Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens
Abstract
:1. Introduction
2. Case Description
3. Materials and Methods
3.1. Histopathology
3.2. DNA Extraction, PCR, and Sequencing
3.3. IHC
3.4. ISH
3.4.1. ISH Probes Used in This Study
3.4.2. ISH Using the PNA Probe
3.4.3. ISH Using dsDNA and Oligonucleotide DNA Probes
4. Results
5. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Tissue Organ | Heart | Lung | Liver | Spleen | Kidney | Colon | ||
---|---|---|---|---|---|---|---|---|
Histopathology | Area of Fungal element/Total area of FFPE | 70% | 60% | 50% | 80% | 50% | 40% | |
Density of fungal components | High | Medium | Low | Medium | Low | Low | ||
Necrosis background | − | − | + | + | − | − | ||
PCR | Panfungal | ITS1-ITS2 | − | − | − | − | − | − |
ITS3-ITS4 | − | − | − | − | − | − | ||
ITS1-ITS4 | − | − | − | − | − | − | ||
NL1-NL4 | + | − | − | − | − | − | ||
Mucorales | ZM1-ZM2 | − | − | − | − | − | − | |
ZM1-ZM3 | + | + | + | − | + | + | ||
IHC | Anti-Aspergillus antibody | ab20419 | − | − | − | − | − | − |
Anti-Rhizopus arrhizus antibody | WSSA-RA-1 | + | + | + | + | + | + | |
ISH | Panfungal | PNA probe | + | + | +(focal) | − | +(focal) | +(focal) |
18S rRNA probe | + | + | + | +(focal) | + | + | ||
Oligo nucleotide DNA probe | − | − | − | − | − | − | ||
Mucormycosis | 28S rRNA probe | + | + | + | + | + | + | |
18S rRNA probe | + | + | + | + | + | + | ||
Aspergillosis | A. fumigatus alkaline proteinase gene | - | NT | NT | NT | NT | NT | |
Mucor, Rhizomucor, Rhizopus, Saksenaea | Oligonucleotide DNA probe | − | NT | NT | NT | NT | NT | |
Absida | − | NT | NT | NT | NT | NT | ||
Cunninghamella | + | − | + | − | + | + |
Method | Accessibility | Standardization | Time for Detection | Cost | Automation Technique | Advantage | Disadvantage |
---|---|---|---|---|---|---|---|
Histopathology | Easy | Yes | Minutes | Low | Yes | Low cost, Fast, High sensitivity. | Difficult for identifying up to species level. |
IHC | Easy-Limited | No | Hours | Intermediate | Yes | It can be fully automated. Good sensitivity. | Commercially available antibody is few. Specificity depends on the quality of the antibody. |
ISH | Limited | No | Hours-days | Intermediate | Partial or no | Good sensitivity with good specify. | Takes time. Specific probes needed for detecting different species. |
Broad range PCR with sequencing | Easy-Limited | Yes | Hours-day | Intermediate | Partial or no | Can be identify up to the species level. | Contamination of ubiquitous fungi can happen. |
Real-time PCR | Limited | Yes | Hours | High | Partial | The result can be shown by real-time with quantification. | Detectible species depend on the primer use. |
NGS | Limited | No | Hours | High | Partial | Can potentially detect any fungal pathogen. | Limited evidence. High cost and special equipment should be needed. |
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Sadamoto, S.; Mitsui, Y.; Nihonyanagi, Y.; Amemiya, K.; Shinozaki, M.; Murayama, S.Y.; Abe, M.; Umeyama, T.; Tochigi, N.; Miyazaki, Y.; et al. Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens. J. Fungi 2022, 8, 337. https://doi.org/10.3390/jof8040337
Sadamoto S, Mitsui Y, Nihonyanagi Y, Amemiya K, Shinozaki M, Murayama SY, Abe M, Umeyama T, Tochigi N, Miyazaki Y, et al. Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens. Journal of Fungi. 2022; 8(4):337. https://doi.org/10.3390/jof8040337
Chicago/Turabian StyleSadamoto, Sota, Yurika Mitsui, Yasuhiro Nihonyanagi, Kazuki Amemiya, Minoru Shinozaki, Somay Yamagata Murayama, Masahiro Abe, Takashi Umeyama, Naobumi Tochigi, Yoshitsugu Miyazaki, and et al. 2022. "Comparison Approach for Identifying Missed Invasive Fungal Infections in Formalin-Fixed, Paraffin-Embedded Autopsy Specimens" Journal of Fungi 8, no. 4: 337. https://doi.org/10.3390/jof8040337