TABLE 3.
Summary of categorical agreement, very major errors, and major errors per species WGS-based susceptibility prediction in comparison with broth microdilutiona
| Species | No. of compounds | No. of isolates | Categorical agreement (%) | VME (%) | ME (%) | TP | TN | FP | FN |
|---|---|---|---|---|---|---|---|---|---|
| Acinetobacter baumannii | 11 | 19 | 199/209 (95.2) | 5/146 (3.4) | 5/63 (7.9) | 141 | 58 | 5 | 5 |
| Escherichia coli | 15 | 46 | 653/690 (94.6) | 26/143 (18.2) | 11/547 (2.0) | 117 | 536 | 11 | 26 |
| Klebsiella pneumoniae | 15 | 48 | 677/720 (94.0) | 13/110 (11.8) | 30/610 (4.9) | 97 | 580 | 30 | 13 |
| Serratia marcescens | 12 | 28 | 314/336 (93.5) | 11/26 (42.3) | 11/310 (3.5) | 15 | 299 | 11 | 11 |
| Staphylococcus aureus | 9 | 128 | 950/1038 (91.5) | 37/341 (10.9) | 51/697 (7.3) | 304 | 646 | 51 | 37 |
| Proteus mirabilis | 10 | 21 | 192/210 (91.4) | 5/52 (9.6) | 13/158 (8.2) | 47 | 145 | 13 | 5 |
| Klebsiella oxytoca | 9 | 13 | 101/117 (86.3) | 7/20 (35.0) | 9/97 (9.3) | 13 | 88 | 9 | 7 |
| Morganella morganii | 7 | 2 | 12/14 (85.7) | 2/10 (20.0) | 0/4 (0.0) | 8 | 4 | 0 | 2 |
| Pseudomonas aeruginosa | 10 | 135 | 1153/1350 (85.4) | 84/294 (28.6) | 113/1056 (10.7) | 210 | 943 | 113 | 84 |
| Enterobacter cloacae | 10 | 37 | 313/370 (84.6) | 21/79 (26.6) | 36/291 (12.4) | 58 | 255 | 36 | 21 |
| Citrobacter freundii | 8 | 4 | 26/32 (81.3) | 4/5 (80.0) | 2/27 (7.4) | 1 | 25 | 2 | 4 |
| Stenotrophomonas maltophilia | 4 | 60 | 193/240 (80.4) | 35/123 (28.5) | 12/117 (10.3) | 88 | 105 | 12 | 35 |
| Klebsiella aerogenes | 9 | 25 | 173/225 (76.9) | 13/43 (30.2) | 39/182 (21.4) | 30 | 143 | 39 | 13 |
a
Categorical agreement, very major errors, and major errors were calculated from the overall number of true positives (TP), true negatives (TN), false positives (FP), and false negatives (FN) obtained per species. Data are sorted by categorical agreement in descending order.