TABLE 2.
Species distribution and sensitivity of the new panfungal qPCR assay for 60 clinical samples included in the validation assaya
| Clinical group and fungal organism (no. of samples) | No. of organisms identified to species or genus level by: |
||
|---|---|---|---|
| Panfungal qPCRb | Molecular beaconc | Melting curved | |
| Proven IFI (37) | 29 | 18 (62.1%) | 15 (51.7%) |
| Aspergillus spp. (6) | 6 | 6 | 4 |
| Aspergillus fumigatus (2) | 2 | 2 | 1 |
| Aspergillus flavus (3) | 3 | 3 | 2 |
| Aspergillus penicilloides (1) | 1 | 1 | 1 |
| Mucormycetes (10) | 7 | 6 | 5 |
| Rhizopus oryzae (7) | 5 | 5 | 3 |
| Rhizopus microsporus (1) | 1 | 1 | 1 |
| Lichtheimia ramosa (1) | 1 | 0 | 1 |
| Rhizomucor pusillus (1) | 0 | 0 | 0 |
| Endemic mycoses (10) | 6 | 6 | 4 |
| Histoplasma capsulatum (8) | 4 | 4 | 2 |
| Coccidioides immitis (1) | 1 | 1 | 1 |
| Paracoccidioides brasiliensis (1) | 1 | 1 | 1 |
| Candida spp. (3) | 3 | 0 | 2 |
| Candida albicans (2) | 2 | 0 | 1 |
| Candida glabrata (1) | 1 | 0 | 1 |
| Other (8) | 7 | 0 | 0 |
| Fusarium sp. (1) | 1 | 0 | 0 |
| Cryptococcus neoformans (1) | 1 | 0 | 0 |
| Phoma exigua (1) | 0 | 0 | 0 |
| Bipolaris spicifera (1) | 1 | 0 | 0 |
| Microsphaeropsis arundinis (1) | 1 | 0 | 0 |
| Pythium insidiosum (1) | 1 | 0 | 0 |
| Cladophialophora bantiana (1) | 1 | 0 | 0 |
| Emmonsia crescens (1) | 1 | 0 | 0 |
| Probable IFI (23) | 21 | 10 (47.6%) | 7 (33.3%) |
| Aspergillus spp. (11) | 10 | 9 | 7 |
| Aspergillus fumigatus (6) | 6 | 6 | 4 |
| Aspergillus flavus (3) | 3 | 2 | 2 |
| Aspergillus terreus (1) | 1 | 1 | 1 |
| Aspergillus nomius (1) | 0 | 0 | 0 |
| Mucormycetes (1) | 1 | 1 | 0 |
| Rhizopus oryzae (1) | 1 | 1 | 0 |
| Candida spp. (6) | 6 | 0 | 0 |
| Candida albicans (2) | 2 | 0 | 0 |
| Candida parapsilosis (2) | 2 | 0 | 0 |
| Candida tropicalis (2) | 2 | 0 | 0 |
| Other (5) | 4 | 0 | 0 |
| Scedosporium sp. (1) | 1 | 0 | 0 |
| Aureobasidum pullulans (1) | 1 | 0 | 0 |
| Acremonium sp. (1) | 1 | 0 | 0 |
| Exophiala sp. (1) | 0 | 0 | 0 |
| Schizophyllum commune (1) | 1 | 0 | 0 |
| Total (60) | 50 | 28 (56%) | 22 (44%) |
a
Values in last three columns are numbers (percentage relative to positive samples by panfungal qPCR) of samples in which the organism was identified.
b
Overall identification of fungal species by the new panfungal qPCR assay by positive signal of Resolight dye followed by sequencing.
c
Identification of species or genus by positive signal of molecular beacon probes.
d
Identification of fungal species by melting curve analysis.