Table 3:
Results of WGS for Prediction of AMR among clinical VRE isolates
| Antibiotic | No. Isolates |
Phenotypic Resistance |
Genotypic Resistance |
Concordance with Disk Diffusion (%) |
Sensitivity (95% CI) (%) |
Specificity (95% CI) (%) |
PPV (95% CI) (%) |
NPV (95% CI) (%) |
|
|---|---|---|---|---|---|---|---|---|---|
| Automated No, (%) |
Disk Diffusion, No, (%) |
Inferred resistant by WGS No. (%) |
|||||||
| Vancomycin | 100 | 100 (100) |
96 (96.0) |
96 (96.0) |
100 | 100 (96.2-100) |
100 (39.8-100) |
100 (96.2-100) |
100 (39.8-100) |
| Linezolid1 | 96 | 3 (3.1) |
2 (2.1) |
0 | 97.9 | 0 (0-84.2) |
100 (96.2-100) |
n/a | 97.9 (97.9-97.9) |
| Erythromycin | 56 | 56 (100) |
56 (100) |
56 (100) |
100 | 100.00 (93.6-100) |
n/a | 100 (93.6-100) |
n/a |
| Tetracycline | 48 | 44 (91.7) |
45 (93.8) |
47 (97.9) |
95.8 | 100 (92.1-10) |
33.3 (0.82-90.6) |
95.7 (91.0-98.0) |
100 (5.0-100) |
| Total2,3 | 300 | 203 (67.7) |
199 (66.3) |
199 (66.3) |
98.7 | 99.0 (96.4-99.9) |
98.0 (93.0-99.8) |
99.0 (96.1-99.7) |
98.0 (92.6-99.5) |
1
With the additional step of examining for point mutations in housekeeping genes concordance and NPV were increased to 100% (95 CI, 96.2-100%)
2
Total results for all VRE isolate/antibiotic combinations
3
Additional identification of point mutations in housekeeping genes increased the concordance to 99.3%, sensitivity to 100% (95% CI, 99.1-100%) and NPV to 100% (95% CI, 96.8-100%).