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Table 9 Histological Characterization of Neighboring Sections of the Materials That Were Used for NGS Assessment. Samples of Cases with Invasive Mycosis Had Been Assessed by HE, Giemsa, PAS, and Grocott Staining [13], Samples of Cases with Invasive Amebiasis by PAS Staining [7]. Especially in the Case of Filamentous Fungi, No Quantification Had Been Attempted, Because Elements of a Multiply-cut Filament Were Indistinguishable from Single Cuts of Multiple Filaments

From: Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment

Sample Histological diagnosis Microscopic confirmation of pathogens in neighboring sections of the materials for NGS assessment
1 Chromoblastomycosis Microorganisms seen, no quantification performed
2 Mucormycosis Microorganisms seen, no quantification performed
3 Histoplasmosis Microorganisms seen, < 10 pathogens per unit area (160 μm × 210 μm)
4 Mucormycosis Microorganisms seen, no quantification performed
5 Histoplasmosis or cryptococcosis Microorganisms seen, < 10 pathogens per unit area (160 μm × 210 μm)
6 Chromoblastomycosis Microorganisms seen, no quantification performed
7 Rhinosporidiosis Microorganisms seen, no quantification performed
8 Mycetoma Microorganisms seen, no quantification performed
9 Rhinosporidiosis Microorganisms seen, no quantification performed
10 Mycetoma Microorganisms seen, no quantification performed
11 Histoplasmosis Microorganisms seen, < 10 pathogens per unit area (160 μm × 210 μm)
12 Histoplasmosis Microorganisms seen, < 10 pathogens per unit area (160 μm × 210 μm)
13 Chromoblastomycosis Microorganisms seen, no quantification performed
14 Histoplasmosis Microorganisms seen, < 10 pathogens per unit area (160 μm × 210 μm)
15 Coccidioidomycosis Microorganisms seen, no quantification performed
16 Coccidioidomycosis Microorganisms seen, no quantification performed
17 Mycetoma Microorganisms seen, no quantification performed
18 Invasive amebiasis Microorganisms seen, > 5 pathogens per unit area (160 μm × 210 μm)
19 Invasive amebiasis Negative microscopy in neighboring sections
20 Invasive amebiasis Microorganisms seen, > 5 pathogens per unit area (160 μm × 210 μm)
21 Invasive amebiasis Microorganisms seen, < 0.5 pathogens per unit area (160 μm × 210 μm)
22 Invasive amebiasis Negative microscopy in neighboring sections
23 Invasive amebiasis Uncertain microscopic result in neighboring sections