Detection and identification of fungi from fungus balls of the maxillary sinus by molecular techniques

Aspergillus fumigatus-induced biogenic silver nanoparticles' efficacy as antimicrobial and antibiofilm agents with potential anticancer activity: An in vitro investigation

A worldwide hazard to human health is posed by the growth of pathogenic bacteria that have contaminated fresh, processed, cereal, and seed products in storage facilities. As the number of multidrug-resistant (MDR) pathogenic microorganisms rises, we must find safe, and effective antimicrobials. The use of green synthesis of nanoparticles to combat microbial pathogens has gained a rising interest. The current study showed that Aspergillus fumigatus was applied as a promising biomass for the green synthesis of biogenic silver nanoparticles (Ag NPs). The UV-visible spectra of biosynthesized Ag NPs appeared characteristic surface plasmon absorption at 475 nm, round-shaped with sizes ranging from 17.11 to 75.54 nm and an average size of 50.37 ± 2.3 nm. In vitro tests were conducted to evaluate the antibacterial, antioxidant, and anticancer effects of various treatment procedures for Ag NP applications. The synthesized Ag NPs was revealed antimicrobial activity against Aspergillus flauvas, A. niger, Bacillus cereus, Candida albicans, Esherichia coli, Pseudomonas aerugonosa, and Staphylococcus aureus under optimum conditions. The tested bacteria were sensitive to low Ag NPs concentrations (5, 10, 11, 8, 7, 10, and 7 mg/mL) which was observed for the mentioned-before tested microorganisms, respectively. The tested bacterial pathogens experienced their biofilm formation effectively suppressed by Ag NPs at sub-inhibitory doses. Antibacterial reaction mechanism of Ag NPs were tested using scanning electron microscopy (SEM) to verify their antibacterial efficacy towards S. aureus and P. aeruginosa. These findings clearly show how harmful Ag NPs are to pathogenic bacteria. The synthesized Ag NPs showed antitumor activity with IC50 at 5 μg/mL against human HepG-2 and MCF-7 cellular carcinoma cells, while 50 mg/mL was required to induce 70 % of normal Vero cell mortality. These findings imply that green synthetic Ag NPs can be used on cancer cell lines in vitro for anticancer effect beside their potential as a lethal factor against some tested pathogenic microbes.

Pathogenesis, Diagnosis, and Treatment of Infectious Rhinosinusitis

Rhinosinusitis is a common inflammatory disease of the sinonasal mucosa and paranasal sinuses. The pathogenesis of rhinosinusitis involves a variety of factors, including genetics, nasal microbiota status, infection, and environmental influences. Pathogenic microorganisms, including viruses, bacteria, and fungi, have been proven to target the cilia and/or epithelial cells of ciliated airways, which results in the impairment of mucociliary clearance, leading to epithelial cell apoptosis and the loss of epithelial barrier integrity and immune dysregulation, thereby facilitating infection. However, the mechanisms employed by pathogenic microorganisms in rhinosinusitis remain unclear. Therefore, this review describes the types of common pathogenic microorganisms that cause rhinosinusitis, including human rhinovirus, respiratory syncytial virus, Staphylococcus aureus, Pseudomonas aeruginosa, Aspergillus species, etc. The damage of mucosal cilium clearance and epithelial barrier caused by surface proteins or secreted virulence factors are summarized in detail. In addition, the specific inflammatory response, mainly Type 1 immune responses (Th1) and Type 2 immune responses (Th2), induced by the entry of pathogens into the body is discussed. The conventional treatment of infectious sinusitis and emerging treatment methods including nanotechnology are also discussed in order to improve the current understanding of the types of microorganisms that cause rhinosinusitis and to help effectively select surgical and/or therapeutic interventions for precise and personalized treatment.

Impact of Zinc Oxide on the Development of Aspergillus-Induced Maxillary Sinusitis Rabbit Model

Aspergillus fumigatus is commonly found in the airway and is associated with airway inflammatory diseases. Zinc oxide (ZO) is known to be an essential microelement that facilitates fungal survival, growth, and proliferation. This study aimed to investigate the impact of ZO on A. fumigatus-induced fungal sinusitis in rabbits. Twenty-eight New Zealand white rabbits were divided into four groups for this study. Group 1 (6 sides) was treated with intramaxillary phosphate buffer saline (PBS) served as the negative control, Group 2 (6 sides) received intramaxillary PBS and ZO, Group 3 (8 sides) was treated with intramaxillary A. fumigatus alone, and Group 4 (8 sides) treated with intramaxillary A. fumigatus with ZO. After 4 and 12 weeks, sinus mucosal cytokine and transcription factor expressions were determined. A histological analysis was performed to determine inflammatory cell infiltration, number of secretory cells, and mucosal thickness. Fungal biofilm formation was determined using confocal laser microscopy. The intramaxillary instillation of A. fumigatus conidia led to an increase in protein and mRNA expression of interleukin (IL)-1β and IL-8 in the maxillary sinus mucosa. They were associated with mitogen-activated protein kinase and activator protein-1. Furthermore, intramaxillary instillation of fungal conidia resulted in significant enhancement of inflammatory cell infiltration, epithelial thickening, and fungal biofilm formation. However, intramaxillary ZO did not have a significant impact on A. fumigatus-induced cytokine protein and mRNA expression, and inflammatory cell infiltration and epithelial thickness in sinonasal mucosa. While intramaxillary instillation of A. fumigatus increased mucosal inflammation, cytokine production, and biofilm formation, the intramaxillary application of ZO did not have a significant influence on inflammation in the maxillary sinus mucosa.

Candida spp. DNA Extraction in the Age of Molecular Diagnosis

The standard procedure for the detection of candidemia is blood culture, a method that might require 3-5 days for a positive result. Compared with culturing, molecular diagnosis techniques can provide faster diagnosis. The current paper aimed to present the main strengths and constraints of current molecular techniques for Candida spp. DNA extraction, analyzing their efficiency from a time, price, and ease of usage point of view. A comprehensive search was conducted using the PubMed NIH database for peer-reviewed full-text articles published before October 2022. The studies provided adequate data on the diagnosis of the infection with the Candida spp. DNA extraction is a relevant step in yielding pure qualitative DNA to be amplified in molecular diagnostic techniques. The most used fungal DNA extraction strategies are: mechanical (bead beating, ultrasonication, steel-bullet beating), enzymatic (proteinase K, lysozyme, lyticase), and chemical extraction (formic acid, liquid nitrogen, ammonium chloride). More clinical studies are needed to formulate adequate guidelines for fungal DNA extraction as the current paper highlighted discrepancies in the reported outcome.

