TABLE 2.
Studies evaluating the performance of in-house MALDI-TOF MS databases for identification of filamentous fungia
| MALDI system(s) | Order(s) and/or group(s) | Organism(s) studied (no. of species) | No. of species (no. of strains) in DB | Acceptance criterion for ID (Bruker Biotyper ID score) | No. of correctly identified isolates while challenging DB/total no. of isolates while challenging DB | Accuracy (%) | Comparative method(s) | Sequence(s) used for ID | Reference |
|---|---|---|---|---|---|---|---|---|---|
| Bruker Daltonics | Eurotiales, Mucorales, Hypocreales | Aspergillus (sections Fumigati, Flavi, Terrei, Nigri, Nidulantes, Usti, Circumdati, Aspergillus, Candidi) (33), Mucor spp. (5), Lichtheimia spp. (2), Rhizopus spp. (2), Rhizomucor spp. (2), Fusarium spp. (12) | 55 | ≥2.0; 1.7–2.0 | 91/94; 3/94 | 96.8; 3.2 | MB | ITS1-5.8S-ITS2, β-tubulin, calmodulin, elongation factor Iα | 42 |
| Bruker Daltonics | Eurotiales, Hypocreales, Mucorales, Microascales, dermatophytes, dimorphic, other | Aspergillus spp. (63), Penicillium spp. (10), Paecilomyces spp. (15), Fusarium spp. (15), Pseudallescheria spp. (11), Scedosporium spp. (11), Mucor spp. (15), other (154) | 152 (294) | ≥2.0; 1.7–2.0 | 370/421; 18/421 | 87.9; 4.3 | MB, MO | ITS, D1/D2 domains of the 23S rDNA complex, β-tubulin, elongation factor Iα | 14 |
| Bruker Daltonics | Eurotiales, Hypocreales, other | Aspergillus spp. (77), Penicillium spp. (45), Paecilomyces spp. (7), Fusarium spp. (14), dematiaceous species (11), dermatophytes (46), other (130) | 347 (708) | NR | 257/262 | 98.1 | MB, MO | D1-D2 variable region of the 28S gene; ITS2 | 24 |
| Bruker Daltonics | Eurotiales, Hypocreales, Mucorales, Microascales, other | Aspergillus spp. (256), Penicillium spp. (37), Fusarium spp. (20), Scedosporium spp. (16), Cladosporium spp. (10), other (39) | 472 (760) | ≥2.0; 1.7–2.0 | 372/390 | 95.4 | MO, MB | ITS, β-tubulin, elongation factor Iα, LSU rDNA | 23 |
| Bruker Daltonics | Eurotiales, Hypocreales, Microascales, other | Aspergillus spp. (43), Penicillium spp. (16), Scedosporium spp. (18), Fusarium spp. (11), other (68) | 63 (146) | ≥2.0; 1.7–2.0 | 150/156 | 96.15 | MO, MB | ITS1-5.8S-ITS2, D1-D2 domains of the 28S rDNA complex | 1 |
| Bruker Daltonics | Eurotiales | Aspergillus spp. (23) | 14 | ≥2.0 | 24/24 | 100 | MB, MO | Calmodulin, β-tubulin | 29 |
| Bruker Daltonics | Hypocreales | Fusarium spp. (19) | 40 (289) | ≥2.0 | 222/268 | 82.8 | MB, MO | ITS, partial ribosomal LSU, β-tubulin, elongation factor Iα | 36 |
| Bruker Daltonics | Mucorales | Rhizopus arrhizus | 2 (38) | NR | 25/25 | 100 | MB | ITS, actin, elongation factor Iα | 27 |
| Rhizopus microsporus | NR | 13/13 | 100 | MB | |||||
| Bruker Daltonics | Eurotiales | Talaromyces marneffei | 1 (21) | ≥2.0 | 39/39 | 100 | MB | MPI, PM-ATPase, PK | 28 |
