL AND METHODS

We compared four different methods for Aspergillus DNA isolation - one method with enzymatic lysis of the fungal cell wall and three methods that combine chemical and mechanical lysis (using high speed cell disruption with glass beads). Peripheral blood samples were inoculated with defined amount of Aspergillus fumigatus suspension and used for DNA isolation. Isolated DNA was then quantitatively analyzed with in-house real-time PCR method using specific probe.

RESULTS

Enzymatic method seems not to be useful in a routine diagnostics mainly because of its low efficiency and too long processing time. Better could be the methods using both chemical and mechanical cell disruption that can isolate fungal DNA with high efficiency in a relatively short time.

CONCLUSIONS

The method using ZR Fungal/Bacterial DNA Kit (Zymo Research, USA) was chosen for routine use in our laboratory because it is cheap, fast and very efficient.

Diagnostic value of DNA, (1-3)-β-d-glucan, and galactomannan detection in serum and bronchoalveolar lavage of mice experimentally infected with Aspergillus terreus

The aim of this study was to evaluate the diagnostic value of Aspergillus terreus-specific DNA, (1-3)-beta-d-glucan (BDG), and galactomannan (GM) in immunosuppressed mice infected intravenously with A. terreus conidia and sacrificed in groups of 12 each on days 1, 3, 5, 7, and 9. A. terreus-specific DNA, BDG, and GM in serum and bronchoalveolar lavage (BAL) were detected by nested polymerase chain reaction (nPCR), Fungitell kit (Associates of Cape Cod, E. Falmouth, MA), and Aspergillus Platelia kit (Bio-Rad, Marnes-laCoquette, France), respectively. Cultures of lung homogenate of all the animals yielded A. terreus. The BDG positivity, GM positivity, and nPCR positivity in serum specimens were 43%, 78%, and 73%, respectively. Combined detection enhanced the positivity to 95% for A. terreus DNA and GM, 83% for GM and BDG, and 95% for DNA, GM, and BDG. In BAL, the GM positivity and nPCR positivity were 80% and 81%, respectively, whereas combined detection increased the positivity to 98%. Detection of GM and DNA offers a sensitive and specific diagnostic option for invasive aspergillosis.

Comparative evaluation of (1, 3)-beta-D-glucan, mannan and anti-mannan antibodies, and Candida species-specific snPCR in patients with candidemia

BACKGROUND

Candidemia is a major infectious complication of seriously immunocompromised patients. In the absence of specific signs and symptoms, there is a need to evolve an appropriate diagnostic approach. A number of methods based on the detection of Candida mannan, nucleic acid and (1,3)-beta- D- glucan (BDG) have been used with varying specificities and sensitivities. In this retrospective study, attention has been focused to evaluate the usefulness of two or more disease markers in the diagnosis of candidemia.

METHODS

Diagnostic usefulness of Platelia Candida Ag for the detection of mannan, Platelia Candida Ab for the detection of anti-mannan antibodies, Fungitell for the detection of BDG, and of a semi-nested PCR (snPCR) for the detection Candida species-specific DNA have been retrospectively evaluated using 32 sera from 27 patients with culture-proven candidemia, 51 sera from 39 patients with clinically suspected candidemia, sera of 10 women with C. albicans vaginitis, and sera of 16 healthy controls.

RESULTS

Using cut-off values recommended by the manufacturers, the sensitivity of the assays for candidemia patients were as follows: Candida snPCR 88%, BDG 47%, mannan 41%, anti-mannan antibodies 47%, respectively. snPCR detected 5 patients who had candidemia due to more than one Candida species. The sensitivities of the combined tests were as follows: Candida mannan and anti-mannan antibodies 75%, and Candida mannan and BDG 56%. Addition of snPCR data improved the sensitivity further to 88%, thus adding 10 sera that were negative by BDG and/or mannan. In clinically suspected, blood culture negative patients; the positivities of the tests were as follows: Candida DNA was positive in 53%, BDG in 29%, mannan in 16%, and anti-mannan antibodies in 29%. The combined detection of mannan and BDG, and mannan, BDG and Candida DNA enhanced the positivity to 36% and 54%, respectively. None of the sera from Candida vaginitis patients and healthy subjects were positive for Candida DNA and mannan.