High CT Attenuation Values Relative to the Brainstem Predict Fungal Hyphae Within the Sinus

Objectives

There is currently no established objective diagnostic indicator for the differentiation of sinus fungal ball (SFB) from unilateral nonfungal chronic sinusitis (UCRS). This study evaluated whether computed tomography (CT) attenuation values relative to those of the brainstem (relative CT number) are useful for differentiating SFB from UCRS.

Materials and Methods

Consecutive patients who were pathologically diagnosed with SFB or UCRS between 2013 and 2021 were retrospectively identified. The relative CT numbers of region of interest (ROIs) within the sinuses were compared between the two patient groups. Factors with predictive power for differentiating SFBs from UCRSs were identified by uni/multivariable logistic regression analyses.

Results

One hundred and eighty-three patients with unilateral chronic sinusitis were finally analyzed (SFB, 86 cases; UCRS, 97 cases). Regardless of the presence or absence of calcified lesions, the relative CT numbers in SFB were significantly higher than those in UCRS. ROIs showing high relative CT numbers were those where fungal hyphae were present. In the uni/multivariable logistic regression analysis, age (p < 0.001), relative CT number (p < 0.001), and calcification (p = 0.002) had predictive value for distinguishing SFB from UCRS. Within those cases not showing calcification, age (p = 0.004) and relative CT number (p < 0.001) were predictive factors for differentiating SFB from UCRS. A relative CT number >1.5 was significantly associated with SFB (sensitivity, 70%; specificity, 91%), with a significantly larger area under the receiver operating characteristics curve than age.

Conclusions

High relative CT numbers within the sinus are strongly associated with the presence of fungal hyphae, and measurement of relative CT number is a powerful adjunctive diagnostic method for distinguishing between SFB and UCRS.

Asian Sand Dust Particles Enhance the Development of Aspergillus fumigatus Biofilm on Nasal Epithelial Cells

Background: Asian sand dust (ASD) and Aspergillus fumigatus are known risk factors for airway mucosal inflammatory diseases. Bacterial and fungal biofilms commonly coexist in chronic rhinosinusitis and fungus balls. We evaluated the effects of ASD on the development of A. fumigatus biofilm formation on nasal epithelial cells. Methods: Primary nasal epithelial cells were cultured with A. fumigatus conidia with or without ASD for 72 h. The production of interleukin (IL)-6, IL-8, and transforming growth factor (TGF)-β1 from nasal epithelial cells was determined by the enzyme-linked immunosorbent assay. The effects of ASD on A. fumigatus biofilm formation were determined using crystal violet, concanavalin A, safranin staining, and confocal scanning laser microscopy. Results: ASD and A. fumigatus significantly enhanced the production of IL-6 and IL-8 from nasal epithelial cells. By coculturing A. fumigatus with ASD, the dry weight and safranin staining of the fungal biofilms significantly increased in a time-dependent manner. However, the increased level of crystal violet and concanavalin A stain decreased after 72 h of incubation. Conclusions: ASD and A. fumigatus induced the production of inflammatory chemical mediators from nasal epithelial cells. The exposure of A. fumigatus to ASD enhanced the formation of biofilms. The coexistence of ASD and A. fumigatus may increase the development of fungal biofilms and fungal inflammatory diseases in the sinonasal mucosa.

Evaluating a semi-nested PCR to support histopathology reports of fungal rhinosinusitis in formalin-fixed paraffin-embedded tissue samples

BACKGROUND

Fungal rhinosinusitis (FRS) encompasses a various spectrum of diseases. Histopathology is the "reference method" for diagnosing FRS, but it cannot determine the genus and species. Moreover, in more than 50% of the histopathologically proven cases, the culture elicited no reliable results. This study was an attempt to evaluate the diagnostic efficiency of semi-nested polymerase chain reaction (PCR) from formalin-fixed paraffin-embedded (FFPE) functional endoscopic sinus surgery (FESS) in FRS patients.

METHODS

One hundred ten specimens were subjected to DNA extraction and histopathology examination. The amplification of the β-globin gene by conventional PCR was used to confirm the quality of extracted DNA. The semi-nested PCR was performed using ITS1, ITS2, and ITS4 primers during two steps. Sequencing the internal transcribed spacer region (ITS1-5.8S-ITS2) to identify causative agents was performed on PCR products.

RESULTS

Sixty-four out of 110 samples were positive by histopathology evidence, of which 56 samples (87.5%) were positive by PCR. Out of 46 negative samples by histopathological methods, five samples (10.9%) yielded positive results by PCR. Sensitivity, specificity, positive predictive value, and negative predictive value of the semi-nested PCR method were reported 87.5%, 89.2%, 92.7%, and 85.2%, respectively. The kappa factor between PCR and histopathological methods was 0.76, indicating substantial agreements between these two tests.

CONCLUSION

Due to the acceptable sensitivity and specificity of the present method, it might be used to diagnose fungal sinusitis infections along with microscopic techniques. This method is recommended to confirm the diagnose of suspected fungal sinusitis with negative histopathology results.

Isolated Fungal Balls in Urinary Bladder Presenting as Acute Retention of Urine

A 52-year-old male presented to surgery emergency with acute retention of urine. Patient was relieved in the emergency setting by catheterization and bladder irrigation. Urine was sterile; however, microscopy revealed field full of RBCs (>50/high-power field) and pus cells (>20/hpf). Cystoscopy revealed fungal balls in the urinary bladder which upon histopathological examination showed Aspergillus species. Patient was managed with systemic voriconazole and bladder wash with diluted povidone iodine. Predisposing factors diabetes mellitus and benign prostatic hyperplasia were medically managed, and patient recovered well. This case stresses the importance of considering isolated fungal urinary infections in predisposed individuals.

Clinical Characteristics Other Than Intralesional Hyperdensity May Increase the Preoperative Diagnostic Accuracy of Maxillary Sinus Fungal Ball

Objectives

This study aimed to evaluate the clinical characteristics of maxillary sinus fungus ball (MFB) to increase the preoperative diagnostic accuracy.

Methods

A retrospective review of 247 patients who underwent endoscopic sinus surgery for unilateral maxillary sinusitis from January 2015 to December 2017 at a single institution was performed. Patients with pathologically proven MFB were compared to those with unilateral chronic maxillary sinusitis (CMS). Patient demographics and computed tomography (CT) findings were evaluated. The CT features were categorized as intralesional hyperdensity (calcification), the irregular lobulated protruding lesion (fuzzy appearance), maxillary sinus full haziness without mass effect, maxillary sinus full haziness with mass effect, and others. A regression tree analysis was performed.

