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Table 5 Comparison of the NGS Results in Terms of Percentage of Species-specific Reads of Investigated Fungal Species Per Total Number of Reads in the Sample with the Respective Largest Standard Deviation above the Mean of All Samples in Multiples of the Standard Deviation (SD), Depicted for the Samples from Patients with Invasive Mycoses. “Positive” = matching of the molecular results with histology. “Negative” = inconsistency of molecular results with histology. “Partially positive” = detection of both matching and nonmatching molecular results compared with histology. “Contaminated” = Detection of environmental fungi only. “Match” = NGS result matching the histological findings. “Mismatch” = NGS results not matching the histological findings, “No match” = No evidence for relevant fungal species above the respective standard deviation (SD), “Not performed” in “Specific PCR” = No specific PCR performed. Highest standard deviations (SD) are shown

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 Specific PCR [13] Panfungal PCRs [13] NGS > 1st SD NGS > 2nd SD NGS > 3rd SD NGS > 4th SD
1 Chromoblastomycosis Not performed Contaminated Matchd No match No match No match
2 Mucormycosis Negative Contaminated No match No match No match No match
3 Histoplasmosis Negative Contaminated Mismatche Mismatchf No match No match
4 Mucormycosis Positivea Contaminated No match No match No match Matchg
5 Histoplasmosis or cryptococcosis Negative Contaminated No match No match No match Matchh
6 Chromoblastomycosis Not performed Contaminated Mismatchi Matchj No match No match
7 Rhinosporidiosis Not performed Contaminated No match No match No match No match
8 Mycetoma Not performed Contaminated Mismatchk Mismatchl No match Matchm
9 Rhinosporidiosis Not performed Contaminated Mismatchn No match No match No match
10 Mycetoma Not performed Contaminated Mismatcho No match No match No match
11 Histoplasmosis Negative Contaminated No match No match No match No match
12 Histoplasmosis Negative Contaminated Mismatchp Mismatchq Mismatchr No match
13 Chromoblastomycosis Not performed Contaminated No match No match No match No match
14 Histoplasmosis Positive Partially positiveb No match No match No match Matchs
15 Coccidioidomycosis Not performed Contaminated Mismatcht No match No match No match
16 Coccidioidomycosis Not performed Contaminated No match No match No match No match
17 Mycetoma Not performed Partially positivec No match No match No match Matchu
  1. aLichtheimia / Absidia corymbifera, bHistoplasma capsulatum in 2 out of 5 panfungal PCRs, cMadurella mycetomatis in 1 out of 5 panfungal PCRs, d0.004% Cladophialophora yegresii, e0.0004% Capronia epimyces, f0.0002% Cladophialophora carrionii, g0.00004% Rhizopus oryzae, h0.00001% Cryptococcus carnescens, i0.00009% Fusarium graminearum, j0.0002% Cladophialophora psammophila, k0.0004% Bipolaris oryzae, l0.0005% Paracoccidioides sp. ‘lutzii’, m0.02% Fusarium pseudograminearum, n0.004% Cladophialophora yegresii, o0.004% Cladophialophora yegresii, p0.0003% Bipolaris sorokiniana, 0.004% Cladophialophora yegresii, 0.0003% Coccidioides immitis, 0.0004% Paracoccidioides sp. ‘lutzii’, q0.0006% Capronia epimyces, 0.0006% Chaetomium globosum, 0.0004% Chaetomium thermophilum var. Thermophilum, 0.0002% Cladophialophora psammophila, 0.0002% Cryptococcus neoformans, 0.0002% Exophiala dermatitidis, 0.0006% Paracoccidioides brasiliensis, r0.0005% Coccidioides posadasii, 0.0005% Cyphellophora europaea, 0.0002% Fusarium graminearum, s0.02% Histoplasma capsulatum, t0.004% Cladophialophora yegresii, u0.001% Madurella mycetomatis. Matches with the histological findings are depicted in underlined print