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Sadamoto S, Mitsui Y, Nihonyanagi Y, Amemiya K, Shinozaki M, Murayama SY, Abe M, Umeyama T, Tochigi N, Miyazaki Y, Shibuya K. Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens. J Fungi (Basel) 2022; 8:jof8040337. [PMID: 35448568 PMCID: PMC9030445 DOI: 10.3390/jof8040337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Invasive fungal infection (IFI) has a high mortality rate in patients who undergo hematopoietic stem cell transplantation, and it is often confirmed by postmortem dissection. When IFI is initially confirmed after an autopsy, the tissue culture and frozen section are challenging to secure, and in many cases, formalin-fixed, paraffin-embedded (FFPE) samples represent the only modality for identifying fungi. Histopathological diagnosis is a useful method in combination with molecular biological methods that can achieve more precise identification with reproducibility. Meanwhile, polymerase chain reaction (PCR) using fungal-specific primers helps identify fungi from FFPE tissues. Autopsy FFPE specimens have a disadvantage regarding the quality of DNA extracted compared with that of specimens obtained via biopsy or surgery. In the case of mucormycosis diagnosed postmortem histologically, we examined currently available molecular biological methods such as PCR, immunohistochemistry (IHC), and in situ hybridization (ISH) to identify fungi. It is reasonable that PCR with some modification is valuable for identifying fungi in autopsy FFPE specimens. However, PCR does not always correctly identify fungi in autopsy FFPE tissues, and other approaches such as ISH or IHC are worth considering for clarifying the broad classification (such as the genus- or species-level classification).
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Affiliation(s)
- Sota Sadamoto
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
- Department of Fungal Infection, National Institute of infectious Diseases, Tokyo 162-8640, Japan; (S.Y.M.); (M.A.); (T.U.); (Y.M.)
| | - Yurika Mitsui
- Department of Hematology and Oncology, Toho University School of Medicine, Tokyo 143-8541, Japan;
| | - Yasuhiro Nihonyanagi
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
| | - Kazuki Amemiya
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
| | - Minoru Shinozaki
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
| | - Somay Yamagata Murayama
- Department of Fungal Infection, National Institute of infectious Diseases, Tokyo 162-8640, Japan; (S.Y.M.); (M.A.); (T.U.); (Y.M.)
| | - Masahiro Abe
- Department of Fungal Infection, National Institute of infectious Diseases, Tokyo 162-8640, Japan; (S.Y.M.); (M.A.); (T.U.); (Y.M.)
| | - Takashi Umeyama
- Department of Fungal Infection, National Institute of infectious Diseases, Tokyo 162-8640, Japan; (S.Y.M.); (M.A.); (T.U.); (Y.M.)
| | - Naobumi Tochigi
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
- Correspondence:
| | - Yoshitsugu Miyazaki
- Department of Fungal Infection, National Institute of infectious Diseases, Tokyo 162-8640, Japan; (S.Y.M.); (M.A.); (T.U.); (Y.M.)
| | - Kazutoshi Shibuya
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo 143-8541, Japan; (S.S.); (Y.N.); (K.A.); (M.S.); (K.S.)
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Lockhart SR, Bialek R, Kibbler CC, Cuenca-Estrella M, Jensen HE, Kontoyiannis DP. Molecular Techniques for Genus and Species Determination of Fungi From Fresh and Paraffin-Embedded Formalin-Fixed Tissue in the Revised EORTC/MSGERC Definitions of Invasive Fungal Infection. Clin Infect Dis 2021; 72:S109-S113. [PMID: 33709128 PMCID: PMC7952508 DOI: 10.1093/cid/ciaa1836] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The EORTC/MSGERC have revised the definitions for proven, probable, and possible fungal diseases. The tissue diagnosis subcommittee was tasked with determining how and when species can be determined from tissue in the absence of culture. The subcommittee reached a consensus decision that polymerase chain reaction (PCR) from tissue, but not immunohistochemistry or in situ hybridization, can be used for genus or species determination under the new EORTC/MSGERC guidelines, but only when fungal elements are identified by histology. Fungal elements seen in tissue samples by histopathology and identified by PCR followed by sequencing should fulfill the definition of a proven fungal infection, identified to genus/species, even in the absence of culture. This summary discusses the issues that were deliberated by the subcommittee to reach the consensus decision and outlines the criteria a laboratory should follow in order to produce data that meet the EORTC/MSGERC definitions.
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Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ralf Bialek
- LADR GmbH MVZ Dr. Kramer und Kollegen, Geesthacht, Germany
| | | | - Manuel Cuenca-Estrella
- Laboratorio de referencia e investigación en Micología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Spain
| | - Henrik E Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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Shinozaki M, Tochigi N, Sadamoto S, Yamagata Murayama S, Wakayama M, Nemoto T. [Histopathological Diagnosis of Invasive Fungal Infections in Formalin-Fixed and Paraffin-Embedded Tissues in Conjunction with Molecular Methods]. Med Mycol J 2018; 59:E7-E18. [PMID: 29491339 DOI: 10.3314/mmj.17-00016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
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.
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Affiliation(s)
- Minoru Shinozaki
- Department of Pathology, Toho University Graduate School of Medicine
| | - Naobumi Tochigi
- Department of Pathology, Toho University Graduate School of Medicine.,Department of Surgical Pathology, Toho University School of Medicine
| | - Sota Sadamoto
- Department of Pathology, Toho University Graduate School of Medicine.,Department of Surgical Pathology, Toho University School of Medicine
| | | | - Megumi Wakayama
- Department of Pathology, Toho University Graduate School of Medicine.,Department of Surgical Pathology, Toho University School of Medicine
| | - Tetsuo Nemoto
- Department of Surgical Pathology, Toho University School of Medicine
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Liu K, Yan X, Mao B, Wang S, Deng L. Aptamer-based detection of Salmonella enteritidis using double signal amplification by Klenow fragment and dual fluorescence. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1692-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Rickerts V. Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods. Fungal Biol 2015; 120:279-87. [PMID: 26781382 DOI: 10.1016/j.funbio.2015.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/28/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
Abstract
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.
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Affiliation(s)
- Volker Rickerts
- Robert Koch Institut, FG 16, Nordufer 20, 13353 Berlin, Germany.
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Song Y, Li W, Duan Y, Li Z, Deng L. Nicking enzyme-assisted biosensor for Salmonella enteritidis detection based on fluorescence resonance energy transfer. Biosens Bioelectron 2014; 55:400-4. [DOI: 10.1016/j.bios.2013.12.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
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