Results

In total, 247 patients were analyzed; among them, 179 (72.5%) had MFB and 68 (27.5%) had CMS. MFB showed predominance in older individuals. Among the radiological features, intralesional hyperdensity was most commonly associated with MFB. The presence of a fuzzy appearance or full opacity with mass effect was also associated with MFB. The highest area under the curve was noted with the regression tree analysis based on the model, which included the presence of intralesional hyperdensity, demographic data (age), and presence of fuzzy appearance or maxillary sinus full haziness with mass effect in case of absence of intralesional hyperdensity (0.904).

Conclusion

A simple algorithm to optimize the preoperative diagnosis of MFB was developed. Physicians should be aware of such findings in the management of patients presenting with unilateral CMS.

Nested PCR for the detection of Aspergillus species in maxillary sinus samples of patients with chronic sinusitis

BACKGROUND

Fungal rhinosinusitis has become an increasingly recognized disease, being Aspergillus species responsible for most of the cases. Its diagnosis is quite difficult because of the non-specific symptoms and low sensitivity of the current diagnostic methods.

AIMS

An Aspergillus-specific nested polymerase chain reaction (PCR) assay using biopsy specimens taken from the maxillary sinuses was performed in order to assess its usefulness. Conventional diagnostic methods (histology and culture) were also carried out.

METHODS

A case-control study was performed in the Institute of Stomatology, Jagiellonian University in Kraków, between 2011 and 2014. The case group consisted of 21 patients with suspected rhinosinusal mycetoma while the control group included 46 patients with no suspicion of fungal rhinosinusitis. The two-step PCR assay amplified an Aspergillus specific portion of the 18S rRNA gene. Interval estimation of sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were calculated to assess the diagnostic test performance. The agreement between the PCR and the other tests was evaluated using the Kappa coefficient (k).

RESULTS

Ninety percent of the samples obtained from patients diagnosed with mycetoma yielded positive PCR results. The PCR showed almost perfect concordance with histology (k=0.88). Sensitivity, specificity, PPV and NPV estimates were 90%; 95% CI: (55.5-99.7%), 98.3%; 95% CI: (90.9-100%), 90%; 95% CI: (55.5-99.7%) and 98.3%; 95% CI: (90.9-100%), respectively. One clinical sample showed growth of Aspergillus fumigatus and positive PCR despite the negative histological examination.

CONCLUSIONS

Nested PCR assay is a promising diagnostic tool to evaluate the presence of Aspergillus in the tissue of maxillary sinus from patients with suspicion of sinus aspergillosis.

[Histopathological Diagnosis of Invasive Fungal Infections in Formalin-Fixed and Paraffin-Embedded Tissues in Conjunction with Molecular Methods]

The main objective of this study was to evaluate the relationship between histopathology, polymerase chain reaction (PCR), and in situ hybridization (ISH) for the identification of causative fungi in formalin-fixed and paraffin-embedded (FFPE) tissue specimens. Since pathogenic fungi in tissue specimens can be difficult to identify morphologically, PCR and ISH have been usually employed as auxiliary procedures. However, little comparison has been made on the sensitivity and specificity of PCR and ISH using FFPE specimens. Therefore, to compare and clarify the reproducibility and usefulness of PCR and ISH as auxiliary procedures for histological identification, we performed histopathological review, PCR assays, and ISH to identify pathogenic fungi in 59 FFPE tissue specimens obtained from 49 autopsies. The following are the main findings for this retrospective review: i) even for cases classified as "mold not otherwise specified" (MNOS), two cases could be identified as Aspergillus species by molecular methods; ii) all cases classified as non-zygomycetes mold (NZM) were Aspergillus species and were not identified by molecular methods as other fungi; iii) all 3 cases classified as zygomycetes mold (ZM) could be identified by molecular methods as Mucorales; iv) except for 1 case identified by molecular methods as Trichosporon spp., 5 cases were originally identified as dimorphic yeast (DY). As a measure of nucleic acid integrity, PCR and ISH successfully detected human and fungal nucleic acids in approximately 60% of the specimens. Detection of Aspergillus DNA by nested PCR assay and by ISH against the A. fumigatus ALP gene were similarly sensitive and significant (p<0.01). Thus, our findings demonstrated the potential risk of error in the classification of fungi based on pathological diagnosis. Combining molecular methods such as ISH and PCR on FFPE specimens with pathological diagnosis should improve diagnostic accuracy of fungal infection.

Identification of fungal causative agents of rhinosinusitis from Mashhad, Iran

Background and Purpose:

Rhinosinusitis is a common disorder, influencing approximately 20% of the population at some time of their lives. It was recognized and reported with expanding recurrence over the past two decades worldwide. Undoubtedly, correct diagnosis of fungi in patients with fungal rhinosinusitis affects the treatment planning and prognosis of the patients. Identification of the causative agents using the standard mycological procedures remains difficult and time-consuming.

Materials and Methods:

Based on clinical and radiological parameters, 106 patients suspected of fungal rhinosinusitis were investigated in this cross-sectional prospective study from April 2012 to March 2016 at an otorhinolaryngology department. In this study, internal transcribed spacer (ITS) and calmodulin (CaM) sequencing were respectively validated as reliable techniques for the identification of Mucorales and Aspergillus to species level (both agents of fungal rhinosinusitis).

Results:

Of these, 63 (59.4%) patients were suspected of allergic fungal rhinosinusitis (AFRS), 40 (37.7%) patients suspected of acute invasive fungal rhinosinusitis (AIFRS), and 3 (2.8%) patients suspected of mycetoma. In patients suspected of AFRS, AIFRS, and mycetoma only 7, 29, and 1 had positive fungal culture, respectively. After ITS and CaM sequencing, Aspergillus flavus was the most common species isolated from non-invasive forms, and A. flavus and Rhizopus oryzae were more frequently isolated from invasive forms.

Conclusion:

Aspergillus flavus is the most common agent of fungal rhinosinusitis in Iran, unlike most other reports from throughout the world stating that A. fumigatus is the most frequent causative agent of this disease.

