Clinical use of fungal PCR from deep tissue samples in the diagnosis of invasive fungal diseases: a retrospective observational study

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.

PCR diagnostic platforms for non-Aspergillus mold infections: ready for routine implementation in the clinic?

INTRODUCTION

While Aspergillus spp. remain the predominant cause of invasive mold infections, non-Aspergillus molds, such as the Mucorales or Fusarium spp., account for an increasing proportion of cases. The diagnosis of non-Aspergillus invasive mold infections (NAIMI) is challenging because of the low sensitivity and delay of conventional microbiological tests. Therefore, there is a particular interest to develop molecular tools for their early detection in blood or other clinical samples.

AREAS COVERED

This extensive review of the literature discusses the performance of Mucorales-specific PCR and other genus-specific or broad-range fungal PCR that can be used for the diagnosis of NAIMI in diverse clinical samples, with a focus on novel technologies.

EXPERT OPINION

PCR currently represents the most promising approach, combining good sensitivity/specificity and ability to detect NAIMI in clinical samples before diagnosis by conventional cultures and histopathology. Several PCR assays have been designed for the detection of Mucorales in particular, but also Fusarium spp. or Scedosporium/Lomentospora spp. Some commercial Mucorales PCRs are now available. While efforts are still needed for standardized protocols and the development of more rapid and simpler techniques, PCR is on the way to becoming an essential test for the early diagnosis of mucormycosis and possibly other NAIMIs.

Clinical performance of metagenomic next-generation sequencing for diagnosis of invasive fungal disease after hematopoietic cell transplant

Background

Timely diagnosis and appropriate antifungal therapy are critical for improving the prognosis of patients with invasive fungal disease (IFD) after hematopoietic stem cell transplantation (HSCT). We evaluated the performance of metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT), as well as the diagnosis, therapeutic management, and outcomes of IFD after HSCT.

Methods

We retrospectively studied 189 patients who underwent HSCT and were considered at risk for IFD. In total, 46 patients with IFD were enrolled in this study. The IFD consensus was followed for classifying IFD incidents.

Results

Forty-six patients were diagnosed with proven/probable (n = 12), possible (n = 27), and undefined (n = 7) IFD. Aspergillus was the most commonly detected fungal genus. Mucormycosis was found in 15 patients; two had Aspergillus, and one had Candida infections. Compared to CMT, mNGS significantly reduced the time required to identify pathogens (P = 0.0016). mNGS had a much higher sensitivity than CMT (84.78% vs. 36.96%; P < 0.0001). A total of 76.09% of patients received antifungal prophylaxis during fungal infections. All Pneumocystis infections occurred later than 100 days after transplantation. Among patients with Pneumocystis infection, 71.43% occurred following sulfonamide withdrawal, and subsequent treatment with sulfonamide alone or in combination with other drugs was effective. Based on the empirical antifungal treatment, the dosages, modes of administration, frequency of administration, or antifungal of 55.26% of the patients were changed according to the mNGS results. The 4-year overall survival rate of patients diagnosed with IFD after transplantation was 71.55% (95% CI, 55.18%-85.82%). Hypoproteinemia and corticosteroid use are independent risk factors for IFD.

Conclusion

mNGS, which has a high sensitivity and a short detection time, aids in the diagnosis and prognosis of pathogenic fungi. As a powerful technology, mNGS can influence treatment decisions in patients with IFD following HSCT.

Fungal Spectrum and Susceptibility Against Nine Antifungal Agents in 525 Deep Fungal Infected Cases

Background

Deep fungal infection has become an important cause of infection and death in hospitalized patients, and this has worsened with increasing antifungal drug resistance.

Objective

A 3-year retrospective study was conducted to investigate the clinical characteristics, pathogen spectrum, and drug resistance of deep fungal infection in a regional hospital of Guangzhou, China.

Methods

Non-duplicate fungi isolates recovered from blood and other sterile body fluids of in-patients of the clinical department were identified using biochemical tests of pure culture with the API20C AUX and CHROMagar medium. Antifungal susceptibilities were determined by Sensititre YeastOne^® panel trays.

