Table 2.

The accuracy of Streptococcus pneumoniae detection in paired saliva samples and nasopharyngeal swabs from n = 394 children.

Method	Sensitivity % (95% CI)	Specificity % (95% CI)	PPV % (95% CI)	NPV % (95% CI)	Accuracy % (95% CI)
Isolation of viable S. pneumoniae from culture of NPS	96.9 (91.23–99.36)	100.00 (98.77–100.00)	100.00	99.00 (97.01–99.67)	99.24 (97.79–99.84)
Isolation of viable S. pneumoniae from culture of saliva	6.19 (2.30–12.98)	100.00 (98.77–100.00)	100.00	76.55 (75.62–77.45)	76.90 (72.42–80.90)
qPCR on culture-enriched NPS	95.88 (89.66–98.87)	90.57 (86.66–93.64)	76.86 (69.96–82.57)	98.53 (96.26–99.43)	91.88 (88.73–94.38)
qPCR on culture-enriched saliva	53.61 (43.19–63.80)	86.20 (81.74–89.91)	55.91 (47.46–64.03)	85.05 (82.05–87.62)	78.17 (73.76–82.15)

Samples were tested using culture method and molecular methods applied to DNA extracted from culture-enriched (CE) samples and applying thresholds of < 40 C_T in piaB- and lytA-specific qPCRs for a sample positivity. Measures of diagnostic accuracy were calculated by comparing the number of samples positive by a method with the overall number of n = 97 children identified as carriers of S. pneumoniae based on isolation of viable pneumococcus either from saliva or nasopharyngeal sample.

NPS nasopharyngeal swab, PPV positive predictive value, NPV negative predictive value, 95% CI 95% confidence interval.