CONCLUSION

The observations made in this study reinforce the diagnostic value of snPCR in the sensitive and specific diagnosis of candidemia and detection of more than one Candida species in a given patient. Additionally, in the absence of a positive blood culture, snPCR detected Candida DNA in sera of more than half of the clinically suspected patients. While detection of BDG, mannan and anti-mannan antibodies singly or in combination could help enhancing sensitivity and eliminating false positive tests, a more extensive evaluation of these assays in sequentially collected serum samples is required to assess their value in the early diagnosis of candidemia.

Avances y limitaciones del diagnóstico precoz de las infecciones invasoras causadas por levaduras

In the last years, the main advances in the serological diagnosis of mycoses caused by yeasts have occurred in the area of antibody and (1-3)-beta-D-glucan detection. Commercialization of the Candida albicans IFA IgG test and detection of antibodies against recombinant antigens Hwp1 and enolase are the most important contributions to the first area. Detection of (1-3)-beta-D-glucan confirms its usefulness as a good marker for the diagnosis of invasive candidiasis. The most recent studies suggest that combination of two tests to detect antígen, antibodies, (1-3)-beta-D-glucan and DNA will be needed to optimize the diagnosis of systemic yeast infections.

Estado actual del diagnóstico precoz de las infecciones invasoras causadas por Aspergillus y otros hongos filamentosos emergentes

The usefulness of surrogate markers in the diagnosis of invasive fungal infections caused by Aspergillus and other emerging mycelial fungi is based on the ability of surrogate markers to detect the infection caused by different species of mycelial fungi. Conventional microbiological methods for diagnosis of fungal disease are slow and insensitive. Antigen based assays or measurement of (1-3)-beta-D-glucan in blood have been developed and validated in clinical laboratories. We review these diagnostic contemporary tools, their clinical application and impact.

[Detection of Candida DNA in simulated blood samples by polymerase chain reaction]

Although blood culture method is accepted as gold standard in the laboratory diagnosis of invasive candidiasis seen in immunocompromised patients, cultivation of blood is considered as not a reliable and rapid method for the diagnosis of candidemia, since it may be negative in approximately half of the patients, slow growth rate of Candida in routine culture media and requirement of large amounts of blood for the isolation. The aim of this study was to detect Candida DNA in simulated blood samples by using polymerase chain reaction (PCR). Simulated samples were prepared by using blood samples of healthy volunteers. These samples were inoculated into tubes with EDTA and BACTEC 9240 blood culture bottles in which no growth was detected and with standard strains of C. albicans, C. tropicalis, C. parapsilosis, C. krusei, Escherichia coli and Staphylococcus aureus together with the clinical isolates of Aspergillus fumigatus, C. kefyr, C. glabrata, C. lusitaniae, C. guilliermondii and Rhodotorula sp. Additionally, blood culture samples of 23 cases whose blood culture bottles signaled as positive and revealed growth of Candida in agar plates were examined. DNA extraction of all samples were performed according to the standard procedure proposed by the MN Nucleospin Tissue Kit (Macherey-Nagel, Germany) for tissue samples; following the pre-treatment with erythrocyte, leukocyte and fungus cell wall lysis buffers. DNAs were amplified with PCR, using primers specific for the 5S rDNA region (PCon 1 and PCon 2 primers) and PCR products were obtained by electrophoresis in 2% agarose gel. Presence of a 105 base pair (bp) product was considered as positive. The lowest detection limit of PCR has been determined as 10(2)-10(3) cfu/ml Candida for our simulated samples. The presence of a 105 bp band has been observed in samples prepared with all Candida strains included in the study. Blood samples spiked with E. coli, S. aureus, A. fumigatus and Rhodotorula sp. and negative blood samples has been found negative in terms of Candida DNA. The same 105 bp product has been observed for blood culture samples with Candida growth. The PCR method applied in this study takes approximately seven hours and the cost was calculated approximately 6.00 U.S. dollars per patient. As a result, it has been determined that Candida DNA can be detected in a shorter time by PCR using specific primers for 5S rDNA gene from simulated samples prepared with either blood or BACTEC blood culture bottles.