Results

In this study, 525 patients (283 female, 242 male) with deep fungal infection were included, half of them were elderly patients (≥60 years) (54.67%, n=286). A total of 605 non-repetitive fungi were finally isolated from sterile samples, of which urine specimens accounted for 66.12% (n=400). Surgery, ICU, and internal medicine were the top three departments that fungi were frequently detected. The mainly isolated fungal species were Candida albicans (43.97%, n=266), Candida glabrata (20.00%, n=121), and Candida tropicalis (17.02%, n=103), which contributed to over 80% of fungal infection. The susceptibility of the Candida spp. to echinocandins, 5-fluorocytosine, and amphotericin B remained above 95%, while C. glabrata and C. tropicalis to itraconazole were about 95%, and the dose-dependent susceptibility of C. glabrata to fluconazole was more than 90%. The echinocandins had no antifungal activity against Trichosporon asahi in vitro (MIC₉₀>8 μg/mL), but azole drugs were good, especially voriconazole and itraconazole (MIC₉₀ = 0.25 μg/mL).

Conclusion

The main causative agents of fungal infection were still the genus of Candida. Echinocandins were the first choice for clinical therapy of Candida infection, followed with 5-fluorocytosine and amphotericin B. Azole antifungal agents should be used with caution in Candida glabrata and Candida tropicalis infections.

The clinical significance of Aspergillus-positive respiratory samples

BACKGROUND

Aspergilli moulds are frequently detected in sputum and other respiratory samples. It is not known what the significance of these findings is, or how to differentiate contamination, temporary or persistent colonisation from clinical infection when Aspergilli are found in respiratory samples.

OBJECTIVES

In this study we studied the clinical significance of Aspergillus findings from respiratory samples.

METHODS

We retrospectively evaluated 299 patients who had provided Aspergillus-positive respiratory samples in 2007-2016, which provided a follow-up time of 3-13 years. Data were collected from laboratory registry and Helsinki University Hospital medical records. Underlying diseases, immunosuppression, reasons for sample collection, clinical significance of positive Aspergillus culture, antifungal medication, and patient survival were assessed.

RESULTS

Underlying pulmonary disease had 88% of patients, most commonly asthma (44%), bronchiectasis (30%) or COPD (21%). Corticosteroids (orally or inhalation therapy) prior to positive samples used 78%; the use of corticosteroids did not explain the development of Aspergillus disease. Pulmonary disease caused by Aspergillus was identified in 88 (29%) of the reviewed patients; remaining samples did not represent clinical disease. Chronic cavitary or fibrosing pulmonary aspergillosis (CCPA or CFPA) had 44 (49%) of the diseased. The probability of Aspergillus disease increased when Aspergillus-positive samples were given repeatedly within 1 year (p = .001). Mortality for all reasons was 45%. The repeated positive samples did not predict survival (p = .084), but the diagnosis of CPA did (p < .001).

CONCLUSIONS

The possibility of Aspergillus disease increases when Aspergilli are found repeatedly, collection of samples should be repeated due to method insensitivity. Diagnosis of CPA predicted significantly lower survival.

Molecular Diagnosis of Endemic Mycoses

Diagnosis of endemic mycoses is still challenging. The moderated availability of reliable diagnostic methods, the lack of clinical suspicion out of endemic areas and the limitations of conventional techniques result in a late diagnosis that, in turn, delays the implementation of the correct antifungal therapy. In recent years, molecular methods have emerged as promising tools for the rapid diagnosis of endemic mycoses. However, the absence of a consensus among laboratories and the reduced availability of commercial tests compromises the diagnostic effectiveness of these methods. In this review, we summarize the advantages and limitations of molecular methods for the diagnosis of endemic mycoses.

Evaluation of the Performance of a Multiplex Real-Time PCR Assay for the Identification of Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii Simultaneously from Sputum in Multicenter

Purpose

To evaluate the performance of a multiplex real-time polymerase chain reaction (PCR) assay for the simultaneous identification of Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii from sputum.

Patients and Methods

Sputum samples (n=537) from patients with suspected invasive fungal infection (IFI) were collected from four centers; they were tested by both multiplex real-time PCR assay and DNA sequencing. DNA sequencing was considered as the reference method, and the performance of the multiplex real-time assay was evaluated by determining the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The interference experiment, repeatability, reproducibility, and stability of the multiplex real-time PCR assay were also evaluated.