Direct identification of molds by sequence analysis in fungal chronic rhinosinusitis

Fungi are widely implicated in chronic rhinosinusitis. Direct microscopic examination (DME) is used to confirm the biological diagnosis of fungal rhinosinusitis (FRS). Diagnostic sensitivity of DME is better than culture, however DME does not allow fungal species identification. In this study, we included 54 sinus samples demonstrating hyphae on DME. Direct sequencing was compared to culture for the identification of the fungal species. Sequence analysis identified fungi in 81.5% of cases while culture was positive in only 31.5%. The most common genus was Aspergillus and the identified species belonged to section Fumigati or to section Flavi. Among other fungi identified by sequence analysis, Schizophyllum commune was present in three samples attesting to the importance of this Basidiomycetes in FRS. Our results clearly demonstrate the superiority of sequencing compared to culture when performed on specimens with hyphal elements at DME, and contributes to the epidemiological knowledge of fungi involved in FRS.

Contribution of molecular tools for the diagnosis and epidemiology of fungal chronic rhinosinusitis

Chronic rhinosinusitis (CRS) rank second at chronic inflammatory diseases in industrialized countries and are an important public health concern. Diagnosis relies on a set of arguments including clinical signs, imaging, histopathologic and mycological analyses of sinus specimens, collected during nasal endoscopy. The sensitivity of fungal cultures is reported to be poor, even when direct examination is positive, thus the epidemiology of fungal chronic sinusitis is ill-known. This study evaluated the sensitivity of molecular diagnosis in 70 consecutive samples (61 patients with CRS) analysed at the University Hospital of Rennes during a 3-year period. DNA detection was performed using a conventional PCR method targeting the ITS1/ITS2 sequence and the resulting amplification products were sequenced. Fungal CRS was proven in 42 patients (69%), of which only 20 (48%) had a positive culture. 37/42 (88%) patients were diagnosed with a fungus ball, 3 with allergic fungal CRS and 2 with undetermined fungal CRS. PCR was positive in all 42 cases and direct sequencing allowed to identify fungi in all cases but one, and detected multiple infection in 3. Aspergillus fumigatus was present in 69% of patients; Cladosporium cladosporoides in 9.5%, Scedosporium sp., A. nidulans and A. flavus in 7% each. In 2/19 patients with negative direct examination, sequencing analysis revealed the presence of Capnobotryella sp. and C. cladosporoides, in clinical settings compatible with fungal sinusitis. In conclusion, ITS1/ITS2 PCR had a twice better sensitivity than culture, and combined sequencing provides accurate epidemiological data on fungal CRS.

Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods

The etiology of invasive fungal infections (IFI) is incompletely understood due to diagnostic limitations including insensitivity of cultures and failure of histopathology to discriminate between different species. This diagnostic gap precludes the optimal use of antifungals, leading to adverse patient outcomes. The identification of fungal pathogens from Formalin-fixed, Paraffin-embedded tissue (FFPE) blocks by molecular methods is emerging as an alternative approach to study the etiology of IFI. PCR assays, including species specific- and broadrange fungal tests are used with FFPE samples from patients with proven IFI. Fungal species identification is achieved in 15-90% of the samples. This heterogeneity may be explained by the samples studied. However, comparison of different studies is impaired, as controls ruling out false positive-, false negative test results or PCR inhibition are frequently not reported. Studies using in situ hybridization also vary in the clinical samples included and the targeted fungi. In addition, target sequences, the probe chemistry and the detection of hybridization signals also account for the differences in diagnostic sensitivity. Using both approaches in parallel yields additive insights, potentially leading to a superior identification of fungal etiology and awareness of the limitations of both molecular diagnostic approaches.

Analysis of fungal ball rhinosinusitis by culturing fungal clumps under endoscopic surgery

OBJECTIVE

This study was designed to investigate the clinical microbiology of fungal ball (FB) rhinosinusitis by culturing fungal clumps collected under endoscopic surgery.

METHODS

From April to November of 2012, fungal clumps were sampled by endoscopic surgery from patients diagnosed with FB using clinical and histopathological methods. The specimens were subjected to smear microscopy, and cultured for bacteria and fungi analysis.

RESULTS

Out of the 81 specimens from 80 patients, 69 (69/81, 85.19%) specimens were detected a mixed infection of bacteria and fungi. However, only 25 (25/81, 30.86%) specimens resulted in fungal growth. There were 12 (12/81, 14.81%) specimens with fungal infections alone. The cultured fungi included 36 strains belonging to five genera, and most of them were Aspergillus spp. (30/36, 83.3%). The cultured bacteria included 94 strains belonging to 16 genera, and the most frequently seen was Staphylococcus spp. (23/94, 35.94%). When it was fungal and Pseudomonas aeruginosa mixed infection, the fungal growth was inhibited (P = 0.002).

CONCLUSION

Patients with fungal ball usually have mixed fungal and bacterial infections. The fungi from these samples are sometimes difficult to culture, which may be the result of the inhibition by bacteria in vitro and in vivo.

Performances of two different panfungal PCRs to detect mould DNA in formalin-fixed paraffin-embedded tissue: what are the limiting factors?

BACKGROUND

Detection of fungal DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is challenging due to degradation of DNA and presence of PCR inhibitors in these samples. We analyzed FFPE samples of 26 patients by panfungal PCR and compared the results to the composite diagnosis according to the European Organization for Research and Treatment of Cancer (EORTC) criteria. Additionally we analyzed the quality of human and fungal DNA and their level of age-dependent degradation, as well as the existence of PCR inhibition in these tissue samples.

METHODS

We evaluated two 45-cycle panfungal PCR tests that target the internal transcribed spacer 2 (ITS2) as well as the ITS1-5.8S-ITS2 (ITS1-2) region. The PCRs were applied to 27 FFPE specimens from 26 patients with proven invasive fungal disease (IFD), and one patient with culture and histologically negative but PCR-positive fungal infection collected at our institution from 2003 to 2010. Quality of DNA in FFPE tissue samples was evaluated using fragments of the beta-globin gene for multiplex PCR, inhibition of PCR amplification was evaluated by spiking of C. krusei DNA to each PCR premix.

RESULTS

In 27 FFPE samples the ITS2 PCR targeting the shorter fragment showed a higher detection rate with a sensitivity of 53.8% compared to the ITS1-2 fragment (sensitivity 38%). Significant time-dependent degradation of human DNA in FFPE sample extracts was detected based on partial beta-globin gene amplification which was not in correlation to successful panfungal PCR identification of fungal organisms. The analytical sensitivity of both assays compared with culture was 60 CFU/ml of a Candida krusei reference strain. The performance of the two tests in an Aspergillus proficiency panel of an international external quality assessment programme showed considerable sensitivity.