Real-time PCR assay to detect DNA in sera for the diagnosis of deep-seated trichosporonosis

Deep-seated trichosporonosis due to Trichosporon asahii is life-threatening and has high mortality. A real-time PCR assay to detect T. asahii DNA in sera for diagnosis of this fungal infection was developed. The assay showed a higher sensitivity than polysaccharide antigen detection method. Our new real-time PCR assay may be used for diagnosing deep-seated trichosporonosis due to T. asahii.

Detection of imported histoplasmosis in serum of HIV-infected patients using a real-time PCR-based assay

A new real-time PCR-based assay was used for detecting DNA of Histoplasma capsulatum in serum samples collected from four HIV-infected patients with proven histoplasmosis. The assay targeted the ITS1 region of rDNA and its in vitro sensitivity, specificity and reproducibility were evaluated. The technique detected DNA of H. capsulatum in all of the HIV-infected patients with proven histoplasmosis (4/4, 100%). The PCR result was positive for seven of the ten (70%) samples studied. The assay's specificity was determined to be 100%, since the method was negative for 25 other serum samples (10 from patients with proven aspergillosis and 15 from healthy controls). The PCR assay is a new and promising diagnostic alternative and further investigation is warranted.

Candiduria in critically ill patients: an early candidemia marker when coupled with multiple blood specimens PCR assays?

BACKGROUND/AIMS

Can repeated blood PCR assays in critically ill patients with culture-confirmed candiduria help in the early detection of candidemia?

METHODOLOGY

Urine samples were obtained on the day of admission and if negative were repeated on the 5th ICU day. Upon laboratory confirmation of candiduria, preemptive antifungal therapy was commenced. Whole blood samples were tested simultaneously with conventional cultures and PCR repeated twice weekly for two weeks.

RESULTS

In ICU patients with candiduria, preemptive antifungal therapy resulted in candiduria clearance and clinical improvement in 94% of them. Candida DNAemia (detected in 64 out of 136 repeated PCR assays) persisted for 1 or 2 weeks in a significant number of patients. Even after multiple positive PCR assays from each individual candiduric patient, the specificity and positive predictive value of the assay in the early detection of candidemia were low (negative predictive value was 100%). No differences were detected on demographics among patients with or without candiduria. The correlations (PCR with culture) with kappa test presented a poor agreement (K = 0.103, Kmin= -0679, Kmax = 0.103).

CONCLUSIONS

PCR in the blood should not be used in early diagnosis of (but it could help in excluding) candidemia, in ICU patients with candiduria.

[Comparison of different methods of DNA extraction from blood to detect fungal DNA by PCR]

Comparison of different methods of DNA extraction from blood to detect fungal DNA by PCR. Invasive fungal infections (IFI) are associated with high mortality by reaching levels of 50%, and also with a significant failure in antifungical treatments. This fact mostly obeys to difficulties in obtaining a fast and accurate mycologic diagnosis due to the low sensitivity of conventional methods, mainly in neutropenic and AIDS patients. Various methods based on fungal DNA study are currently being used for the diagnosis of mycotic infections. We herein evaluated two procedures of extraction and purification of fungal DNA in blood for their use in PCR detection. Both of them showed equal efficiency in obtaining high performance DNA with universal primers ITS land ITS 4 as target.

Serial Aspergillus antigen monitoring in pediatric bone marrow transplant patients

Invasive aspergillosis carries a high mortality rate in immunocompromised patients, such as bone marrow transplant patients. Favorable outcomes are dependent on early detection and treatment. Positive galactomannan antigenemia has been included as a microbiological criterion for probable or possible diagnosis of invasive aspergillosis. Detection of circulating Aspergillus DNA in the first positive galactomannan sample, with serial monitoring, could help in diagnosis of invasive aspergillosis in bone marrow transplant patients. Morbidity and mortality from aspergillosis can possibly be reduced if an early diagnosis is made and appropriate treatment initiated. An effective and accurate way of early detection of invasive aspergillosis is serial Aspergillus antigen monitoring.

