Detection of Tropical Fungi in Formalin-Fixed, Paraffin-Embedded Tissue: Still an Indication for Microscopy in Times of Sequence-Based Diagnosis?

Table 3

Comparison of histological and sequencing results. (Details on PCR results and sequencing quality can be found in supplementary materials 2–5.)

Sample I.D.	Histological diagnosis	PCR 1	PCR 2	PCR 3	PCR 4	PCR 5
Case  1	Chromoblastomycosis	Multiple species, no discrimination possible	Noninterpretable, poor/overlapping sequences	Umbilicaria torrefacta/Placynthium nigrum	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences
Case  2	Mucormycosis	Aspergillus spp./Penicillium spp.	Candida parapsilosis	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Candida parapsilosis
Case  3	Histoplasmosis	Cryptococcus carnescens/Cryptococcus psychrotolerans/Cryptococcus peneaus/Taphrina maculans	Noninterpretable, poor/overlapping sequences	Various Umbilicaria spp.	Various Penicillium spp.	—
Case  4	Mucormycosis	Delitschia didyma	Various Candida spp./Yarrowia spp./Candida galli	—	Multiple species, no discrimination possible/Neofusicoccum spp.	—
Case  5	Histoplasmosis or cryptococcosis	Lactarius indigo/Candida piceae/Glomus spp.	Noninterpretable, poor/overlapping sequences	Various Umbilicaria spp.	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences
Case  6	Chromoblastomycosis	Xylomyces spp./Speiropsis spp./Jahnula spp./Brachiosphaera spp./Megalohypha spp./Lactarius indigo  Candida piceae/Glomus spp.	Noninterpretable, poor/overlapping sequences	—	Noninterpretable, poor/overlapping sequences	—
Case  7	Rhinosporidiosis	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Candida spp./Malassezia spp./Starmerella spp.	—
Case  8	Mycetoma/maduromycosis	Lactarius indigo/Candida piceae/Glomus spp.	—	—	Noninterpretable, poor/overlapping sequences	—
Case  9	Rhinosporidiosis	Multiple species, no discrimination possible	Noninterpretable, poor/overlapping sequences	Various Umbilicaria spp.	Rhizoctonia solani	Noninterpretable, poor/overlapping sequences
Case  10	Mycetoma/maduromycosis	Multiple fungal species including Penicillium spp./Aspergillus spp.	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Various Penicillium spp./Talaromyces flavus	Noninterpretable, poor/overlapping sequences
Case  11	Histoplasmosis	Noninterpretable, poor/overlapping sequences	Candida parapsilosis	Noninterpretable, poor/overlapping sequences	Trametes spp./Tricholoma spp./Phellinus spp.	—
Case  12	Histoplasmosis	Candida parapsilosis	Candida parapsilosis	Candida parapsilosis	Candida parapsilosis	Candida parapsilosis/Tremellalesspp./Saccharomycetales spp.
Case  13	Chromoblastomycosis	Multiple fungal species including Penicillium spp./Aspergillus spp.	Candida parapsilosis/various Candida spp.	Penicillium spp.	Aspergillus spp./Ajellomyces capsulatus/Histoplasma capsulatum	Candida parapsilosis
Case  14	Histoplasmosis	Ajellomyces capsulatus/Histoplasma capsulatum	Noninterpretable, poor/overlapping sequences	Paecilomyces variotii	Ajellomyces  capsulatus/ Histoplasmacapsulatum	—
Case  15	Coccidioidomycosis	Multiple species, no discrimination possible	Candida parapsilosis	Noninterpretable, poor/overlapping sequences	Candida parapsilosis	Candida parapsilosis
Case  16	Coccidioidomycosis	Delitschia didyma	Candida parapsilosis	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences
Case  17	Mycetoma/maduromycosis	Delitschia didyma	Noninterpretable, poor/overlapping sequences	Myceliophthora thermophila/Thielavia terrestris/Neurospora crassa	Madurella mycetomatis	Noninterpretable, poor/overlapping sequences
Control 1	Negative control	Funneliformis spp./Glomus spp./Candida salmanticensis	Noninterpretable, poor/overlapping sequences	Various Umbilicaria spp.	Davidiella tassiana	—
Control 2	Negative control	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Various Umbilicaria spp.	Noninterpretable, poor/overlapping sequences	—
Control 3	Negative control	Noninterpretable, poor/overlapping sequences	Noninterpretable, poor/overlapping sequences	Umbilicaria spp./Lasallia spp./Boreoplaca ultrafrigida/Rhizoplaca huashanensis	Noninterpretable, poor/overlapping sequences	—