CONCLUSION

Panfungal diagnostic PCR assays applied on FFPE specimens provide accurate identification of molds in highly degraded tissue samples and correct identification in samples stored up to 7 years despite sensitivity limitations, mainly caused by partial PCR inhibition and DNA degradation by formalin.

Comparison between the effectiveness of polymerase chain reaction and in situ hybridization in detecting the presence of pathogenic fungi by using the preserved DNA in formalin-fixed and paraffin-embedded tissues

In situ hybridization (ISH) has been recognized as an important technique for identifying the causative fungi in the foci of infection observed in histopathological specimens which was processed from formalin-fixed and paraffin-embedded (FFPE) tissues. However, few basic studies have conducted an evaluation of the DNA preservation for use in ISH in comparison to polymerase chain reaction (PCR). The latter is a DNA amplification-based modality. In the present study, we analyzed 65 FFPE lung tissue specimens collected from autopsy cases for comparing the usefulness of ISH and PCR analysis. As a result, the positive identification rates for PCR were strikingly low; a majority of these results can be assumed to be false negative because the presence of fungi had been confirmed by histopathological analysis. In contrast, panfungal ISH targeting of the 28S rRNA showed a higher sensitivity than the 230-bp panfungal PCR primers did (80.0% versus 4.6%, respectively). Furthermore, over 60% of the samples we examined showed a favorable intensity of the ISH signal. Therefore, in conventional postmortem FFPE tissues, the state of DNA preservation may be more favorable for ISH than PCR analysis.

Identification of fungi in fungal ball sinusitis: comparison between MUC5B immunohistochemical and Grocott methenamine silver staining

CONCLUSION

MUC5B immunohistochemical staining was a valuable method for identifying fungi in fungal ball sinusitis, especially in distinguishing aspergillus and mucor. Combined infection with Aspergillus and Mucor fungi was the most common pattern in fungal ball sinusitis.

OBJECTIVE

To assess the value of MUC5B immunohistochemical staining in identifying fungi in fungal ball sinusitis by comparing it with conventional Grocott methenamine silver (GMS) staining.

METHODS

GMS staining and MUC5B immunohistochemical staining were used to identify fungi in mucopurulent cheesy or clay-like tissues from sinuses in 180 fungal ball sinusitis patients, and the examination results were compared.

RESULTS

In 180 samples of fungal ball sinusitis, GMS staining showed Aspergillus in 130, Mucor in 88, and Candida albicans in 6, while MUC5B immunohistochemical staining identified Aspergillus in 166, Mucor in 172, and Candida albicans in 16. The fungal detection rate for MUC5B immunohistochemical staining was markedly greater than that for GMS staining (p < 0.01). This implies that MUC5B immunohistochemical staining was more sensitive than GMS staining in identifying fungi in fungal ball sinusitis. Mixed infection of Aspergillus and Mucor was present in 146 of 180 patients (81.1%).

Associations between quantitative measures of fungi in home floor dust and lung function among older adults with chronic respiratory disease: a pilot study

OBJECTIVE

Many fungi may cause allergic reactions and increase asthma symptoms prevalence and severity. One susceptible, vulnerable population subgroup of increasing size in industrialized countries and of public health concern who spends the majority of their time at home is older adults. Older adults diagnosed with chronic obstructive pulmonary disease (COPD) are at risk of exposure to fungi. Currently, species identification is based on observation of microscopic and macroscopic morphologies, which may underestimate concentrations compared to quantitative polymerase chain reaction (qPCR)-based measurements which are toxicologically more relevant to exposure science.

METHODS

This article analyzes quantitative indoor exposure data on fungi in floor dust (cells/cm(2) floor) by real-time qPCR-based detection with quantitative outcome data via field spirometry in a pilot community-based study in Visalia, Tulare County, California, between July 2009 and January 2010. Subjects (n = 9, five females, four males) were Caucasian, English-speaking, nonsmoking older adults with doctor-diagnosed asthma and/or COPD.

RESULTS

While certain results did not reach statistical significance (p ≤ .10) due to sample size-overall and by gender-we found consistent trends and statistically significant associations for total fungal DNA (summer data) with forced vital capacity and forced expiratory volume in 1 second.

CONCLUSIONS

The results of this pilot study are novel and suggest adverse effects of exposure inside homes to certain fungal species. This pilot study supports the need for larger prospective epidemiologic studies of older adults with asthma and/or chronic bronchitis based on quantitative environmental and clinical measures.

Enhanced fungal DNA-extraction from formalin-fixed, paraffin-embedded tissue specimens by application of thermal energy

Determining the etiology of invasive fungal infections (IFI) is critical for patient management as fungi vary in their susceptibility to antifungals. However, the etiology remains obscure in many cases due to negative culture results. The identification of fungal DNA by PCR in pathology blocks and sequencing it is an alternative approach to determine the cause of IFI. Previous studies identified fungal DNA in only 50% of samples with positive histopathology results, probably due to DNA damage by tissue fixation. We used realtime PCR to quantify human and fungal DNA from formalin-fixed, paraffin-embedded tissue specimens in order to study the effect of thermal energy during extraction on the yield of amplifiable DNA and subsequent identification of fungal DNA. Tissue sections from eight patients with proven IFI were subjected to DNA extraction with varying exposure to thermal energy. Amplifiable DNA increased up to 76-fold by increasing the incubation temperature from 65°C to 90°C and an additional increase was documented by incubating samples for up to 6 hours at this temperature. The augmented amplification of fungal DNA was associated with improved species identification by the sequencing of the PCR amplicons. This may help illuminate the etiology of IFI and thereby improve patient management by guiding antifungal therapy.

Degradation of fungal DNA in formalin-fixed paraffin-embedded sinus fungal balls hampers reliable sequence-based identification of fungi

Identification of the etiologic agent responsible for sinus fungal ball (SFB) is rarely obtained due to either the culture of patient specimens not being ordered or if cultures were inoculated they proved to be negative. Obviously, this has a significant impact on the design of appropriate therapeutic strategies. We investigated whether paraffin-embedded (PE) tissues, the only materials often available, were suitable for the correct identification of the responsible fungi. We obtained PE tissues of SFB from 16 different patients who had risk factors for invasive fungal infections. DNA was extracted using an automated extractor and the internal transcribed spacer (ITS) sequenced following amplification with two sets of primers designed to amplify >300 bp fragments. This was attempted in parallel with a real-time quantitative PCR assay targeting Aspergillus spp. mitochondrial DNA designed to amplify <150 bp fragments. ITS sequencing succeeded in appropriately identifying the etiologic agents in 10 of the 16 samples (nine Aspergillus fumigatus, one Lewia spp.). In contrast, the <150 bp PCR assay amplified all specimens correctly except the one involving Lewia spp. If fungal identification is warranted to understand the pathophysiology of SFB and guide clinicians, we cannot rely only on ITS sequencing of the DNA obtained from PE tissues. The main reason is probably due to the fact that formalin prevents amplification of long DNA fragments and consequently, frozen or fresh tissues should be employed.