Evaluation of polymerase chain reaction for the detection of Paracoccidioides brasiliensis DNA on serum samples from patients with paracoccidioidomycosis

The aim of this study was to demonstrate the DNA of Paracoccidioides brasiliensis in human serum samples of patients with paracoccidioidomycosis using the polymerase chain reaction (PCR). The diagnosis of paracoccidioidomycosis (PCM) was defined by microscopic observation of the fungus on direct exam or histopathology, culture, and serological positivity. DNA from serum of 33 patients with PCM was extracted and submitted to nested-PCR using primers from the gp 43 gene. Only one sample was positive on nested-PCR. We conclude that the prevalence of fungemia in patients with different clinical forms of PCM is low, limiting the use of serum DNA detection as an alternative diagnostic tool.

Use of DNA sequencing analysis to confirm fungemia due to Trichosporon dermatis in a pediatric patient

This is the first reported case of human disease caused by Tricosporon dermatis, an organism recently transferred to the genus Trichosporon from Cryptococcus and now confirmed to be a human pathogen.

Use of quantitative real-time PCR to study the kinetics of extracellular DNA released from Candida albicans, with implications for diagnosis of invasive Candidiasis

Quantitative real-time PCR (qPCR) is considered one of the most sensitive methods to detect low levels of DNA from pathogens in clinical samples. To improve the design of qPCR for the detection of deeply invasive candidiasis, we sought to develop a more comprehensive understanding of the kinetics of DNA released from Candida albicans in vitro and in vivo. We developed a C. albicans-specific assay targeting the rRNA gene complex and studied the kinetics of DNA released from C. albicans alone, in the presence of human blood monocytes (H-MNCs), and in the bloodstream of rabbits with experimental disseminated candidiasis. The analytical qPCR assay was highly specific and sensitive (10 fg). Cells of C. albicans incubated in Hanks balanced salt solution (+/-10% bovine serum albumin [BSA]) or RPMI (+/-10% BSA) showed a significant release of DNA at T equal to 24 h compared to T equal to 0 h (P < or = 0.01). C. albicans incubated with H-MNCs exhibited a greater release of DNA than C. albicans cells alone over 24 h (P = 0.0001). Rabbits with disseminated candidiasis showed a steady increase of detectable DNA levels in plasma as disease progressed. Plasma cultures showed minimal growth of C. albicans, demonstrating that DNA extracted from plasma reflected fungal cell-free DNA. In summary, these studies of the kinetics of DNA release by C. albicans collectively demonstrate that cell-free fungal DNA is released into the bloodstream of hosts with disseminated candidiasis, that phagocytic cells may play an active role in increasing this release over time, and that plasma is a suitable blood fraction for the detection of C. albicans DNA.

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.

Polymerase chain reaction screening for fungemia and/or invasive fungal infections in patients with hematologic malignancies

INTRODUCTION

Invasive fungal infections (IFIs) are a life-threatening complication in patients with hematologic malignancies, mainly in acute leukemia patients, following chemotherapy. IFI incidence is increasing, and associated mortality remains high due to unreliable diagnosis. Antifungal drugs are often limited by inadequate antimicrobial spectrum and side effects. Thus, the detection of circulating fungal DNA has been advocated as a rapid, more sensitive diagnostic tool.

PATIENTS AND METHODS

Between June 01 and January 03, weekly blood samples (1,311) were screened from 193 patients undergoing intensive myelosuppressive or immunosuppressive therapy. IFI cases were classified according to European Organization for Research and Treatment of Cancer/Mycoses Study Group criteria. Fungal DNA was extracted from whole blood and amplified using polymerase chain reaction (PCR) published primers that bind to the conserved regions of the fungal 18S rRNA gene sequence. In our study, two or more consecutive positive samples were always associated with fungal disease.