Results

The detection performance of the multiplex real-time assay, compared with that of DNA sequencing, for the three pathogens was as follows: sensitivity, specificity, PPV, and NPV for Aspergillus, Cryptococcus neoformans, and Pneumocystis jirovecii were 99.40%, 98.64%, 97.09%, and 99.73%; 100%, 99.59%, 96.36%, and 100.00%; and 99.28%, 98.50%, 95.80%, and 99.75%, respectively. The consistency of the two methods was almost perfect: the kappa value was between 0.97 and 0.98. The minimum detection limit of the multiplex real-time assay for each of the three pathogens was 1250 copies/mL. Interference experiment showed that blood and normally used antifungal drugs had no effect on the results. No cross-reactivity was detected for any bacteria or fungi. In 40 patients, mixed infections by Aspergillus and/or Cryptococcus neoformans and/or Pneumocystis jirovecii were detected by the multiplex real-time assay. Among these patients, those with acquired immune deficiency syndrome (AIDS) ranked first, with Aspergillus and Pneumocystis mixed infection accounting for 75%.

Conclusion

The multiplex real-time PCR assay is fast, sensitive, and specific and has good clinical application prospects.

Development and evaluation of a novel fast broad-range PCR and sequencing assay (FBR-PCR/S) using dual priming oligonucleotides targeting the ITS/LSU gene regions for rapid diagnosis of invasive fungal diseases: multi-year experience in a large Canadian healthcare zone

Background

This study evaluated the performance of a novel fast broad range PCR and sequencing (FBR-PCR/S) assay for the improved diagnosis of invasive fungal disease (IFD) in high-risk patients in a large Canadian healthcare region.

Methods

A total of 114 clinical specimens (CS) including bronchoalveolar lavages (BALs) were prospectively tested from 107 patients over a 2-year period. Contrived BALs (n = 33) inoculated with known fungi pathogens were also tested to increase diversity. Patient characteristics, fungal stain and culture results were collected from the laboratory information system. Dual-priming oligonucleotide (DPO) primers targeted to the internal transcribed spacer (ITS) (~ 350 bp) and large subunit (LSU) (~ 550 bp) gene regions were used to perform FBR-PCR/S assays on extracted BALs/CS. The performance of the molecular test was evaluated against standard microbiological methods and clinical review for the presence of IFD.

Results

The 107 patients were predominantly male (67, 62.6%) with a mean age of 59 years (range = 0–85 years): 74 (69.2%) patients had at least one underlying comorbidity: 19 (34.5%) had confirmed and 12 (21.8%) had probable IFD. Culture recovered 66 fungal isolates from 55 BALs/CS with Candida spp. and Aspergillus spp. being most common. For BALs, the molecular assay vs. standard methods had sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), and efficiency of 88.5% vs.100%, 100% vs. 61.1%, 100% vs. 88.5%, 61.1% vs. 100%, and 90.2% for both. For other CS, the molecular assay had similar performance to standard methods with sensitivity, specificity, PPV, NPV and efficiency of 66.7%, 87.0%, 66.7%, 87.0% and 81.3% for both methods. Both methods also performed similarly, regardless of whether CS stain/microscopy showed yeast/fungal elements. FBR-PCR/S assays results were reported in ~ 8 h compared to fungal cultures that took between 4 and 6 weeks.

Conclusions

Rapid molecular testing compared to standard methods have equivalent diagnostic efficiency but improves clinical utility by reporting a rapid species-level identification the same dayshift (~ 8 h).

Utility of Panfungal PCR in the diagnosis of invasive fungal infections in febrile neutropenia

Background:

The prevalence of invasive fungal infections (IFIs) is increasing due to the increasing population of immunocompromised patients. Fungal culture is the gold standard for diagnosis but not sensitive and the turnaround time is long. Samples for histopathology are difficult to obtain because of profound cytopenias. We conducted this study with the aim to evaluate panfungal PCR for the diagnosis of IFIs in patients of febrile neutropenia.

Methods:

This was a single-centre, cross-sectional observational study. Patients of febrile neutropenia suspected of having IFI were included in the study. Panfungal PCR was performed on the blood of included patients along with other investigations for diagnosis of IFI. The sensitivity, specificity, positive predictive value, and negative predictive value of panfungal PCR were calculated using EORTC/MSG 2008 criteria as the gold standard.

