TABLE 2.
Samples grouped by their clonal complexes and the concordant and discrepant WGS and microarray typing results calculated for each CC (percentages per CC given in parentheses)a
| Clonal complex (no. of isolates) | No. concordant (n = 27,119; 96.8 %) |
No. discrepant (n = 909; 3.2 %) |
No. unknown | Total no. | |||||
|---|---|---|---|---|---|---|---|---|---|
| Positive | Negative | False positive |
False negative |
||||||
| Microarray | LFM | Microarray | LFM | WGS | |||||
| CC1 (7) | 541 (42.5) | 703 (55.2) | 0 | 0 | 4 (0.3) | 0 | 26 (2.0) | 0 | 1,274 |
| CC5 (17) | 1,375 (44.4) | 1,615 (52.2) | 2 (0.1) | 1 (<0.1) | 1 (<0.1) | 0 | 99 (3.2) | 1 (<0.1) | 3,094 |
| CC6 (6) | 448 (41.0) | 611 (56.0) | 5 (0.5) | 1 (0.1) | 0 | 0 | 27 (2.5) | 0 | 1,092 |
| CC7 (6) | 423 (38.7) | 633 (58.0) | 11 (1.0) | 1 (0.1) | 7 (0.6) | 0 | 15 (1.4) | 2 (0.2) | 1,092 |
| CC8 (16) | 1,258 (43.2) | 1,542 (53.0) | 38 (1.3) | 3 (0.1) | 0 | 1 (<0.1) | 70 (2.4) | 0 | 2,912 |
| CC9 (2) | 143 (39.3) | 210 (57.7) | 2 (0.5) | 0 | 1 (0.3) | 0 | 6 | 2 (0.5) | 364 |
| CC15 (28) | 2,152 (42.2) | 2,864 (56.2) | 33 (0.6) | 0 | 21 (0.4) | 0 | 26 (0.5) | 0 | 5,096 |
| CC22 (8) | 496 (34.1) | 831 (57.1) | 16 (1.1) | 5 (0.3) | 51 (3.5) | 2 (0.1) | 54 (3.7) | 1 (0.1) | 1,456 |
| CC30 (13) | 937 (39.6) | 1,352 (57.1) | 13 (0.5) | 6 (0.3) | 0 | 0 | 55 (2.3) | 3 (0.1) | 2,366 |
| CC45 (12) | 829 (38.0) | 1,271 (58.2) | 17 (0.8) | 1 (0.3) | 30 (1.4) | 2 (0.1) | 33 (1.5) | 1 (<0.1) | 2,184 |
| CC80 (1) | 75 (41.2) | 99 (54.4) | 2 (1.1) | 0 | 2 (1.1) | 0 | 1 (0.5) | 3 (1.6) | 182 |
| CC88 (4) | 312 (42.9) | 398 (54.7) | 0 | 0 | 1 (0.1) | 0 | 17 (1.6) | 0 | 728 |
| CC121 (18) | 1,469 (44.8) | 1,711 (52.2) | 33 (1.0) | 10 (0.3) | 3 (0.1) | 0 | 50 (1.5) | 0 | 3,276 |
| CC152 (16) | 916 (31.5) | 1,905 (65.4) | 30 (1.0) | 0 | 36 (1.2) | 0 | 10 (0.3) | 15 (0.5) | 2,912 |
| Total (154) | 11,374 | 15,745 | 202 | 28 | 157 | 5 | 489 | 28 | 28,028 |
a
Comparison of typing concordance of WGS typing and the traditional DNA microarray. In total, 182 targets in 154 samples were analyzed, resulting in 28,028 individual typing results. The discrepant results are subdivided by false-positive and false-negative typing results and different causes of error. Results that were assumed to be false negatively typed by the two methods are not considered in this table (n = 4). WGS results were summarized in one column irrespective of the cause of error.