RESULTS

PCR screening predicted the development of IFI to be 17 days (median). This test had a specificity of 91.1% and a sensitivity of 75%. IFI incidence was 7.8%.

DISCUSSION

Therefore, our results confirm the potential usefulness of PCR serial screening and the clinical applicability in everyday routine. PCR screening offers a noninvasive repeatable aid to the diagnosis of IFI.

Use of real-time PCR to process the first galactomannan-positive serum sample in diagnosing invasive aspergillosis

Positive galactomannan (GM) anti-genemias are included as a microbiological item in the diagnosis of probable or possible invasive aspergillosis (IA). Because false-positive GM results frequently occur, at least two positive results on two different samples are required. Waiting for clinical specimens can delay the initiation of treatment. As an alternative, we wondered whether detection of circulating Aspergillus DNA on the first positive GM serum sample could aid in diagnosing IA. Therefore, we retrospectively screened the first GM-positive serum samples from 29 patients from our hematology unit for Aspergillus DNA using real-time PCR. We compared the real-time PCR results with the final classification of proven, probable, and possible IA according to consensual criteria. No clear correlation between PCR results and the classification with the medical files could be shown. However, a positive PCR result was associated with a poor prognosis (Fisher's test; P=0.01). Our preliminary data suggest that a positive PCR result could indicate a more advanced stage of the disease. Therefore, concomitant positive PCR and GM results may justify the initiation of antifungal therapy in neutropenic patients. In contrast, a negative PCR on the first positive GM sample may argue for postponing costly antifungal administration until additional arguments for the diagnosis of IA are presented.

Detection of Aspergillus fumigatus and a mutation that confers reduced susceptibility to itraconazole and posaconazole by real-time PCR and pyrosequencing

A real-time PCR and pyrosequencing method was developed to detect Aspergillus fumigatus in whole blood by amplifying the cyp51A gene and sequencing the codon for glycine 54. Mutations in this codon can result in amino acid substitutions that confer reduced susceptibility to itraconazole and posaconazole.

A prospective study of real-time panfungal PCR for the early diagnosis of invasive fungal infection in haemato-oncology patients

A blinded prospective study was performed to determine whether screening of whole blood using a real-time, panfungal polymerase chain reaction (PCR) technique could predict the development of invasive fungal infection (IFI) in immunocompromised haemato-oncology patients. In all, 78 patients (125 treatment episodes) were screened twice weekly by real-time panfungal PCR using LightCyclertrade mark technology. IFI was documented in 19 treatment episodes (five proven, three probable and 11 possible), and in 12, PCR was sequentially positive. PCR positivity occurred in: 4/5 proven; 2/3 probable; 6/11 possible; and 29/106 with no IFI. In 8/12 with IFI and sequentially positive PCR results, PCR positivity occurred before (median 19.5 days) and in 4/12 (median 10.5 days) after the initiation of empirical antifungal therapy. Based on sequential positive results for proven/probable IFI sensitivity, specificity, positive predictive value and negative predictive value were 75, 70, 15 and 98%, respectively. Real-time panfungal PCR is a sensitive tool for the early diagnosis of IFI in immunocompromised haemato-oncology patients. It may be most useful as a screening method in high-risk patients, either to direct early pre-emptive antifungal therapy or to determine when empirical antifungal therapy can be withheld in patients with antibiotic--resistant neutropenic fever. However, these strategies require further assessment in comparative clinical trials.

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.