Results:

Fifty patients of febrile neutropenia were included in the study, of which 52% were diagnosed positive by panfungal PCR assay. The sensitivity, specificity, positive predictive value, and negative predictive value of panfungal PCR assay was found to be 82.76%, 90.48%, 92.31% and 79.17% respectively.

Conclusion:

Panfungal PCR is a promising and highly sensitive diagnostic test for screening at-risk patients suspected to have IFIs. The use of panfungal PCR assay in combination with other diagnostic modalities and clinical judgment can be very helpful in the early diagnosis of IFI.

Clinical characteristics and evaluation of the incidence of cryptococcosis in Finland 2004-2018

BACKGROUND

Cryptococcosis is one of the major causes of mortality among HIV patients worldwide. Though most often associated with late stage HIV infection/AIDS, a significant number of cases occur in other immunocompromised patients such as solid organ transplant recipients and patients with hematological malignancies. Immunocompromised patients are a heterogeneous group and their number increases constantly. Since little is known about the incidence and the clinical features of cryptococcosis in Northern Europe, our aim was to investigate the clinical characteristics of cryptococcosis patients in Finland.

METHODS

We retrospectively reviewed the laboratory confirmed cryptococcosis cases in Finland during 2004-2018. Only those who were treated for cryptococcosis were included in the study. Initial laboratory findings and medical records were also collected.

RESULTS

A total of 22 patients with cryptococcosis were included in our study. The annual incidence of cryptococcosis was 0.03 cases per 100,000 population. Ten patients were HIV-positive and 12 out of 22 were HIV-negative. Hematological malignancy was the most common underlying condition among HIV-negative patients.

CONCLUSIONS

To our knowledge, this is the first study of the clinical presentation and incidence of cryptococcosis in Finland. We demonstrate that invasive cryptococcal infection occurs not only in HIV/AIDS patients or otherwise immunocompromised patients but also in immunocompetent individuals. Even though cryptococcosis is extremely rare in Finland, its recognition is important since the prognosis depends on rapid diagnostics and early antifungal therapy.

Ménétrier-like disease in a Pointer with concurrent granulomatous gastritis, helicobacteriosis and leishmaniosis: a case report

Background

Ménétrier-like disease is a rare hypertrophic canine gastropathy, reported in only seven dogs. Clinical signs are vomiting, anorexia and weight loss. Macroscopically, giant cerebriform gastric mucosal folds are typically seen in the corpus and fundus of the stomach. Histopathologically, fundic mucous cell hyperplasia and loss of parietal and chief cells are typical.

Case presentation

A nine-year-old spayed female Pointer had a history of intermittent vomiting, marked weight loss and hypoalbuminaemia. A gastroduodenoscopy was performed three times within three months with macroscopic changes remaining the same. The gastric mucosa of the corpus, fundus and proximal antrum was markedly irregular, with cerebriform mucosal folds. In the first gastric biopsies, histopathology revealed a moderate granulomatous gastritis, with a severe manifestation of Helicobacter-like organisms. Treatment for Helicobacter spp. decreased the vomiting slightly. The dog was diagnosed with concurrent leishmaniosis; the conventional anti-Leishmania treatment decreased the vomiting moderately, the hypoalbuminaemia resolved and the dog gained weight back to a normal body condition. Granulomatous gastritis was not present in the gastric biopsies after these treatments. The dog increased vomiting when palliative treatment (maropitant citrate, ondansetron and esomeprazole) was discontinued, and thus, full-thickness biopsies of the stomach were taken and Ménétrier-like disease was diagnosed. The affected area was too large to be surgically removed; thus, palliative treatment was reinstated. The dog remained clinically well 39 months after the first clinical presentation.

Conclusions

This is the first report of Ménétrier-like disease in a dog with a simultaneous manifestation of granulomatous gastritis, helicobacteriosis and leishmaniosis. The clinical signs decreased after treatment of helicobacteriosis and leishmaniosis, but vomiting remained probably as a sign of Ménétrier-like disease. Treatment options for dogs are surgical removal of the abnormal area or palliative treatment. In humans, promising results for a cure have been shown with cetuximab treatment, a human monoclonal antibody, but no canine antibody is commercially available yet. The dog here was doing well 39 months after first presentation, which is the longest reported survival time for Ménétrier-like disease with only palliative treatment in dogs. Full-thickness biopsies are preferred in macroscopic hypertrophic lesions of the stomach for better assessment of Ménétrier-like disease.