Allergic fungal rhinosinusitis: detection of fungal DNA in sinus aspirate using polymerase chain reaction

Objective:

This study investigated allergic fungal rhinosinusitis cases, and aimed to compare the detection of fungi in sinus aspirate by culture and by polymerase chain reaction assay, and to relate the presence of fungi in the nasal sinuses to the type of fungal allergen causing disease.

Methods:

Sixty-eight cases of allergic fungal rhinosinusitis underwent fungal culture and polymerase chain reaction assay for universal fungal, aspergillus and bipolaris DNA. Aspergillus-specific immunoglobulin E levels were measured in sinus aspirate, and total serum immunoglobulin E levels were calculated. A control group of 10 cases was included in the study.

Results:

Of the 68 allergic fungal rhinosinusitis cases, only 42 (61.7 per cent) had positive fungal cultures; of the 10 controls, only three (30 per cent) had positive cultures. Species from the dematiaceous family were most commonly grown, being isolated in 30 cases (71.4 per cent). Bipolaris was the most commonly isolated species (18 cases) followed by curvularia (11 cases) and alternaria (one case). Polymerase chain reaction assay detected fungal DNA in all the allergic fungal rhinosinusitis cases and also in four controls (40 per cent). Ten patients (of 68; 14.7 per cent) were positive forAspergillus fumigatusspecific immunoglobulin E. The mean concentration of this immunoglobulin was 11.32 ± 4.12 IU/ml in patients and 0 IU/ml in controls, a statistically significant difference.

Conclusion:

Detection of fungal DNA in nasal aspirate by polymerase chain reaction was superior to fungal cultures as a method of detecting fungal growth. In allergic fungal rhinosinusitis, fungal growth is not always accompanied by an allergic reaction.

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

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

Negative impact of Aspergillus galactomannan and DNA detection in the diagnosis of fungal rhinosinusitis

A proportion of patients with chronic rhinosinusitis, especially if nasal polyps are present, have a diagnosis of fungal rhinosinusitis. The diagnosis is difficult to establish because the symptoms and clinical and radiological signs are non-specific. Also current diagnostic methods, i.e. histology, fungal staining and culture, are insensitive. The performance of the Aspergillus galactomannan (GM) ELISA and real-time PCR for Aspergillus fumigatus mitochondrial DNA was evaluated for the detection of Aspergillus in sinus mucus samples from 25 patients with chronic rhinosinusitis with nasal polyposis. The results were compared with those from nasal lavage fluid from 19 healthy volunteers. Seven patients (28 %) were diagnosed as having fungal rhinosinusitis according to the presence of filaments in histology or direct microscopy using Calcofluor white. All fungal rhinosinusitis patients were negative in the GM ELISA. GM ELISA was positive in five patients whose samples were negative using conventional methods and A. fumigatus PCR. Two out of seven patients with fungal rhinosinusitis were positive by A. fumigatus PCR: one also had a positive A. fumigatus culture, and one had hyphae consistent with Aspergillus in histology. One additional patient had a weak positive PCR result, but other fungal tests were negative. In control subjects, the GM ELISA was positive in 21 %, whereas direct microscopy, culture and A. fumigatus PCR were negative in all samples. Direct microscopy and culture together with histology remain pivotal in defining fungal rhinosinusitis diagnosis. A. fumigatus PCR may have additional value in allowing the diagnosis to be made sooner, whereas the GM ELISA is not reliable in diagnosing Aspergillus infection of the paranasal sinuses.

Scedosporium apiospermum infection after near-drowning

Scedosporium apiospermum and its teleomorph (sexual form) Pseudallescheria boydii are ubiquitous saprophytic fungi, which under specific conditions, such as near-drowning, may cause therapy-refractory and life-threatening infections. We reviewed 22 cases (eight children and 14 adults) of S. apiospermum infection after near-drowning reported in the literature including an additional paediatric case from our institution. Scedosporiosis after near-drowning was associated with high mortality (16/23, 70%) even in immunocompetent hosts. It affected mainly young (mean age 24 years) and immunocompetent (83% with no apparent immune defect) males (male to female ratio 2.5 : 1). Scedosporiosis after near-drowning was a slow progressive disease (mean survival time 87 days) involving virtually all body organs. However, central nervous system (CNS) dissemination predominated (21/23, 91%) presenting mainly as multiple brain abscesses (15/23, 65%). All 23 patients showed preceding clinical and/or radiological evidence of lung disease indicating the mode of invasion. Diagnosis was delayed (median time to diagnosis 28 days) and was made by culture (16/23, 69.5%) or culture and tissue examination (7/23, 30.5%). The majority of the patients (20/23, 87%) received antifungal treatment and underwent neurosurgery. While the optimal treatment remains undefined, the most recent reports indicated voriconazole as a potentially effective option. Better knowledge of scedosporiosis after near-drowning could lead to improved intervention and ultimately to more favourable outcome.

Diagnosis of invasive aspergillosis and mucormycosis in immunocompromised patients by seminested PCR assay of tissue samples

Aspergillosis and mucormycosis are the most common mold infections in patients with hematological malignancies. Infections caused by species of the genus Aspergillus and the order Mucorales require different antifungal treatments depending on the in vitro susceptibility of the causative strain. Cultures from biopsy specimens frequently do not grow fungal pathogens, even from histopathologically proven cases of invasive fungal infection. Two seminested PCR assays were evaluated by amplifying DNA of zygomycetes and Aspergillus spp. from organ biopsies of 21 immunocompromised patients. The PCR assays correctly identified five cases of invasive aspergillosis and six cases of mucormycosis. They showed evidence of double mold infection in two cases. Both assays were negative in five negative controls and in two patients with yeast infections. Sequencing of the PCR products was in accordance with culture results in all culture-positive cases. In six patients without positive cultures but with positive histopathology, sequencing suggested a causative organism. Detection of fungal DNA from biopsy specimens allows rapid identification of the causative organism of invasive aspergillosis and mucormycosis. The use of these PCR assays may allow guided antifungal treatment in patients with invasive mold infections.