Diagnosing invasive aspergillosis during antifungal therapy by PCR analysis of blood samples

We evaluated the value of Aspergillus PCR as a tool for diagnosing invasive aspergillosis from whole-blood samples during antifungal therapy. In a 3-year study, 36 patients receiving antifungal therapy due to chest radiographic findings highly suggestive of fungal pneumonia were evaluated. The PCR results from whole-blood samples were compared to those obtained from bronchoalveolar lavage fluids and/or tissue specimens. A total of 205 whole-blood samples, 15 fine-needle aspirations or tissue biopsy specimens, and 21 bronchoalveolar lavage fluids and tracheal secretions were analyzed using PCR. Of the 36 patients, 15 had proven, 9 had probable, and 12 had possible invasive Aspergillus infection according to European Organization for Research and Treatment of Cancer/Mycosis Study Group definitions. For patients with proven infection the sensitivity values of PCR in lung and blood samples were 100 and 40%, respectively. The negative predictive value of blood monitoring under conditions of antifungal treatment was 44%. Clearance of fungal DNA from blood was associated with resolution of clinical symptoms in six of nine patients with proven infection. Repeated positive PCR results for Aspergillus were associated with fatal outcome, as three of six patients died. For patients with probable infection the sensitivity values of PCR in lung fluid and blood were 66 and 44%, respectively. The benefit of PCR diagnosis using whole-blood samples is limited when sampling takes place after treatment has been started. Performance of Aspergillus PCR using tissue samples is recommended in addition to microscopic examination and culture technique for sensitive detection of fungal infection.

PCR-enzyme immunoassay of rDNA in the diagnosis of candidemia and comparison with amplicon detection by agarose gel electrophoresis

We have developed a semi-nested PCR-enzyme immunoassay (snPCR-EIA) for the detection of Candida species in serum specimens, and the sensitivity of amplicon detection was compared with the detection of amplified product by agarose gel electrophoresis (AGE). The universal outer primers amplified the 3' end of 5.8S and the 5' end of 28S rDNA including the internally transcribed spacer 2 (ITS2) in PCR with genomic DNA as template from all the tested Candida species. The biotin-labeled species-specific primers derived from ITS2 from the four commonly encountered Candida species, viz. C. albicans, C. tropicalis, C. parapsilosis and C. glabrata, together with digoxigenin-labeled reverse primer amplified species-specific DNA in the reamplification step of the snPCR. The snPCR-EIA was positive for genomic DNA recovered from 0.06 Candida cells in culture and one organism/ml in spiked serum specimens. Evaluation of snPCR-EIA and snPCR-AGE for specific identification of Candida species with 26 clinical Candida isolates showed 100% concordant results with Vitek and ID32C yeast identification systems. Further evaluation of snPCR-EIA and snPCR-AGE for detection of Candida species in serum samples from culture proven (n = 6) and suspected (n = 10) patients showed concordance with the corresponding species isolated in culture. The serum samples from none of the healthy volunteers (n = 10) were positive for the presence of Candida DNA by snPCR-EIA or snPCR-AGE. Our results show that the snPCR-EIA has the same sensitivity as snPCR-AGE, however, it offers additional advantages of simultaneous testing of a large number of serum samples and avoids the use of ethidium bromide, a potent mutagen. The snPCR-EIA could, therefore, be a method of choice for the diagnosis of candidemia.

Amplification of coccidioidal DNA in clinical specimens by PCR

Coccidioides DNA was amplified from serum by a PCR using coccidioid-specific primers. A 239-bp product was visualized when 10 fg of exogenous coccidioidal DNA was subjected to amplification. This product was demonstrated in some human and mouse sera prior to the detection of coccidioidal antibodies.

Comparison of different methods of isolation of DNA of commonly encountered Candida species and its quantitation by using a real-time PCR-based assay

