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

OBJECTIVES: To assess the clinical use of panfungal PCR for diagnosis of invasive fungal diseases (IFDs). We focused on the deep tissue samples. METHODS: We first described the design of panfungal PCR, which is in clinical use at Helsinki University Hospital. Next we retrospectively evaluated the results of 307 fungal PCR tests performed from 2013 to 2015. Samples were taken from normally sterile tissues and fluids. The patient population was nonselected. We classified the likelihood of IFD according to the criteria of the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG), comparing the fungal PCR results to the likelihood of IFD along with culture and microscopy results. RESULTS: There were 48 positive (16%) and 259 negative (84%) PCR results. The sensitivity and specificity of PCR for diagnosing IFDs were 60.5% and 91.7%, respectively, while the negative predictive value and positive predictive value were 93.4% and 54.2%, respectively. The concordance between the PCR and the culture results was 86% and 87% between PCR and microscopy, respectively. Of the 48 patients with positive PCR results, 23 had a proven or probable IFD. CONCLUSIONS: Fungal PCR can be useful for diagnosing IFDs in deep tissue samples. It is beneficial to combine fungal PCR with culture and microscopy.

In vitro fungistatic effects of natural coniferous resin from Norway spruce (Picea abies).

Resins (rosin, pitch) are natural products of the coniferous trees and are antimicrobial against a wide range of microbes. The antifungal effectiveness of resin, purified from Norway spruce (Picea abies), was studied against human pathogenic fungi and yeasts with the agar plate diffusion tests and electron microscopy (EM). The fungistatic effect of these resin mixtures (resin salves) was tested against a set of Candida yeasts, dermatophytes, and opportunistic fungi. Transmission and scanning EM was done from samples of fungi (Trichophyton mentagrophytes). In agar diffusion tests, the resin was strongly antifungal against all dermatophytes tested, e.g., against all fungi of the genus Trichophyton, but it was not antifungal against the Candida yeasts or against the opportunistic fungi tested. According to EM, resin caused damages in the cell hyphae and cell wall structures. We conclude that, in the agar plate diffusion test, coniferous resins are strongly fungistatic against the dermatophytic fungi only.

Deep, respiratory tract and ear infections caused by Pseudallescheria (Scedosporium) and Microascus (Scopulariopsis) in Finland. A 10-year retrospective multi-center study.

Deep, respiratory tract and ear infections due to Microascaceae (Pseudallescheria, Scedosporium, Microascus or Scopulariopsis) were studied nationwide in Finland during 1993-2002. The data were based on 52,000 fungal cultures that represented about 50% of all such specimens in Finland and included all Finnish cases of profound immunosuppression. There were 39 cases that were re-evaluated as clinically significant, i.e., three pneumonias, two deep pedal infections and five wound infections, 11 sinusitis and 18 ear infections. The pedal infections and most pneumonias occurred in immunocompromised patients. Most cases, except the ear infections, were due to Pseudallescheria boydii. Two patients had lethal P. boydii pneumonia and a deep P. boydii infection of the foot contributed to a third lethal case. Two of the patients with lethal outcomes had received an allogeneic haematopoietic stem cell transplantation (AHSCT). Two patients with haematological malignancies were cured of deep site infections by a prolonged course of itraconazole. Wound, sinus and ear infections were cured or improved by local surgery or topical therapy. There were 0.8-1.7 cases of any type of infection per million inhabitants per year (MY) and 3.4 cases/1000 AHSCT. Mortality associated with Microascaceae in any type of patient was 0.06-0.12 MY.

Radiologically guided fine needle lung biopsies in the evaluation of focal pulmonary lesions in allogeneic stem cell transplant recipients.

Lung problems are common in allogeneic stem cell transplant (SCT) recipients. To evaluate the feasibility and diagnostic yield of radiologically guided fine needle lung biopsy (FNLB) in allogeneic SCT recipients with focal pulmonary lesions, a retrospective analysis was carried out. Between 1989 and 1998, radiologists performed a total of 30 FNLBs in 21 allogeneic SCT recipients, guided either by ultrasound (n = 17) or computed tomography (n = 13). The median time from SCT to the first FNLB was 131 days (20-343 days). Prophylactic platelet transfusions were given in 19 procedures (66%). The complications of FNLB included clinically insignificant pneumothorax in four procedures (13%) and self-limiting haemoptysis in one case (3%). The first FNLB was suggestive of invasive pulmonary aspergillosis (IPA) in five patients (24%). Additional clinically useful findings of FNLB included Pseudomonas (two patients) and Nocardia (one patient). The final diagnosis of pulmonary lesions was IPA in 14 patients, immunological lung problems in four patients and other in three patients. Radiologically guided FNLB is feasible in allogeneic SCT recipients and has a low complication rate. The diagnostic yield is high especially for IPA.

Pulmonary infection caused by an unusual, slowly growing nontuberculous Mycobacterium.