Characteristics of late recurrent candidemia in adult patients

BACKGROUND AND OBJECTIVES

Candida species are one of the most common causes of health care-associated bloodstream infections. However, recurrent candidemia is rare, and the characteristics of late recurrent (LR) candidemia are partly unclear. Our aim was to evaluate the characteristics of LR candidemia in adult patients.

PATIENTS AND METHODS

A retrospective cohort study was performed in the hospital district of Helsinki and Uusimaa in Finland (2007-2016). All candidemia cases were searched in an electronic database during the study period. Patients with LR candidemia were compared with patients with a single candidemia episode to evaluate the characteristics of LR candidemia. LR candidemia was defined as having at least two episodes of candidemia more than 30 days apart.

RESULTS

We identified 24 episodes of LR candidemia in 20 patients. Patients with LR candidemia represented 6% of all patients with candidemia during the study period, and most of these cases were nosocomial. The median time between the first and the recurrent episode was 5.1 months. One-year mortality in LR candidemia was 45%. Underlying gastrointestinal disease (OR 7.21, 95% CI 2.52-20.61) and history of intra-venous drug use (IVDU) (OR 3.62, 95% CI 1.03-12.69) were independent risk factors for LR candidemia in the multivariable analysis.

CONCLUSION

Our study indicates that the gastrointestinal tract may be a continuous source of infection in patients with chronic gastrointestinal diseases. Gastrointestinal diseases and IVDU should be regarded as risk factors for LR candidemia.

Clinical evaluation of an in-house panfungal real-time PCR assay for the detection of fungal pathogens

PURPOSE

Due to an increasing incidence of invasive fungal infections, the availability of reliable diagnostic tools for the fast detection of a wide spectrum of fungal pathogens is of vital importance. In this study, we aimed to conduct an extensive clinical evaluation of a recently published in-house panfungal PCR assay on samples from suspected invasive fungal infections.

METHODS

Overall 265 clinical samples from 232 patients with suspected invasive fungal disease (96 deep airway samples, 60 sterile fluids, 50 tissue biopsies, and 59 blood samples) were included. All samples underwent standard culture-based diagnostics and were additionally analyzed with our panfungal PCR assay.

RESULTS

Overall, 55.1% of agreement between culture and the panfungal PCR was observed; in 17% of all samples partial concordance was noted, while results between culture and our PCR assay were not in agreement in 27.9%. Our panfungal assay performed better in samples from normally sterile sites, while samples from the deep airways yielded the highest rate of discordant (39.6%) results. In two tissue and three blood samples an invasive pathogen was only detected by PCR while cultures remained negative.

CONCLUSION

In combination with routine methods, our panfungal PCR assay is a valuable diagnostic tool. Patients at risk for invasive fungal infections might profit from the reduced time to pathogen identification.

A New Age in Molecular Diagnostics for Invasive Fungal Disease: Are We Ready?

Invasive fungal diseases (IFDs) present an increasing global burden in immunocompromised and other seriously ill populations, including those caused by pathogens which are inherently resistant or less susceptible to antifungal drugs. Early diagnosis encompassing accurate detection and identification of the causative agent and of antifungal resistance is critical for optimum patient outcomes. Many molecular-based diagnostic approaches have good clinical utility although interpretation of results should be according to clinical context. Where an IFD is in the differential diagnosis, panfungal PCR assays allow the rapid detection/identification of fungal species directly from clinical specimens with good specificity; sensitivity is also high when hyphae are seen in the specimen including in paraffin-embedded tissue. Aspergillus PCR assays on blood fractions have good utility in the screening of high risk hematology patients with high negative predictive value (NPV) and positive predictive value (PPV) of 94 and 70%, respectively, when two positive PCR results are obtained. The standardization, and commercialization of Aspergillus PCR assays has now enabled direct comparison of results between laboratories with commercial assays also offering the simultaneous detection of common azole resistance mutations. Candida PCR assays are not as well standardized with the only FDA-approved commercial system (T2Candida) detecting only the five most common species; while the T2Candida outperforms blood culture in patients with candidemia, its role in routine Candida diagnostics is not well defined. There is growing use of Mucorales-specific PCR assays to detect selected genera in blood fractions. Quantitative real-time Pneumocystis jirovecii PCRs have replaced microscopy and immunofluorescent stains in many diagnostic laboratories although distinguishing infection may be problematic in non-HIV-infected patients. For species identification of isolates, DNA barcoding with dual loci (ITS and TEF1α) offer optimal accuracy while next generation sequencing (NGS) technologies offer highly discriminatory analysis of genetic diversity including for outbreak investigation and for drug resistance characterization. Advances in molecular technologies will further enhance routine fungal diagnostics.