| Bruker Daltonics | Eurotiales | T. marneffei | 1 (4) | ≥2.0 | 23/28 | 82.1 | MB, MO | ITS1, ITS4 | 25 |
| Bruker Daltonics | Eurotiales | Paecilomyces spp. (4) | 8 (8) | ≥2.0; ≥1.8 | 67/71 | 94.30 | MB, MO | ITS1-5.8S-ITS2, D1/D2 region, β-tubulin | 33 |
| Bruker Daltonics | Dermatophytes | Trichophyton spp. (6), Microsporum spp. (4), Epidermophyton floccosum | 13 (24) | >2.0; 1.7–2.0 | 64/64 | 100 | MB, MO | 5.8S-ITS2 rDNA | 26 |
| Bruker Daltonics | Eurotiales, Hypocreales, Mucorales, Microascales, Onygenales, other | Aspergillus spp. (115), Fusarium spp. (33), Penicillium spp. (60, Paecilomyces spp. (5), Scedosporium spp. (20), Trichophyton spp. (183), other (85) | 938 | ≥20 | 435/501; 26/501 | 87.35; 5.22 | MB | ITS, β-tubulin, elongation factor | 18b |
| Bruker Daltonics | Pleosporales, Chaetothyriales, Capnodiales, other | Alternaria spp. (9), Cladophialophora spp. (10), Cladosporium spp. (8), Fonsecaea pedrosoi (10), Bipolaris spp. (10), other (70) | 29 (59) | ≥2.0; 1.75–1.99 | 75/117; 42/117 | 64.1; 35.9 | MB | ITS, 28S rDNA | 15 |
| Bruker Daltonics | Eurotiales, Hypocreales, Microascales | Aspergillus spp. (55), Fusarium spp. (45), Scedosporium spp. (17) | 28 (117) | ≥2.0; 1.7–1.99 | 105/117; 8/117 | 90; 6.8 | MB, MO | ITS, β-tubulin, elongation factor Iα | 20 |
| Bruker Daltonics | Eurotiales | Aspergillus (sections Fumigati, Flavi, Terrei, Nigri, Nidulantes, Usti, Circumdati, Versicolores) | 53 (23) | ≥2.0; 1.7–2.0 | 165/190; 25/190 | 86.8; 13.2 | MB, MO | β-Tubulin, calmodulin | 30 |
| Bruker Daltonics | Eurotiales, Hypocreales, Microascales | Aspergillus spp. (55), Fusarium spp. (45), Scedosporium spp. (17) | 6 (13) | ≥2.0; 1.7–2.0 | 90/111; 14/111 | 81.8; 12.6 | MB | ITS1, ITS4 | 43 |
| Bruker Daltonics | Hypocreales, Microascales, Mucorales | Fusarium spp. (19), Scedosporium spp. (24), Lichtheimia (8), other (12) | 15 (63) | ≥1.8; ≥1.6 | 94/101; 7/101 | 91.3; 8.7 | MB | ITS, β-tubulin, elongation factor Iα | 44 |
| Bruker Daltonics, Andromas | Eurotiales | Aspergillus (sections Fumigati, Flavi, Terrei, Nigri, Nidulantes, Usti, Circumdati) | 28 | ≥66% of common peaks of the reference strains | 138/140 | 98.6 | MB | β-Tubulin, calmodulin | 45 |
a
Within a row where there is a pair of entries separated by semicolons in the “Acceptance criterion for ID” column, there is a one-to-one correspondence between that pair, the pair in the “No. of correctly identified isolates while challenging DB/total no. of isolates while challenging DB” column, and the pair in the “Accuracy” column. Abbreviations: DB, database; ID, identification; MB, molecular biology; MO, morphology; NR, not reported; LSU, large subunit; MPI, mannose phosphate isomerase; PM-ATPase, plasma membrane H+ ATPase; PK, pyruvate kinase.
b
A combination of an in-house database and online software (MSI) was used.