Molecular diagnosis based on genomic amplification methods such as real-time PCR assay has been reported as an alternative to conventional culture for early detection of invasive candidiasis. However, a major limitation of the molecular method is the difficulty associated with breaking fungal cell walls since the DNA extraction step still requires more than half of a working day. It has been suggested that PCR detection of free template DNA in serum is preferred over the use of whole blood for the diagnosis of systemic candidiasis. In this study, two conventional procedures (the first [the HLGT method] consists of boiling sera in an alkaline guanidine-phenol-Tris reagent, and the second [the PKPC method] uses proteinase K digestion, followed by organic extraction) and three commercially available kits for DNA isolation were evaluated for sensitivity, purity, cost, and use of template for most clinically important Candida species in a TaqMan-based PCR assay. To optimize these procedures, we evaluated the effect of adding 0.5% bovine serum albumin to DNA extracts and found that it decreased the effects of inhibitors. The QIAamp DNA blood kit did significantly shorten the duration of the DNA isolation but was among the most expensive procedures. Furthermore, the QIAamp DNA blood kit proved to be as sensitive as the HLGT DNA isolation method for PCR amplification from 52 serum samples from hematology or oncology patients with clinically proven or suspected systemic Candida infections. All PCR-positive samples showed approximately the same Candida species load by both procedures (100% correspondence), whereas one discordant result was obtained between PCR and blood culture.

The diagnosis of hepatosplenic candidiasis by DNA analysis of tissue biopsy and serum

Hepatosplenic candidiasis is traditionally diagnosed by blood culture, magnetic resonance imaging (MRI), and histological analysis. The limitations of these methods include: low sensitivity (blood culture) and failure to isolate the organism (MRI/histology). This report describes a case of hepatosplenic candidiasis diagnosed by simultaneous polymerase chain reaction (PCR) analysis of liver biopsy and serum. PCR of biopsy and/or serum may offer a sensitive and specific diagnostic test for hepatosplenic candidiasis. Candida species can be identified, which helps guide antifungal chemotherapy, an important aspect in this difficult to treat infection.

Detection of Aspergillus DNA by a nested PCR assay is superior to blood culture in an experimental murine model of invasive aspergillosis

For diagnosing invasive aspergillosis (IA), an increasing clinical problem in immunocompromised patients, molecular tools are gaining in importance. Detection of Aspergillus DNA in blood samples was investigated by a nested PCR assay in a murine model of experimentally induced IA. Ex vivo, the detection threshold of the PCR assay was determined in blood and organ homogenates of mice. After intravenous injection of Aspergillus fumigatus conidia on different days, growth of colonies was determined in cultures of blood and organs from immunocompetent and immunosuppressed mice and Aspergillus DNA was detected from blood samples by a nested PCR assay. The detection threshold of the PCR assay was as low as 1 c.f.u. ml(-1). The assay proved to be more sensitive than cultures of blood, with sensitivity rates between 17.6 and 87.5 % depending on the fungal burden. In conclusion, the nested PCR assay is superior to cultural methods in detecting Aspergillus spp. in murine blood samples.

Early detection and identification of commonly encountered Candida species from simulated blood cultures by using a real-time PCR-based assay

In a recent study, Candida species in clinical blood samples were detected using a real-time PCR-based method (Maaroufi et al, J Clin Microbiol 2003, 41:3293-3298). For the present study, we evaluated the efficiency of this method as an adjunct to the BACTEC blood culture system to early detection of positivity and negativity of simulated low candidemias. We first established an in vitro correlation between the inoculum of the most frequently encountered Candida species and the time to positivity of these microorganisms. Then, aliquots from blood culture bottles infected with a final average candidal inoculum of 3.18 colony-forming units (CFU)/culture bottle (range, 1 to 6 CFU) were collected at increasing incubation times, and DNA was extracted and submitted to the TaqMan-based PCR assay. To optimize this assay, we evaluated the effect of adding 0.5% bovine serum albumin (BSA) to DNA extracts and found that it decreased the effects of inhibitors. Using specific probes for the tested Candida species, the PCR assay was positive on blood culture aliquots collected from the BACTEC system after a minimum culture turnaround time (TAT) of 3.11 +/- 1.24 hours. Addition of BSA to PCR reaction mixtures improves the TAT (1.84 +/- 0.41 hours). Hence, the combination of DNA "amplification" in the culture bottles by normal growth with an additional DNA amplification by PCR might be a reliable tool facilitating the early diagnosis of low candidemias.

[Laboratory diagnosis of invasive aspergillosis]

Invasive aspergillosis is major cause of morbility and mortality in immunosuppressed patients, in part due to the inability to identify infected patients at an early stage of the disease. Diagnosis is based on a combination of imaging (high-resolution computed tomography) and a number of laboratory techniques including direct examination, culture and circulating markers (galactomannan and Aspergillus DNA) which can be detected at early stages of the infection.

