TABLE 1.

Analysis of unenriched and SWGA-enriched specimens by RT-PCR and sequencing

Specimen	RT-PCR			% N. meningitidis readsa		Fold enrichmentb	% of N. meningitidis genome with ≥10-fold coverage depth
	ΔCT, sodC	ΔCT, rnp	ΔΔCT	Unenriched	Enriched		Unenriched	Enriched
Ur-1	11.5	−1.1	12.6	0.4	66.1	165	1.8	35.5
Ur-2	17.9	0.9	17.0	0.1	90.5	905	0.03	97.6
Ur-3	15.5	−0.8	16.3	0.05	67.3	1,346	0.01	51.8
Ur-4	11.1	−5.2	16.3	0.03	57.2	1,907	<0.01	48.9
Ur-5	15.6	0	15.6	0.4	77.7	194	0.6	97.6
Ur-6	10.2	1.8	8.4	0.7	1.1	2	7.4	14.1
Ur-7	14.5	−1.4	15.9	0.4	61.9	155	0.6	93.3
Ur-8	16.1	−1.8	17.9	1.6	65.9	41	36.9	40.0
Ur-9	3.3	−3.3	6.6	0.02	3.7	185	<0.01	89.6
Ur-10	5.4	−3.4	8.8	0.04	6.2	155	<0.01	76.3
Ur-11	17.2	10.4	6.8	0.09	21.1	234	<0.01	90.0
Ur-12	7.6	−0.2	7.8	0.04	2.2	55	0.01	3.0
CSF-1	10.5	3.2	7.3	1	33.3	33	7.4	93.5
CSF-2	1.9	1.5	0.4	0.2	0.7	4	0.4	9.1
CSF-3	1.7	1.2	0.5	0.9	1	1	20.7	16.9
CSF-4	12.5	7	5.5	0.2	4.5	23	0.04	74.9
CSF-5	11.2	5.1	6.1	0.4	19.7	49	0.7	91.8
CSF-6	4.4	−0.4	4.8	0.3	6.8	23	0.1	90.8
CSF-7	9.0	3.8	5.2	2.7	61	23	77.7	97.9
CSF-8	1.8	2.4	−0.6	0.9	27.4	30	3.6	56.0
CSF-9	9.4	−0.2	9.6	0.5	65.7	131	1.1	96.0
CSF-10	5.9	2.8	3.1	2.4	22.6	9	50.0	85.8
CSF-11	7.7	1.9	5.8	0.05	15.6	312	<0.01	83.7
CSF-12	10.2	−5.6	15.8	0.3	86.5	288	0.3	97.8

^aN. meningitidis read pairs as a percentage of total read pairs obtained from the specimen.

^bCalculated as percent enriched N. meningitidis reads divided by percent unenriched N. meningitidis reads. Expanded data from RT-PCR and sequencing analysis are available in Table S3.