Table 2. Determination of sensitivity and specificity of RT-PCR assay for N. meningitidis (ctrA), S. pneumoniae (lytA), and H. influenzae (bexA) in cerebrospinal fluid and serum specimens (see text for details).

Pathogen	No.*	Sensitivity	95% CIs	Specificity-Method 1**	No.*	95% CIs	Specificity-Method 2, unadjusted***	No.	95% CIs	Specificity-Method 2, adjusted****	No.*	95% CIs
CEREBROSPINAL FLUID
N. meningitidis	90	100%	96.0–100	100%	51	93.0–100	75.7%	342	70.8–80.2	98.9%	262	96.7–99.8
S. pneumoniae	46	97.8%	88.5–99.9	100%	94	96.2–100	93.5%	386	90.6–95.8	100%	361	99.0–100
H. influenzae	3	66.7%	9.4–99.2	100%	139	97.4–100	99.8%	433	98.7–100	100%	432	99.2–100
SERUM
N. meningitidis	21	57.1%	34.0–78.2	100%	12	73.5–100	83.1%	223	77.4–87.9	94.1%	188	89.8–97.0
S. pneumoniae	10	80.0%	44.4–97.5	100%	25	86.3–100	96.2%	235	92.9–98.2	100%	226	98.4–100
H. influenzae	2	0%	0–84.2	100%	33	89.4–100	100%	243	98.5–100	100%	243	98.5–100

*Number of specimens contributing to the calculation of sensitivity or specificity

**Specificity determined using specimens positive for other organisms

***Specificity determined using specimens positive for other organisms or culture negative

****Specificity determined using specimens positive for other organisms or culture negative but positive for second gene target