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

Table 2

Results of inhibition control PCR (phocid herpesvirus PCR), DNA extraction control PCR (18S rRNA gene PCR), and specific PCR/sequencing results for Histoplasma capsulatum and Mucorales. Ct = cycle threshold. N.a. = not applicable.

Sample I.D.	Histological diagnosis	Ct-value of phocid herpesvirus PCR	Ct-value of human 18S rRNA gene PCR	DNA concentration as measured by Picodrop	Histoplasma-specific nested PCR (and consecutive sequencing)	Mucorales-specific seminested PCR (and consecutive sequencing)
Case  1	Chromoblastomycosis	22	23	12.3 ng/µL	N.a.	N.a.
Case  2	Mucormycosis	18	15	14.6 ng/µL	Negative	Negative
Case  3	Histoplasmosis	18	14	246.3 ng/µL	Negative	Negative
Case  4	Mucormycosis	20	—	26.9 ng/µL	Negative	Positive (100% Lichtheimia/Absidia corymbifera)
Case  5	Histoplasmosis or Cryptococcosis	20	19	157.6 ng/µL	Negative	Negative
Case  6	Chromoblastomycosis	26	30	414.5 ng/µL	N.a.	N.a.
Case  7	Rhinosporidiosis	26	23	62.7 ng/µL	N.a.	N.a.
Case  8	Mycetoma/maduromycosis	22	33	618.9 ng/µL	N.a.	N.a.
Case  9	Rhinosporidiosis	18	22	21.9 ng/µL	N.a.	N.a.
Case  10	Mycetoma/maduromycosis	25	15	16.8 ng/µL	N.a.	N.a.
Case  11	Histoplasmosis	21	30	104.6 ng/µL	Negative	Negative
Case  12	Histoplasmosis	24	15	44.3 ng/µL	Negative	Positive (no interpretable sequence results due to poor sequence quality)
Case  13	Chromoblastomycosis	23	14	33.8 ng/µL	N.a.	N.a.
Case  14	Histoplasmosis	20	17	175.5 ng/µL	Positive (99% Histoplasma capsulatum)	Negative
Case  15	Coccidioidomycosis	24	21	16.8 ng/µL	N.a.	N.a.
Case  16	Coccidioidomycosis	24	14	107.5 ng/µL	N.a.	N.a.
Case  17	Mycetoma/maduromycosis	18	13	26.3 ng/µL	N.a.	N.a.
Control 1	Negative control	22	34	609.7 ng/µL	N.a.	N.a.
Control 2	Negative control	23	25	655.3 ng/µL	N.a.	N.a.
Control 3	Negative control	19	31	676.6 ng/µL	N.a.	N.a.