TABLE 2.

Optimal qPCR cycle threshold C_q and corresponding parameters for Streptococcus pneumoniae carriage detection in nasopharyngeal (n = 1,549) and oropharyngeal (n = 319) samples.

Parameter	Sample	Reference	Optimal threshold piaB (95% CI)	Youden index piaB	Sensitivity piaB	Specificity piaB	Optimal threshold lytA (95% CI)	Youden index lytA	Sensitivity lytA	Specificity lytA
Minimally processed	NP	Primary cultures	37.13 (36.49–37.76)	0.85	0.95	0.90	37.47 (36.44–38.39)	0.82	0.94	0.87
	NP	Primary culture and reculture	37.21 (36.51–38.46)	0.85	0.95	0.90	37.29 (36.52–38.61)	0.83	0.94	0.89
	OP	Primary culture and reculture	38.73 (37.29–39.39)	0.69	0.91	0.78	37.47 (36.52–37.66)	0.69	0.87	0.82
Culture-enriched	NP	Primary cultures	28.71 (26.59–29.69)	0.94	0.98	0.97	29.19 (27.41–30.25)	0.93	0.98	0.95
	NP	Primary culture and reculture	30.26 (29.91–30.47)	0.96	0.98	0.98	29.99 (28.91–30.47)	0.94	0.98	0.96
	OP	Primary culture and reculture	29.78 (28.84–29.93)	0.91	0.96	0.95	30.73 (29.42–30.81)	0.85	0.91	0.94

Results from qPCR were validated in a receiver operating characteristic curve analysis with culture as reference. With S. pneumoniae isolated from only three samples there was insufficient statistical power to perform the receiver operating characteristic curve analysis on oropharyngeal samples with primary cultures as a reference.