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

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

Development and clinical application of a panfungal PCR assay to detect and identify fungal DNA in tissue specimens

Given the rise in the incidence of invasive fungal infections (IFIs) and the expanding spectrum of fungal pathogens, early and accurate identification of the causative pathogen is essential. We developed a panfungal PCR assay that targets the internal transcribed spacer 1 (ITS1) region of the ribosomal DNA gene cluster to detect fungal DNA in fresh and formalin-fixed, paraffin-embedded (PE) tissue specimens from patients with culture-proven (n=38) or solely histologically proven (n=24) IFIs. PCR products were sequenced and compared with sequences in the GenBank database to identify the causal pathogen. The molecular identification was correlated with results from histological examination and culture. The assay successfully detected and identified the fungal pathogen in 93.6% and 64.3% of culture-proven and solely histologically proven cases of IFI, respectively. A diverse range of fungal genera were identified, including species of Candida, Cryptococcus, Trichosporon, Aspergillus, Fusarium, Scedosporium, Exophiala, Exserohilum, Apophysomyces, Actinomucor, and Rhizopus. For five specimens, molecular analysis identified a pathogen closely related to that identified by culture. All PCR-negative specimens (n=10) were PE tissues in which fungal hyphae were visualized. The results support the use of the panfungal PCR assay in combination with conventional laboratory tests for accurate identification of fungi in tissue specimens.

Biology of the pathogenic yeast Candida glabrata

The yeasts, being favorite eukaryotic microorganisms used in food industry and biotechnologies for production of biomass and various substances, are also used as model organisms in genetic manipulation, molecular and biological research. In this respect, Saccharomyces cerevisiae is the best-known species but current situation in medicine and industry requires the use of other species. Here we summarize the basic taxonomic, morphological, physiological, genetic, etc. information about the pathogenic yeast Candida glabrata that is evolutionarily very closely related to baker's yeast.

Fungal speciation using quantitative polymerase chain reaction (QPCR) in patients with and without chronic rhinosinusitis

OBJECTIVES/HYPOTHESIS

The objectives of this study were to determine the mycology of the middle meatus using an endoscopically guided brush sampling technique and polymerase chain reaction laboratory processing of nasal mucous; to compare the mycology of the middle meatus in patients with sinus disease with subjects without sinus disease; to compare the responses on two standardized quality-of-life survey forms between patients with and without sinusitis; and to determine whether the presence of fungi in the middle meatus correlates with responses on these data sets.

STUDY DESIGN

The authors conducted a single-blind, prospective, cross-sectional study.

METHODS

Patients with sinus disease and a control group without sinus disease were enrolled in the study. A disease-specific, validated Sinonasal Outcomes Test survey (SNOT-20) was completed by the subjects and a generalized validated Medical Outcomes Short Form 36 Survey (SF-36) was also completed. An endoscopically guided brush sampling of nasal mucous was obtained from the middle meatus. Fungal specific quantitative polymerase chain reaction (QPCR) was performed on the obtained sample to identify one of 82 different species of fungus in the laboratory. Statistical analysis was used to categorize the recovered fungal DNA and to crossreference this information with the outcomes surveys.

RESULTS

The fungal recovery rate in the study was 45.9% in patients with sinus disease and 45.9% in control subjects. Patients with chronic rhinosinusitis had a mean SNOT-20 score of 1.80 versus the control group mean score of 0.77 (P < .0001). SF-36 data similarly showed a statistically significant difference between diseased and control populations with controls scoring a mean of 80.37 and patients with chronic rhinosinusitis scoring a mean of 69.35 for a P value of .02. However, no statistical significance could be ascribed to the presence or absence of fungi recovered, the type of fungi recovered, or the possible impact of fungi on the quality-of-life survey results.

CONCLUSION

The recovery rate of fungi from the middle meatus of patients with chronic rhinosinusitis and a control population without chronic rhinosinusitis is 45.9% using QPCR techniques. No direct causation with regard to fungal species or presence was proven; however, a species grouping for future studies is proposed based on trends in this data and other reports. Disease-specific outcomes surveys revealed a statistically significant difference between the two groups.

Paranasal sinus fungus ball: epidemiology, clinical features and diagnosis. A retrospective analysis of 173 cases from a single medical center in France, 1989-2002

Over the last decade, we have observed a high frequency of Aspergillus rhinosinusitis in french medical centers. The epidemiological data, clinical presentations, radiology, mycology and histology results of 173 consecutive patients with paranasal sinus fungus balls who were admitted from 1989 to 2002 have been reviewed. The most common symptoms included purulent nasal discharges and nasal obstructions, with the maxillary sinus being the most common site of infection (152 cases, 87.8%). Computed tomography scans (CT scan) were performed in 92% (159/173) of the cases and heterogeneous opacities were observed in 132 patients (83%). Histology examinations were performed in all cases and proved positive in 162 patients. Fungi were recovered, mainly Aspergillus fumigatus, from samples of 50 patients, while specimens from the remaining 123 patients were negative. Since no specific clinical sign could be found, a diagnosis of fungus ball is frequently made after a long term symptomatic period. CT scan findings of metallic or calcified densities within an opacified sinus cavity are highly suggestive of a fungus ball, but mycological and histological studies are essential to confirm the diagnosis. Treatment consisted of functional endonasal sinus surgery and was successful in 172 out of 173 cases.

Rapid identification of clinical Trichoderma longibrachiatum isolates by cellulose-acetate electrophoresis-mediated isoenzyme analysis

Cellulose-acetate electrophoresis was used to investigate isoenzyme polymorphism among ten clinical and 11 non-clinical isolates of Trichoderma. Initial testing of 13 enzyme systems for activity and resolution of bands showed that seven were appropriate for identifying the different species. Each of the enzyme systems investigated (glucose-6-phosphate dehydrogenase, glucose-6-phosphate isomerase, 6-phosphogluconate dehydrogenase, peptidases A, B and D, and phosphoglucomutase) was diagnostic for at least one species. On the basis of the results of isoenzyme analysis, several isolates identified originally as Trichoderma pseudokoningii, T. koningii or T. citrinoviride were re-identified as T. longibrachiatum, in agreement with sequence analysis data for the internal transcribed spacer region of the isolates. The availability of a quick, inexpensive and reliable diagnostic tool for the identification of T. longibrachiatum isolates is important, as most clinical Trichoderma isolates belong to T. longibrachiatum. Furthermore, as many different enzyme systems are available, the method may also be suitable for the identification of other clinically relevant fungal species.

