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
|
- 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