Mycobacterium triplex, a recently described slowly growing nontuberculous mycobacterium, was isolated from a Finnish patient with pulmonary mycobacteriosis. The disease was successfully treated with antimycobacterial drugs. The strain isolated, which was similar to the type strain but differed slightly from the species description, was regarded as a variant of M. triplex sensu stricto. According to present knowledge this variant of the species has never been isolated before.

Panfungal PCR and multiplex liquid hybridization for detection of fungi in tissue specimens.

A procedure based on panfungal PCR and multiplex liquid hybridization was developed for the detection of fungi in tissue specimens. The PCR amplified the fungal internal transcribed spacer (ITS) region (ITS1-5.8S rRNA-ITS2). After capture with specific probes, eight common fungal pathogens (Aspergillus flavus, Aspergillus fumigatus, Candida albicans, Candida krusei, Candida glabrata, Candida parapsilosis, Candida tropicalis, and Cryptococcus neoformans) were identified according to the size of the amplification product on an automated sequencer. The nonhybridized products were identified by sequencing. The performance of the procedure was examined with 12 deep-tissue specimens and 8 polypous tissue biopsies from the paranasal sinuses. A detection level of 0.1 to 1 pg of purified DNA (2 to 20 CFU) was achieved. Of the 20 specimens, PCR was positive for 19 (95%), of which 10 (53%) were hybridization positive. In comparison, 12 (60%) of the specimens were positive by direct microscopy, but only 7 (35%) of the specimens showed fungal growth. Sequencing of the nonhybridized amplification products identified an infecting agent in six specimens, and three specimens yielded only sequences of unknown fungal origin. The procedure provides a rapid (within 2 days) detection of common fungal pathogens in tissue specimens, and it is highly versatile for the identification of other fungal pathogens.

Mycotoxins in crude building materials from water-damaged buildings.

We analyzed 79 bulk samples of moldy interior finishes from Finnish buildings with moisture problems for 17 mycotoxins, as well as for fungi that could be isolated using one medium and one set of growth conditions. We found the aflatoxin precursor, sterigmatocystin, in 24% of the samples and trichothecenes in 19% of the samples. Trichothecenes found included satratoxin G or H in five samples; diacetoxyscirpenol in five samples; and 3-acetyl-deoxynivalenol, deoxynivalenol, verrucarol, or T-2-tetraol in an additional five samples. Citrinine was found in three samples. Aspergillus versicolor was present in most sterigmatocystin-containing samples, and Stachybotrys spp. were present in the samples where satratoxins were found. In many cases, however, the presence of fungi thought to produce the mycotoxins was not correlated with the presence of the expected compounds. However, when mycotoxins were found, some toxigenic fungi usually were present, even if the species originally responsible for producing the mycotoxin was not isolated. We conclude that the identification and enumeration of fungal species present in bulk materials are important to verify the severity of mold damage but that chemical analyses are necessary if the goal is to establish the presence of mycotoxins in moldy materials.

Diagnostic aspects of invasive Aspergillus infections in allogeneic BMT recipients.

To investigate diagnostic aspects of invasive aspergillosis (IA) in allogeneic BMT recipients, the charts of 22 consecutive patients with IA transplanted in 1989-1995 were reviewed. IA was diagnosed 69-466 days (median 131 days) post BMT. In 16 patients (73%), a definite or probable diagnosis of IA was made during life. Respiratory symptoms were the presenting feature in half of the patients followed by neurological symptoms (27%). Chest X-ray revealed single or multiple nodular lesions in 10 patients; cavitation was observed in five patients. Tissue biopsy was the most common method of diagnosis (nine patients: lungs 6, liver 1, subcutaneous tissue 1, brain 1). Five IA cases were detected by nine guided fine needle lung biopsies in eight patients and without complications. Bronchoalveolar lavage was performed in 14 patients with findings suggestive of invasive pulmonary aspergillosis in eight cases. Lungs were the most common organ affected (90%) followed by central nervous system (41%). The diagnosis of IA is still difficult, and a large number of patients have advanced infection at diagnosis. Methods for early diagnosis are needed. Patients with a clinical suspicion of IA should be treated vigorously with antifungal agents during the diagnostic work-up.

Comparison of virulence factors of oral Candida dubliniensis and Candida albicans isolates in healthy people and patients with chronic candidosis.

We determined differences in the expression of certain virulence factors between oral Candida dubliniensis and Candida albicans species. In addition, clonal differences were sought among C. albicans isolates recovered from patients with and without compromised immune system. The material comprised 93 clinical yeast isolates originated in 40 subjects (1-5 isolates per subject). All 26 C. dubliniensis isolates and 46 C. albicans isolates originated from healthy routine dental clinic patients. Additionally, 21 C. albicans isolates were collected from patients with autoimmune polyendocrinopathy-candidosis-ectodermal dystrophy (APECED), who have chronic candidosis as one manifestation of their immunocompromising disease. Polymerase chain reaction amplification using the random sequence primer OPE-03 enabled grouping of the C. dubliniensis isolates in 2 genotypes (I and II) and C. albicans isolates in 15 genotypes (I-XV). No significant difference was found in the distribution of genotypes between the patients with APECED and the healthy subjects. C. dubliniensis isolates exhibited high-frequency phenotypic switching significantly more frequently than did C. albicans isolates, and vice versa regarding phospholipase and proteinase production. Proteinase production was significantly more frequent among C. albicans genotype V than genotype IX isolates. No significant difference was found in expression of virulence factors of C. albicans isolates between the patients with APECED and the healthy subjects.