Scedosporium apiospermum: changing clinical spectrum of a therapy-refractory opportunist*

Current knowledge on the opportunist Scedosporium apiospermum (teleomorph: Pseudallescheria boydii), generated over a period of more than 120 years, is reviewed. The natural environmental habitat of the fungus is unknown; nutrient-rich, brackish waters like river estuaria have been suggested. The fungus is strongly promoted by agricultural and particularly by industrial pollution.

Validation and Clinical Application of Molecular Methods for the Identification of Molds in Tissue

BACKGROUND

Invasive fungal infections due to less-common molds are an increasing problem, and accurate diagnosis is difficult.

METHODS

We used our previously established molecular method, which allows species identification of molds in histological tissue sections, to test sequential specimens from 56 patients with invasive fungal infections who were treated at our institution from 1982 to 2000.

RESULTS

The validity of the method was demonstrated with the establishment of a molecular diagnosis in 52 cases (93%). Confirmation of the causative organism was made in all cases in which a mold had been cultured from the tissue specimen. Less-common molds were identified in 7% of cases and appear to be an increasing problem.

CONCLUSIONS

Our previously established method has proven to be of value in determining the incidence of invasive infection caused by less-common molds. Institutions should continue to pursue diagnosis of invasive fungal infections by means of tissue culture and microbiologic analysis.

Laboratory diagnosis of invasive aspergillosis

Invasive aspergillosis occurs in a wide range of clinical scenarios, is protean in its manifestations, and is still associated with an unacceptably high mortality rate. Early diagnosis is critical to a favourable outcome, but is difficult to achieve with current methods. Deep tissue diagnostic specimens are often difficult to obtain from critically ill patients. Newer antifungal agents exhibit differential mould activity, thus increasing the importance of establishing a specific diagnosis of invasive aspergillosis. For these reasons, a range of alternate diagnostic strategies have been investigated. Most investigative efforts have focused on molecular and serological diagnostic techniques. The detection of metabolites produced by Aspergillus spp and a range of aspergillus-specific antibodies represent additional, but relatively underused, diagnostic avenues. The detection of galactomannan has been incorporated into diagnostic criteria for invasive aspergillosis, reflecting an increased understanding of the performance, utility, and limitations of this technique. Measurement of (1,3)-beta-D glucan in blood may be useful as a preliminary screening tool for invasive aspergillosis, despite the fact that this antigen can be detected in a number of other fungi. There have been extensive efforts directed toward the detection of Aspergillus spp DNA, but a lack of technical standardisation and relatively poor understanding of DNA release and kinetics continues to hamper the broad applicability of this technique. This review considers the application, utility, and limitations of the currently available and investigational diagnostic modalities for invasive aspergillosis.

Assessment of ribosomal large-subunit D1-D2, internal transcribed spacer 1, and internal transcribed spacer 2 regions as targets for molecular identification of medically important Aspergillus species

Molecular approaches are now being developed to provide a more rapid and objective identification of fungi compared to traditional phenotypic methods. Ribosomal targets, especially the large-subunit RNA gene (D1-D2 region) and internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions), have shown particular promise for the molecular identification of some fungi. We therefore conducted an assessment of these regions for the identification of 13 medically important Aspergillus species: Aspergillus candidus, Aspergillus (Eurotium) chevalieri, Aspergillus (Fennellia) flavipes, Aspergillus flavus, Aspergillus fumigatus, Aspergillus granulosus, Aspergillus (Emericella) nidulans, Aspergillus niger, Aspergillus restrictus, Aspergillus sydowii, Aspergillus terreus, Aspergillus ustus, and Aspergillus versicolor. The length of ribosomal regions could not be reliably used to differentiate among all Aspergillus species examined. DNA alignment and pairwise nucleotide comparisons demonstrated 91.9 to 99.6% interspecies sequence identities in the D1-D2 region, 57.4 to 98.1% in the ITS1 region, and 75.6 to 98.3% in the ITS2 region. Comparative analysis using GenBank reference data showed that 10 of the 13 species examined exhibited a < or = 1-nucleotide divergence in the D1-D2 region from closely related but different species. In contrast, only 5 of the species examined exhibited a < or = 1-nucleotide divergence from sibling species in their ITS1 or ITS2 sequences. Although the GenBank database currently lacks ITS sequence entries for some species, and major improvement in the quality and accuracy of GenBank entries is needed, current identification of medically important Aspergillus species using GenBank reference data seems more reliable using ITS query sequences than D1-D2 sequences, especially for the identification of closely related species.

Fungus culture and PCR in nasal lavage samples of patients with chronic rhinosinusitis

Chronic rhinosinusitis (CRS) affects approximately 15 % of the adult population in industrialized countries. Fungi have been recognized as important pathogens in CRS in the immunocompromised host. Recently, fungi have been detected in more than 90 % of nasal lavages (NLs) in immunocompetent patients with CRS. Employing NLs of immunocompetent patients with CRS in the present study, the detection rates for fungi by culture techniques were compared with the results of different fungus-specific PCR assays. Standard fungal cultures were performed on NLs from 77 patients with CRS. NLs were also tested for the presence of fungal DNA by a panfungal assay with and without specific probes for Candida spp. and Aspergillus spp./Penicillium spp., and an Aspergillus-specific nested PCR assay. Nineteen of the 77 samples (25 %) grew fungi. Fungus-specific DNA was detected in 34 of 77 NLs (44 %). Twelve samples were positive for both culture and panfungal PCR, whereas seven specimens grew fungi in culture, but were negative in panfungal PCR, and an additional seven samples were positive in panfungal PCR, but negative in culture. The combination of culture and all employed PCR assays detected fungi in 39 patients (50 %). This study demonstrated that PCR and conventional culture techniques could be complementary diagnostic techniques to detect fungi in nasal specimens from CRS patients.

Use of paraffin-embedded tissue for identification of Saccharomyces cerevisiae in a baker's lung nodule by fungal PCR and nucleotide sequencing

A 40-year-old healthy male employed in a bakery presented with a single lung nodule and underwent investigations to rule out pulmonary carcinoma. Biopsy was positive for yeast cells, which did not match common fungal pathogens. PCR assay of paraffin-embedded tissue and nucleotide sequencing with ribosomal ITS1-ITS2 universal primers revealed the presence of Saccharomyces cerevisiae.