Table 3.
Correct identification results of isolates from the test set.
| Correct Identification with MALDI-TOF, Direct Smear | Correct Identification with MALDI-TOF, Ethanol | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bruker Databases 1, n (%) |
Custom Databases 1, n (%) |
Bruker Databases 1 + Custom, n (%) |
Biomarker Assignment, n (%) |
Classifier Models, n (%) |
Bruker Databases 1, n (%) |
Custom Databases 1, n (%) |
Bruker Databases 1 + Custom, n (%) |
Biomarker Assignment, n (%) |
Classifier Models, n (%) |
|||||||||||
| Genus | ||||||||||||||||||||
| Shigella (n = 217) | 19 | (9) | 205 | (94) | 205 | (94) | 10 | (5) | 209 | (96) | 12 | (6) | 207 | (95) | 205 | (94) | 15 | (7) | 217 | (100) |
| E. coli (n = 52) | 49 | (94) | 26 | (50) | 29 | (56) | NA | 11 | (21) | 47 | (90) | 35 | (67) | 37 | (71) | NA | 4 | (8) | ||
| Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 257 | (96) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 250 | (93) | 0 | (0) |
| Pathotype | ||||||||||||||||||||
| Shigella/EIEC (n = 248) | NA | 233 | (94) | 241 | (97) | 217 | (88) | 145 | (58) | NA | 245 | (99) | 242 | (98) | 225 | (92) | 147 | (59) | ||
| Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | NA | 14 | (67) | 21 | (100) | 11 | (52) | 13 | (62) | NA | 6 | (29) | ||
| Unassigned 2 | 2 | 1 | (0.4) | 3 | (1) | 46 | (17) | 0 | (0) | 0 | (0) | 0 | (0) | 3 | (1) | 27 | (10) | 0 | (0) | |
| Group | ||||||||||||||||||||
| Shigella (n = 217) | 19 | (9) | 205 | (94) | 205 | (94) | 193 | (89) | 131 | (60) | 12 | (6) | 207 | (95) | 205 | (94) | 195 | (90) | 134 | (62) |
| EIEC (n = 31) | NA | 9 | (29) | 8 | (26) | NA | 2 | (6) | NA | 19 | (61) | 19 | (61) | NA | 0 | (0) | ||||
| Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | NA | 13 | (62) | 21 | (100) | 11 | (52) | 13 | (62) | NA | 7 | (33) | ||
| Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 49 | (23) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 36 | (13) | 0 | (0) |
| Species | ||||||||||||||||||||
| S. dysenteriae (n = 11) | 5 | (45) | 5 | (45) | 5 | (45) | 0 | (0) | 0 | (0) | 4 | (36) | 7 | (64) | 6 | (55) | 0 | (0) | 0 | (0) |
| S. flexneri (n = 77) | NA | 70 | (91) | 70 | (91) | 24 | (31) | 6 | (8) | NA | 73 | (95) | 73 | (95) | 30 | (39) | 3 | (4) | ||
| S. boydii (n = 14) | NA | 1 | (7) | 0 | (0) | 0 | (0) | 0 | (0) | NA | 0 | (0) | 0 | (0) | 0 | (0) | 0 | (0) | ||
| S. sonnei (n = 115) | NA | 110 | (96) | 110 | (96) | 113 | (98) | 92 | (80) | NA | 112 | (97) | 112 | (97) | 108 | (94) | 101 | (88) | ||
| EIEC (n = 31) | NA | 9 | (29) | 8 | (26) | 0 | (0) | 1 | (3) | NA | 19 | (61) | 19 | (61) | 1 | (3) | 3 | (10) | ||
| Other E. coli (n = 21) | 21 | (100) | 6 | (29) | 10 | (48) | 0 | (0) | 12 | (57) | 21 | (100) | 11 | (52) | 13 | (62) | 0 | (0) | 4 | (19) |
| Unassigned 2 | 2 | (1) | 1 | (0.4) | 3 | (1) | 85 | (32) | 0 | (0) | 1 | (0.4) | 0 | (0) | 3 | (1) | 97 | (36) | 0 | (0) |
NA = not applicable, as no discriminating peaks were assigned to these classes. 1 Bruker MALDI Biotyper database (V8.0.0.0) and the Bruker Security-Relevant Library (V1.0.0.0). 2 Number of isolates that could not be assigned to a class.