Diagnostic laparoscopy in patients with acute leukemia and suspected hepatic candidiasis.

To assess the value of laparoscopy in the diagnosis of suspected hepatosplenic candidiasis in patients with acute leukemia, a retrospective analysis of 28 laparoscopies was conducted. In all but two cases, imaging of the liver showed focal lesions before laparoscopy. Diagnosis of hepatic candidiasis was established significantly more often when the biopsy was targeted at white nodules (in 12 of 22 laparoscopies) than when targeted randomly or at scars (0 of 6 laparoscopies) (p = 0.017, chi-square test). Yeast was detected more often if the laparoscopy was performed during the three-week period after recovery from neutropenia (in 8 of 12 laparoscopies) than when performed later (in 4 of 16 laparoscopies) (p = 0.028, chi-square test). In addition to the 12 laparoscopically diagnosed patients, eight (29%) patients were diagnosed with disseminated Candida infection by other methods. In another eight (29%) patients the causative agent was not identified. No bleeding or other problems occurred after the laparoscopy. Laparoscopy-guided liver biopsy is most useful if biopsies are targeted to macroscopic lesions and if laparoscopy is performed soon after recovery from neutropenia.

Incidence and risk factors for invasive fungal infections in allogeneic BMT recipients.

In order to analyze the incidence and risk factors for invasive fungal infection (IFI) after allogeneic BMT, 142 consecutive adult BMT recipients (131 sibling donors, 11 unrelated donors) transplanted in 1989-1993 were retrospectively analyzed. There were 21 cases with definite or probable IFI (incidence 15%) (Aspergillus, 15; Candida, four; Fusarium, one; Absidia, one). The median time to the diagnosis of IFI was 136 days after BMT (range 6-466 days). Only 14% of the IFIs were found during the neutropenic period post-BMT. Of the pretransplant characteristics, hematological disease (MDS vs other) (P = 0.001) and unrelated donor (P = 0.01) were risk factors for IFI. Acute GVHD grade III-IV (P = 0.03) and extensive chronic GVHD (P = 0.0002) were also found to be significant risk factors. Only three patients with IFI (14%) became long-term survivors. Invasive fungal infections tended to develop late after BMT, were usually caused by Aspergillus sp., and were strongly associated with GVHD and its treatment. Better prophylaxis and treatment of IFI are needed. More effective prophylaxis for GVHD might decrease the risk of IFI after allogeneic BMT.

Invasive cutaneous mucormycosis caused by Absidia corymbifera after allogeneic bone marrow transplantation.

Mucormycotic infections caused by fungi of the families Rhizopus, Mucor or Absidia are rare and usually associated with diabetes or immunosuppression. We describe a patient with invasive necrotizing cutaneous mucormycosis caused by Absidia corymbifera shortly after allogeneic BMT. The infection was successfully treated with surgical debridement and liposomal amphotericin B for 6 weeks. Recognition of these rare infections requires a high index of suspicion. These patients should be evaluated with tissue biopsy and cultures and treated without delay.

Mycobacterium branderi sp. nov., a new potential human pathogen.

A number of mycobacterial strains with similar growth characteristics, metabolic properties, and lipid compositions, which were previously placed in the Helsinki group (E. Brander, E. Jantzen, R. Huttunen, A. Juntunen, and M.-L. Katila, J. Clin. Microbiol. 30:1972-1975, 1992), were characterized by performing 16S rRNA gene sequencing. Of the 14 strains studied, 9 had a unique, previously undescribed sequence in the variable region of 16S rRNA. These nine strains, all of which were isolated from respiratory tract specimens, were nonpigmented and grew at 25 degrees C to 45 degrees C, reaching full colony size after 2 to 3 weeks. They produced arylsulfatase, nicotinamidase, and pyrazinamidase and were negative for Tween 80 hydrolysis, catalase, urease, and nitrate reductase activities, and niacin. Their glycolipid patterns were identical. A mycolic acid analysis performed by using thin-layer chromatography showed that these organisms contained alpha-mycolates, ketomycolates, and carboxy mycolates. Gas-liquid chromatography revealed that 2-eicosanol was the major alcohol and hexacosanoic acid was the major mycolic acid cleavage product. On the basis of their growth, biochemical, and lipid characteristics and their unique 16S rRNA sequence, we propose that these organisms should be assigned to a new species, Mycobacterium branderi. Comparative 16S rRNA sequencing revealed that this new species is closely related to Mycobacterium celatum, Mycobacterium cookii, and Mycobacterium xenopi. Strains 52157T (T = type strain) and 43548 have been deposited in the American Type Culture Collection as strains ATCC 51789 and ATCC 51788, respectively.