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

Rickerts, Volker

doi:10.1016/j.funbio.2015.07.002

Cited by 38 publications

(42 citation statements)

References 79 publications

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“…The applications of PCR to identify fungal pathogens from FFPE tissue have gained attention increasingly and may allow the identification of fungi to the genus or the species level, mostly matched with culture results . However, PCR results have been challenging with heterogenic positivity ranging from 15% to 90%, affected by various factors such as DNA extraction methods, fungal loads in FFPE tissue samples and removal of PCR inhibition . In addition, several studies described that contaminating fungal DNA representing clinical or procedural false positive reported from 13% to 20% of FFPE samples …”

Section: Discussionmentioning

confidence: 99%

“…Fluorescence in situ hybridization (FISH), mostly applied in clinical field for rapid identification directly from clinical specimens such as blood or cerebrospinal fluid, has also become a widely used methods for the identification of fungal pathogen in tissue sections by targeting rRNA with DNA, peptide nucleic acid or locked nucleic acid probe. This method does not require prior target amplification because of the high rRNA contents of cells and does not concern about contamination by the target sequences . High specificities above 90% and sensitivities between 50% and 95% have been described for tissue samples from patients with varied fungal infections including both yeast and mould infections .…”

Section: Discussionmentioning

confidence: 99%

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Diagnostic performance of immunohistochemistry for the aspergillosis and mucormycosis

Choi

Song

Kim

et al. 2019

Mycoses

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Summary Objective To investigate the accuracy of immunohistochemistry (IHC) tests for distinguishing between mucormycosis and aspergillosis and compare the clinical characteristics of mucormycosis patients according to galactomannan (GM) results. Methods We evaluated diagnostic performance of IHC test with tissue sections of patients with culture‐proven invasive fungal infection. In addition, we conducted PCR assay with tissue sections of mucormycosis patients with positive GM results to evaluate the possibility of co‐infection. Results In culture‐proven mucormycosis (n = 13) and aspergillosis (n = 20), the sensitivity and specificity of IHC test were both 100% for mucormycosis and 85% and 100%, respectively, for aspergillosis. Among the 53 patients who met the modified criteria for proven mucormycosis and had GM assay results, 24 (45%) were positive. Compared with those with negative GM results (n = 29), mucormycosis patients with positive GM results had significantly higher incidence of gastrointestinal tract infections (6/24 [25%] vs 0/29 [0%], P = .006) and were more likely to be histomorphologically diagnosed as aspergillosis (7/24 [29%] vs 2/29 [7%], P = .06). PCR assay amplified both Aspergillus‐ and Mucorales‐specific DNA in 6 of these 24 cases. Conclusions Immunohistochemistry tests seem useful for compensating for the limitations of histomorphologic diagnosis in distinguishing between mucormycosis and aspergillosis. Some proven mucormycosis patients with positive GM results had histopathology consistent with aspergillosis and gastrointestinal mucormycosis. In addition, about one quarter of these patients revealed the evidence of co‐infection with aspergillosis by PCR assay.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Diagnostic performance of immunohistochemistry for the aspergillosis and mucormycosis

Choi

Song

Kim

et al. 2019

Mycoses

View full text Add to dashboard Cite

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“…Thrombosed vessels in biopsy or autopsy material should always be examined very carefully by the pathologist, and numerous serial sections should be analysed. The detection of fungal pathogens by histopathology and the differentiation may be improved by immunohistochemical examination or using molecular techniques and these tools should be used to identify any fungal pathogen detected in histopathology samples to the genus and preferrentially species level …”

Section: Diagnostic Proceduresmentioning

confidence: 99%

“…Liver biopsies for diagnosing HSC may not always yield diagnostic evidence but using molecular methods may be helpful to prove IFD (eg, chronic disseminated candidosis) [B]. Molecular identification (eg, by PCR and sequencing assays) may allow highly accurate identification of fungi causing IFD from tissue samples . Earlier reports suggested that a liver biopsy during the first 3 weeks after recovery from granulocytopenia provides the highest diagnostic yield .…”

Section: Diagnostic Proceduresmentioning

confidence: 99%

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Diagnosis of invasive fungal diseases in haematology and oncology: 2018 update of the recommendations of the infectious diseases working party of the German society for hematology and medical oncology (AGIHO)

Ruhnke

Behre

Buchheidt

et al. 2018

Mycoses

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Invasive fungal diseases (IFD) are a primary cause of morbidity and mortality in patients with haematological malignancies. These infections are mostly life-threatening and an early diagnosis and initiation of appropriate antifungal therapy are essential for the clinical outcome. Most commonly, Aspergillus and Candida species are involved. However, other Non-Aspergillus moulds are increasingly identified in case of documented IFD. For definite diagnosis of IFD, a combination of diagnostic tools have to be applied, including conventional mycological culture and non-conventional microbiological tests such as antibody/antigen and molecular tests, as well as histopathology and radiology. Although varying widely in cancer patients, the risk of invasive fungal infection is highest in those with allogeneic stem cell transplantation and those with acute leukaemia and markedly lower in patients with solid cancer. Since the last edition of Diagnosis of Invasive Fungal Diseases recommendations of the German Society for Hematology and Oncology in 2012, integrated care pathways have been proposed for the management and therapy of IFDs with either a diagnostic driven strategy as opposed to a clinical or empirical driven strategy. This update discusses the impact of this additional evidence and effective revisions.

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

Ashraf

Kord

Morovati

et al. 2022

Clinical Laboratory Analysis

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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.

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

Cited by 38 publications

References 79 publications

Diagnostic performance of immunohistochemistry for the aspergillosis and mucormycosis

Diagnostic performance of immunohistochemistry for the aspergillosis and mucormycosis

Diagnosis of invasive fungal diseases in haematology and oncology: 2018 update of the recommendations of the infectious diseases working party of the German society for hematology and medical oncology (AGIHO)

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

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