Genotyping of Aspergillus fumigatus in Formalin-Fixed Paraffin-Embedded Tissues and Serum Samples From Patients With Invasive Aspergillosis

Groot, Theun de; Hagen, Ferry; Vreuls, Willem; Verweij, Paul E.; Chowdhary, Anuradha; Meis, Jacques F.

doi:10.3389/fcimb.2018.00377

Cited by 6 publications

(6 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2017 , Schauwvlieghe et al. 2017 , de Groot et al. 2018 , Denis et al.…”

Section: Antifungal Drug Resistance Detection In a Fumigatus : From Phenotypic Assays To Maldi-tof Msunclassified

“…2017 AsperGenius® TR 34 , L98H, Y121F, T289A Plasma (86) 100 % WT White et al. 2017 AsperGenius® TR 34 , L98H, Y121F, T289A Serum (9); tissue (8) 76.5 % 76.5 % WT de Groot et al. 2018 MycoGENIE® TR 34 , L98H BAL fluids (31) 0 % TR 34 /L98H Denis et al.…”

Section: Antifungal Drug Resistance Detection In a Fumigatus : From Phenotypic Assays To Maldi-tof Msmentioning

confidence: 99%

See 1 more Smart Citation

Aspergillus fumigatusand aspergillosis: From basics to clinics

Arastehfar

Carvalho

Houbraken

et al. 2021

Studies in Mycology

158

112

View full text Add to dashboard Cite

The airborne fungus Aspergillus fumigatus poses a serious health threat to humans by causing numerous invasive infections and a notable mortality in humans, especially in immunocompromised patients. Mould-active azoles are the frontline therapeutics employed to treat aspergillosis. The global emergence of azole-resistant A . fumigatus isolates in clinic and environment, however, notoriously limits the therapeutic options of mould-active antifungals and potentially can be attributed to a mortality rate reaching up to 100 %. Although specific mutations in CYP 51A are the main cause of azole resistance, there is a new wave of azole-resistant isolates with wild-type CYP 51A genotype challenging the efficacy of the current diagnostic tools. Therefore, applications of whole-genome sequencing are increasingly gaining popularity to overcome such challenges. Prominent echinocandin tolerance, as well as liver and kidney toxicity posed by amphotericin B, necessitate a continuous quest for novel antifungal drugs to combat emerging azole-resistant A . fumigatus isolates. Animal models and the tools used for genetic engineering require further refinement to facilitate a better understanding about the resistance mechanisms, virulence, and immune reactions orchestrated against A . fumigatus . This review paper comprehensively discusses the current clinical challenges caused by A . fumigatus and provides insights on how to address them.

show abstract

“…2017 , Schauwvlieghe et al. 2017 , de Groot et al. 2018 , Denis et al.…”

Section: Antifungal Drug Resistance Detection In a Fumigatus : From Phenotypic Assays To Maldi-tof Msunclassified

Section: Antifungal Drug Resistance Detection In a Fumigatus : From Phenotypic Assays To Maldi-tof Msmentioning

confidence: 99%

Aspergillus fumigatusand aspergillosis: From basics to clinics

Arastehfar

Carvalho

Houbraken

et al. 2021

Studies in Mycology

158

112

View full text Add to dashboard Cite

show abstract

“…Diagnoses based on histopathological features or on immunohistochemistry (IHC) can be obtained using FFPE tissue, but both have their limitations, including diagnosis only to the genus level 7‐10 . FFPE tissue can even be used for genotyping infections when isolates are not available 11 . When combined with histopathological evidence of fungal organisms, PCR‐based detection of fungal pathogens from FFPE tissue is rapid, sensitive and specific 12‐17 …”

Section: Introductionmentioning

confidence: 99%

“…[7][8][9][10] FFPE tissue can even be used for genotyping infections when isolates are not available. 11 When combined with histopathological evidence of fungal organisms, PCR-based detection of fungal pathogens from FFPE tissue is rapid, sensitive and specific. [12][13][14][15][16][17] Although culture is considered the gold standard for fungal identification from tissue, the sensitivity of culture from tissue is low.…”

mentioning

confidence: 99%

Performance evaluation of fungal DNA PCR amplification from formalin‐fixed paraffin‐embedded tissue for diagnosis: Experience of a tertiary reference laboratory