Mycoses in northeastern Brazil: epidemiology and prevalence of fungal species in 8 years of retrospective analysis in Alagoas

Superficial and cutaneous mycoses are common in tropical countries, caused by dermatophytes, yeast, and non-dermatophyte molds in different clinical specimens. In order to define the epidemiology of mycoses and the profile of their etiological agents in Alagoas (northeastern Brazil) between 2009 and 2016, we obtained data of patients from the main laboratories of Alagoas, by examining clinical samples with direct microscopy and culture on Sabouraud dextrose agar and Chromagar^®Candida. A total of 3316 patients were confirmed with mycoses (595 men/2716 women) and 40.25 of average age. Positive samples totaled 3776, mainly vaginal secretion (1593/42.2%), toenails (876/23.2%), and fingernails (589/15.6%). Yeasts were the most isolated (3129/82.9%), including 3012 Candida spp. (79.8%), 57 Malassezia spp. (1.5%), 42 Trichosporon sp. (1.1%), 10 Geotrichum spp. (0.3%), and 8 Rhodotorula spp. (0.2%). Candida albicans was the most frequent species (715/18.9%), followed by C. krusei (194/5.1%), C. tropicalis (24/0.6%), and 2079 unspecified species (55.1%). Among 17.1% filamentous fungi, 14.8% dermatophytes were distributed as 211 Trichophyton sp. (5.6%), 125 T. rubrum (3.3%), 106 T. tonsurans (2.8%), 72 T. mentagrophytes (1.9%), 2 Microsporum sp. (0.1%), 15 M. canis (0.4%), and 26 Epidermophyton sp. (0.7%). Other fungi represented the minority: Fusarium sp. and Aspergillus sp. These are the first clinical data on the Alagoas population affected by fungi pathogens, confirming a higher incidence of candidiasis (mainly vulvovaginal and onychomycosis) and dermatophytes, providing a better understanding of different mycoses in northeastern Brazil.

Detection of deep fungal infections: a polyphasic approach

PURPOSE

Tissue samples from patients with suspicion of deep or subcutaneous fungal infections were analysed at the Portuguese Reference Mycology Laboratory according to a proposed diagnostic approach, which aims to constitute a rapid and accurate diagnosis for these fungal infections.

METHODOLOGY

Forty-six tissue biopsy samples were analysed over a period of 26 months, using a diagnostic approach that includes culture, panfungal PCR and Aspergillus-directed PCR.Results/Key findings. Overall, 23 samples were reported as negative while the remaining 23 were reported as positive for fungi (PCR, culture and/or histology). PCR showed an estimated detection limit of 12 pg DNA µl^-1. From the 46 samples, 30 were negative for fungal DNA while 16 gave positive results. From these, 12 cases were detected by panfungal PCR and six cases by PCR directed toward Aspergillus. In 61 % of the cases, there was concordance between molecular and cultural methods. Aetiological agents identified were Candida albicans, C. glabrata, C. tropicalis, Trichosporon montevideense, Alternaria spp., Exophiala sp., Trichoderma sp., Histoplasma spp., Aspergillus fumigatus, Trichophyton rubrum and Paracoccidioides brasiliensis.

CONCLUSION

Our results showed that the proposed polyphasic approach appears to be a useful strategy in the detection of fungi from tissue samples, allowing a better prognosis. In further studies, the inclusion of a higher number of samples and the implementation of more genus-specific PCRs will certainly contribute to an increase in the specificity and sensitivity of this method.