TABLE 3.
The accuracy of Streptococcus pneumoniae detection in n = 1,549 nasopharyngeal samples from children (n = 946) and adults (n = 603) tested using conventional diagnostic culture and molecular methods applied to DNA extracted from minimally processed and culture-enriched samples and applying ROCdCq thresholds for a sample positivity in qPCRs.
| Method | Study population | Percent (n) of positive samples (95%CI) |
PPV % (95%CI) |
NPV % (95%CI) |
Sensitivity % (95%CI) |
Specificity % (95%CI) |
Concordance % (95%CI) |
κ (95%CI) |
| Primary culture | All | 28.7 (445) (26.5–31.0) |
100 (99.1–100) |
98.6 (97.8–99.2) |
96.7 (94.7–98.0) |
100 (99.6–100) |
99.0 (98.4–99.4) |
0.98 (0.96–0.99) |
| Children | 44.6 (422) (41.5–47.8) |
100 (99.1–100) |
97.1 (95.3–98.3) |
96.6 (94.4–97.9) |
100 (99.3–100) |
98.4 (97.4–99.0) |
0.97 (0.95–0.98) |
|
| Adults | 3.8 (23) (2.6–5.7) |
100 (85.7–100) |
100 (99.3–100) |
100 (85.7–100) |
100 (99.3–100) |
100 (99.4–100) |
1 | |
| qPCRs on minimally processed samples | All | 33.1 (512) (30.8–35.4) |
83.2 (79.7–86.2) |
96.7 (95.5–97.6) |
92.6 (89.8–94.7) |
92.1 (90.3–93.6) |
92.3 (90.8–93.5) |
0.82 (0.79–0.85) |
| Children | 51.7 (489) (48.5–54.9) |
83.6 (80.1–86.7) |
93.9 (91.3–95.7) |
93.6 (90.9–95.5) |
84.3 (80.9–87.2) |
88.6 (86.4–90.5) |
0.77 (0.73–0.81) |
|
| Adults | 3.8 (23) (2.6–5.7) |
73.9 (53.5–87.5) |
99.0 (97.8–99.5) |
73.9 (53.5–87.5) |
99.0 (97.8–99.5) |
98.0 (96.6–98.9) |
0.73 (0.58–0.88) |
|
| qPCRs on culture-enriched samples |
All | 30.3 (469) (28.0–32.6) |
95.7 (93.5–97.2) |
99.0 (98.2–99.4) |
97.6 (95.8–98.7) |
98.2 (97.2–98.8) |
98.0 (97.2–98.6) |
0.95 (0.94–0.97) |
| Children | 47.3 (447) (44.1–50.4) |
96.0 (93.7–97.4) |
98.4 (96.9–99.2) |
98.2 (96.4–99.1) |
96.5 (94.5–97.8) |
97.3 (96.0–98.1) |
0.94 (0.92–0.97) |
|
| Adults | 3.7 (22) (2.4–5.5) |
90.9 (72.2–97.5) |
99.5 (98.5–99.8) |
87.0 (67.9–95.5) |
99.7 (98.8–99.9) |
99.2 (98.1–99.6) |
0.88 (0.78–0.99) |
Measures of diagnostic accuracy were calculated by comparing the number of detected samples positive per method with the number of (n = 460 for all individuals, and n = 437 and n = 23 for nasopharyngeal samples from children and adults, respectively) individuals positive for S. pneumoniae based on isolation of live pneumococcus either from the primary diagnostic or qPCR-guided culture. PPV, positive predictive value; NPV, negative predictive value; 95%CI, 95% confidence interval; κ, Cohen’s kappa where ≤ 0, 0.01–0.20, 0.21–0.40, 0.41–0.60, 0.61–0.80, > 0.81 are interpreted as poor agreement, slight, fair, moderate, substantial, and almost perfect agreement, respectively.