Lysen

Silva‐Flannery

Zaki

et al. 2021

Mycoses

View full text Add to dashboard Cite

Background Diagnosis of invasive fungal infections from formalin‐fixed paraffin‐embedded (FFPE) tissues by PCR amplification is a developing technology. One of the difficulties of establishing a validated protocol for this testing is that the gold standard, culture, is much less sensitive than the test being validated. Objectives To validate FFPE PCR as a refence laboratory identification methodology in the absence of abundant gold standard specimens. Methods In this validation, PCR from FFPE tissue was compared to other diagnostic methods for genus/species identification. Four different groups of correlative data from FFPE tissues were used to validate this procedure. Thirteen specimens had culture or serology results and FFPE PCR results, 49 specimens had both immunohistochemistry (IHC) identification and FFPE PCR results, 118 specimens had histological evidence of fungal elements, 64 of which also had FFPE PCR results, and 36 fungal mock tissues or fungal negative tissues were used. Results The sensitivity determined from the tissues with positive fungal histopathology was 54%. The specificity of the cases for which there were both culture and FFPE PCR results was 100%. For the correlation with IHC, the specificity was 98%. For the mock tissues and fungal negative tissues, the calculated analytical sensitivity was 94%, specificity was 95%, and accuracy was 94%. Conclusions By uniquely combining various data sources, this study provides a comprehensive framework for how validation can be achieved in the absence of a gold standard and outlines the excellent performance of PCR from FFPE tissue, despite relatively the low sensitivity when compared to histopathology.

show abstract

“…Molecular methods can now be used to rapidly identify fungal species in formalin-fixed paraffin-embedded (FFPE) tissue specimens, 11 and polymerase chain reaction (PCR)-based methods have been devised to detect azole-resistance in FFPE and bronchial alveolar lavage specimens. 12 13 The objectives of this study were to evaluate performance of panfungal PCR assays on FFPE samples for fungal species identification, and the detection of azole-resistance mutations in the A. fumigatus cyp51A gene at a South Korean hospital.…”

Section: Introductionmentioning

confidence: 99%

Identification of Fungal Species and Detection of Azole-Resistance Mutations in the Aspergillus fumigatus cyp51A Gene at a South Korean Hospital

et al. 2020

View full text Add to dashboard Cite

Purpose: With changing fungal epidemiology and azole resistance in Aspergillus species, identifying fungal species and susceptibility patterns is crucial to the management of aspergillosis and mucormycosis. The objectives of this study were to evaluate performance of panfungal polymerase chain reaction (PCR) assays on formalin-fixed paraffin embedded (FFPE) samples in the identification of fungal species and in the detection of azole-resistance mutations in the Aspergillus fumigatus cyp51A gene at a South Korean hospital. Materials and Methods: A total of 75 FFPE specimens with a histopathological diagnosis of aspergillosis or mucormycosis were identified during the 10-year study period (2006-2015). After deparaffinization and DNA extraction, panfungal PCR assays were conducted on FFPE samples for fungal species identification. The identified fungal species were compared with histopathological diagnosis. On samples identified as A. fumigatus, sequencing to identify frequent mutations in the cyp51A gene [tandem repeat 46 (TR46), L98H, and M220 alterations] that confer azole resistance was performed. Results: Specific fungal DNA was identified in 31 (41.3%) FFPE samples, and of these, 16 samples of specific fungal DNA were in accord with a histopathological diagnosis of aspergillosis or mucormycosis; 15 samples had discordant histopathology and PCR results. No azole-mediating cyp51A gene mutation was noted among nine cases of aspergillosis. Moreover, no cyp51A mutations were identified among three cases with history of prior azole use. Conclusion: Panfungal PCR assay with FFPE samples may provide additional information of use to fungal species identification. No azole-resistance mediating mutations in the A. fumigatus cyp51A gene were identified among FFPE samples during study period.

show abstract

Genotyping of Aspergillus fumigatus in Formalin-Fixed Paraffin-Embedded Tissues and Serum Samples From Patients With Invasive Aspergillosis

Cited by 6 publications

References 31 publications

Aspergillus fumigatusand aspergillosis: From basics to clinics

Aspergillus fumigatusand aspergillosis: From basics to clinics

Performance evaluation of fungal DNA PCR amplification from formalin‐fixed paraffin‐embedded tissue for diagnosis: Experience of a tertiary reference laboratory

Identification of Fungal Species and Detection of Azole-Resistance Mutations in the Aspergillus fumigatus cyp51A Gene at a South Korean Hospital

Contact Info

Product

Resources

About