Table 1.

Clinical microbiology results and sequencing information for patients who were positive for S. pneumonia by mNGS

	Clinical microbiology tests			mNGS				qPCR
Patient	Pathogen	Culture (blood/CSF)	Antigen test	Pathogen	Reads	Coverage%	Depth
P1	SP	–	+	SP	262	1.1	1	ND
P2	SP	+	+	SP	1105	11	1.1	ND
P3	SP	+	+	SP	573	2.6	1	+
P4	SP	+	+	SP	429	1.9	1	+
P5	SP	–	+	SP	425	1.9	1	+
P6	SP	–	+	SP	176	1.8	1	ND
P7	SP	+	ND	SP	162	0.75	1	+
P8	SP	+	+	SP	38	0.16	1	ND
P9	SP	–	+	SP	21	0.12	1	ND
P10	SP	+	+	SP	13	0.066	1	ND
P11	SP	+	+	SP	11	0.052	1	ND
P12	SP	+	+	SP	7	0.048	1	–
P13	SP	+	+	SP	6	0.034	1	–
P14	SP	+	+	SP	4	0.041	1	ND
P15	SP	–	+	SP	4	0.016	1	–
P16	SP	–	+	SP	3189	28	1.3	ND
P17	SP	–	+	SP	23,247	75	3.9	ND
P18	SP	+	+	SP	25	0.19	1	+
P19	SP	+	+	SP	2603	7.25	1.06	ND
P20	SP	+	+	SP	341,303	86.68	36.57	+
P21	SP	+	+	SP	165	0.7413	1.01	+
P22	SP	+	+	SP	1335	12.03	1.09	+
P23	SP	+	+	SP	456	5.41	1.04	+
P24	SP	+	+	SP	32	0.0744	1	ND
P25	SP	+	+	SP	218	1.04	1	ND
P26	SP	+	+	SP	20	0.1488	1	–
P27	–	–	–	SP	33	0.31	1	ND
P28	SA	SA	ND	SP	27	0.15	1	–
P29	–	–	–	SP	24	0.12	1	ND
P30	–	–	ND	SP	12	0.95	1	ND
P31	–	–	–	SP	6	0.055	1	ND
P32	–	–	–	SP	4	0.011	1	–

Note: mNGS metagenomic next-generation sequencing, CSF Cerebrospinal fluid, qPCR quantitative real-time PCR, SP Streptococcus pneumonia, SA Streptococcus aureus, E. coli Escherichia coli, + positive, − negative, ND Not done