Table 1.
Comparison of WGS-based genotyping and phenotypic ASTs against the broth microdilution reference. Frequency of isolates assigned to classification groups after phenotypic testing (broth microdilution) and application of interpretive criteria (epidemiological cut-off and clinical breakpoint). Genotype concordance with classification groups is provided for each interpretive criterion. Antimicrobials with ‘-‘values were not assessed due to the absence of established breakpoints or susceptibility test data
| Antimicrobial | Epidemiological cut-off | Clinical breakpoint | ||||
|---|---|---|---|---|---|---|
| Non-Wild Type | Wild Type | Genotype concordance (%) | Resistant | Sensitive | Genotype Concordance (%) | |
| Ampicillin | 57 | 45 | 95.10 | 57 | 45 | 95.10 |
| Chloramphenicol | 49 | 53 | 94.12 | 49 | 53 | 94.12 |
| Ciprofloxacin | 27 | 75 | 96.08 | - | - | - |
| Gentamicin | 8 | 94 | 92.16 | 7 | 95 | 93.14 |
| Nalidixic Acid | 28 | 74 | 95.10 | 28 | 74 | 95.10 |
| Sulfamethoxazole | 69 | 33 | 76.47 | 69 | 33 | 76.47 |
| Streptomycin | 66 | 36 | 89.22 | 26 | 76 | 55.88 |
| Sulfisoxazole | 73 | 29 | 70.59 | - | - | - |
| Trimethoprim-Sulfamethoxazole (1:19) | 33 | 69 | 93.14 | 30 | 72 | 96.08 |
| Tetracycline | 57 | 45 | 89.22 | - | - | - |
| Trimethoprim | 32 | 70 | 96.08 | - | - | - |
| Overall | 499 | 623 | 89.75 | 266 | 448 | 86.55 |