The first isolation of ustilaginomycetous anamorphic yeasts, Pseudozyma species, from patients' blood and a description of two new species: P. parantarctica and P. thailandica

The genus Pseudozyma is ustilaginomycetous anamorphic yeasts, and are mainly isolated from plants. We isolated three Pseudozyma strains from the blood of patients in Thailand. While one isolate was identified as P. antarctica by rDNA sequence analysis, the other two were considered to be new species and were named P. parantarctica and P. thailandica. The three isolates proved to be resistant to 5-flucytosine, and P. thailandica was also resistant to fluconazole and itraconazole. As far as we know, this is the first isolation of Pseudozyma strains from humans. The two new species are described.

Development of a LightCycler PCR assay for detection and quantification of Aspergillus fumigatus DNA in clinical samples from neutropenic patients

The increasing incidence of invasive aspergillosis, a life-threatening infection in immunocompromised patients, emphasizes the need to improve the diagnostic tools for this disease. We established a LightCycler-based real-time PCR assay to detect and quantify rapidly, specifically, and sensitively Aspergillus fumigatus DNA in both bronchoalveolar lavage (BAL) and blood samples from high-risk patients. The primers and hybridization probes were derived from an A. fumigatus-specific sequence of the mitochondrial cytochrome b gene. The assay is linear in the range between 13.2 fg and 1.3 ng of A. fumigatus DNA, corresponding to 3 to 300,000 CFU per ml of BAL fluid or blood. No cross-amplification was observed with human DNA or with the DNA of fungal or bacterial pathogens. For clinical evaluation we investigated 10 BAL samples from nine neutropenic patients with malignant hematological diseases and 12 blood samples from seven neutropenic patients with malignant hematological diseases. Additionally, we tested one blood sample and one BAL sample from each of two neutropenic patients. In order to characterize the validity of the novel PCR assay, only samples that had shown positive results by a previously described sensitive and specific nested PCR assay were tested. Twelve of 12 BAL samples and 6 of 14 blood samples gave positive results by the LightCycler PCR assay. Eight of 14 blood samples gave negative results by the novel method. The LightCycler PCR-mediated quantification of the fungal burden showed 15 to 269,018 CFU per ml of BAL sample and 298 to 104,114 CFU per ml of blood sample. Twenty of 20 BAL samples and 50 of 50 blood samples from subjects without evidence of invasive pulmonary aspergillosis (IPA) were PCR negative. Compared to a previously described nested PCR assay, these preliminary data for the novel real-time PCR assay indicate a less sensitive rate of detection of IPA in high-risk patients, but the assay may be valuable for quantification of the fungal burden in individual clinical samples.

Diagnosis of invasive mold infection by real-time quantitative PCR

We report the design and evaluation of a quantitative real-time polymerase chain reaction (PCR) assay to diagnose invasive mold infection (IMI) by detecting mold DNA in the serum. This assay detected 200 fg to 20 ng (5-log range) mold DNA and permitted a cutoff of 110 fg (3 genomes). Human or candidal DNA was not amplified. Specificity also was demonstrated by negative results in all 35 patients (76 serum samples) with unlikely IMI at the cutoff. For patients with possible, probable, and documented IMI diagnosed by a combination of clinical, microbiologic, and histologic criteria, this real-time PCR showed positivity in 40% (12/30), 68% (19/28), and 85% (11/13) cases, respectively, in testing of multiple serum samples. The overall serum positivity rate for these patients was 15.1% (73/483). Quantitative analysis of the positive serum samples estimated the bodily circulating mold burden to be 1.6 x 10(5) genomes (5.3 ng) by geometric mean with 4.2 x 10(7) genomes (1,400 ng) the highest. These results suggest that for the diagnosis of IMI, this real-time PCR may be a promising alternative to other invasive methods. Further evaluation is underway.