TABLE 4.
The accuracy of Streptococcus pneumoniae detection in paired nasopharyngeal and oropharyngeal samples from n = 319 adults tested using molecular methods applied to DNA extracted from minimally processed and culture-enriched samples and applying ROCdCq thresholds for a sample positivity in qPCRs.
| Method |
Positivity in | 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 alone | NP | 4.7 (15) (2.9–7.6) |
100 (79.6–100) |
92.8 (89.3–95.2) |
40.5 (26.3–56.5) |
100 (98.7–100) |
93.1 (89.8–95.4) |
0.55 (0.36–0.73) |
| OP | 0.9 (3) (0.3–0.7) |
100 (43.9–100) |
89.2 (85.3–92.2) |
8.1 (2.8–21.3) |
100 (98.7–100) |
89.3 (85.5–92.3) |
0.13 (−0.14–0.41) |
|
| Either NP or OP |
5.6 (18) (3.6–8.7) |
100 (82.4–100) |
93.7 (90.4–95.9) |
48.6 (33.4–64.1) |
100 (98.7–100) |
94.0 (90.9–96.2) |
0.63 (0.46–0.79) |
|
| qPCRs on minimally processed samples | NP | 4.7 (15) (2.9–7.6) |
73.3 (48.0–89.1) |
91.4 (87.8–94.1) |
29.7 (17.5–45.8) |
98.6 (96.4–99.4) |
90.6 (86.9–93.3) |
0.38 (0.17–0.59) |
| OP | 15.7 (50) (12.1–20.1) |
34.0 (22.4–47.8) |
92.6 (88.8–95.1) |
45.9 (31.0–61.6) |
88.3 (84.0–91.5) |
83.4 (78.9–87.1) |
0.30 (0.12–0.47) |
|
| Either NP or OP |
19.1 (61) (15.2–23.8) |
41.0 (29.5–53.5) |
95.3 (92.0–97.3) |
67.6 (51.5–80.4) |
87.2 (82.8–90.6) |
85.0 (80.6–88.5) |
0.43 (0.28–0.58) |
|
| qPCRs on culture-enriched samples | NP | 4.7 (15) (2.9–7.6) |
86.7 (62.1–96.3) |
92.1 (88.5–94.6) |
35.1 (21.8–51.2) |
99.3 (88.3–94.4) |
91.8 (88.3–94.4) |
0.46 (0.27–0.66) |
| OP | 12.2 (39) (9.1–16.3) |
61.5 (45.9–75.1) |
95.4 (92.2–97.3) |
64.9 (48.8–78.2) |
94.7 (91.4–96.8) |
91.2 (87.6–93.9) |
0.58 (0.43–0.73) |
|
| Either NP or OP |
16.3 (52) (12.7–20.8) |
67.5 (53.8–78.5) |
99.3 (97.3–99.8) |
94.6 (82.3–98.5) |
94.0 (90.6–96.2) |
94.0 (90.9–96.2) |
0.75 (0.65–0.86) |
Measures of diagnostic accuracy were calculated by comparing the number of detected samples positive per method with the overall number of n = 37 individuals identified as carriers of S. pneumoniae based on isolation of live pneumococcus either at the primary diagnostic or qPCR-guided culture and either from nasopharyngeal or oropharyngeal sample. NP, nasopharyngeal; OP, oropharyngeal; 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.