TABLE 3.
Antibiotic resistance prediction in isolates of P. aeruginosa using genomes
| Resistance alleles | Predicted MICa | Total no. of isolates | MICactual equal to, or with one doubling of MICpredicted |
MICactual greater than MICpredictedb |
MICactual less than MICpredictedb |
|||
|---|---|---|---|---|---|---|---|---|
| No. of isolates | MIC range in mg/liter | No. of isolates | MIC range in mg/liter | No. of isolates | MIC range in mg/liter | |||
| Clinical isolates with MIC predicted to be less than or equal to 1 mg/liter | ||||||||
| No analyzed resistance alleles present | 0.05 to 0.5 | 136 | 112 (99 + 13) | 0.05–1 | 24 | 2–4 | 0 | NA |
| WT gyrA in combination with resistance alleles in other genes nfxB/parC/parE/gyrB and crpP | 0.05 to 0.5 | 63 | 57 (43 + 14) | 0.125–1 | 6 | 2–3 | 0 | NA |
| Only gyrAT83I | MIC = 1 | 28 | 17 | 0.5–2 | 6 | 4–12 | 5 | 0.05–0.25 |
| Clinical isolates with MIC predicted to be greater than 1 mg/liter | ||||||||
| Both gyrAT83I and parCS87L | MIC ≥ 4 | 33 | 31 | ≥4 | 1 | 24 | 1 | 0.125 |
| gyrAT83I and parE | MIC = 2 | 5 | 4 | 2–4 | 0 | NA | 1 | 0.5 |
| gyrAT83I + nfxB + parE/parC | MIC ≥ 2 | 9 | 5 | 2–8 | 1 | 12 | 3 | 0.05–1 |
| Total | 274 | 226 | 0.05–8 | 38 | 2–24 | 10 | 0.05–1 | |
a
Predictions were based on the resistance alleles in genes gyrA, gyrB, parC, parE and nfxB (Table 1) and MICs of mutants carrying those alleles (Table S1).
b
A value of ± 4-fold or more was considered a significant difference between actual and predicted MICs. NA, not applicable.