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

Hagen Frickmann; Carsten Künne; Ralf Matthias Hagen; Andreas Podbielski; Jana Normann; Sven Poppert; Mario Looso; Bernd Kreikemeyer

doi:10.1186/s12866-019-1448-0

BMC Microbiology

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

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