TABLE 4.
Detection of staphylococcal antibiotic resistance genes in sonicate fluid by metagenomic analysisa
| Threshold of total match percentage [applied gene(s)] | Data set (no. of staphylococci) | Antibiotic(s) | No. of staphylococci resistant by phenotype |
No. of staphylococci susceptible by phenotype |
Sensitivity (% [95% CI]) | Specificity (% [95% CI]) | ||
|---|---|---|---|---|---|---|---|---|
| Resistant by genotype | Susceptible by genotype | Resistant by genotype | Susceptible by genotype | |||||
| >22.4% (all genes) | Derivation set (50) | Methicillin | 19 | 7 | 0 | 24 | 73.1 (52.2, 88.4) | 100.0 (85.8, 100.0) |
| Clindamycin | 14 | 6 | 6 | 24 | 70.0 (45.7, 88.1) | 80.0 (61.4, 92.3) | ||
| TMP-SMX | 7 | 2 | 12 | 29 | 77.8 (40.0, 97.2) | 70.7 (54.5, 83.9) | ||
| Vancomycin | 0 | 0 | 0 | 50 | NA | 100.0 (91.1,100.0) | ||
| Validation set (40) | Methicillin | 22 | 5 | 0 | 13 | 81.5 (61.9, 93.7) | 100.0 (75.3, 100.0) | |
| Clindamycin | 9 | 6 | 2 | 23 | 60.0 (32.9, 83.7) | 92.0 (74.0, 99.1) | ||
| TMP-SMX | 10 | 1 | 10 | 19 | 90.9 (58.7, 99.8) | 65.5 (45.7, 82.1) | ||
| Vancomycin | 0 | 0 | 0 | 40 | NA | 100.0 (91.2, 100.0) | ||
| Overall (90) | Methicillin | 41 | 12 | 0 | 37 | 77.4 (63.8, 87.7) | 100.0 (90.5, 100.0) | |
| Clindamycin | 23 | 12 | 8 | 47 | 65.7 (47.8, 80.9) | 85.5 (73.4, 93.5) | ||
| TMP-SMX | 17 | 3 | 22 | 48 | 85.0 (62.1, 96.8) | 68.6 (56.4, 79.2) | ||
| Vancomycin | 0 | 0 | 0 | 90 | NA | 100.0 (95.9, 100.0) | ||
| >23.6% (mecA) | Derivation set (50) | Methicillin | 19 | 7 | 0 | 24 | 73.1 (52.2, 88.4) | 100.0 (85.8, 100.0) |
| Clindamycin | 14 | 6 | 6 | 24 | 70.0 (45.7,88.1) | 80.0 (61.4,92.3) | ||
| >22.4% (erm) | TMP-SMX | 7 | 2 | 10 | 31 | 77.8 (40.0,97.2) | 75.6 (59.7,87.6) | |
| Vancomycin | 0 | 0 | 0 | 50 | NA | 100.0 (91.1,100.0) | ||
| >68.9% (dfr) | Validation set (40) | Methicillin | 22 | 5 | 0 | 13 | 81.5 (61.9, 93.7) | 100.0 (75.3, 100.0) |
| Clindamycin | 9 | 6 | 2 | 23 | 60.0 (32.9,83.7) | 92.0 (74.0,99.1) | ||
| TMP-SMX | 9 | 2 | 10 | 19 | 81.8 (48.2,97.7) | 65.5 (45.7,82.1) | ||
| Vancomycin | 0 | 0 | 0 | 40 | NA | 100.0 (91.2, 100.0) | ||
| Overall (90) | Methicillin | 41 | 12 | 0 | 37 | 77.4 (63.8, 87.7) | 100.0 (90.5, 100.0) | |
| Clindamycin | 23 | 12 | 8 | 47 | 65.7 (47.8, 80.9) | 85.5 (73.4, 93.5) | ||
| TMP-SMX | 16 | 4 | 20 | 50 | 80.0 (56.3, 94.3) | 71.4 (59.4, 81.6) | ||
| Vancomycin | 0 | 0 | 0 | 90 | NA | 100.0 (95.9, 100.0) | ||
a
TMP-SMX, trimethoprim-sulfamethoxazole; CI, confidence interval; NA, not applicable.