TABLE 3.

Discrepancies between conventional culture and NGS methods for pneumococcal identification and serotype prediction

Sample no.	Serotype identified			Repeat culture with 50 μl of NPA sample and identification of up to 200 colonies		Sweep culture DNA for serotype prediction based on CDC PCRs		Direct sample DNA for serotype prediction based on CDC PCRs
	Culture	Sweep culture DNA for NGS	Direct sample DNA for NGS	Pneumococcal identification	Serotype identified	Pneumococcal identification	Serotype identified	Pneumococcal identification	Serotype identified
Additional samples identified as having S. pneumoniae
44	Oral flora	3	3	+	3	+	3	+	3
71	No growth	No growth	Sga 6	−	NAb	−	NA	+	Sg 6
100	Oral flora	19B/19C	19B/19C	−	NA	+	19B/C	+	19B/19C
104	No growth	No growth	23A	−	NA	−	NA	+	23A
143	Oral flora	15B/15C	15B/15C	+	15B/15C	+	15B/15C	+	15B/15C
Samples identified as having second serotype
27	6A	Sg 6 plus 34	Sg 6	+	6A	+	6A	+	6A
117	3	3	3 plus 15A/15F	+	3	+	3	+	3 plus 15A/15F
132	14	14	14 plus 15A/15F	+	14	+	14	+	14 plus 15A/15F
Samples with other discrepancies
95	10A	10A/10B (400 reads) plus 19A (290 reads)	23A (364 reads) plus 19A (248 reads)	+	10A, 19A, 23A	+	10A, 19A	+	10A, 23A
73	Oral flora	1,412 (90%) reads against pneumococcal lytA with <500 reads for serotype sequences	Oral flora	−	NA	−	NA	−	NA
116	Oral flora	No pneumococci	<10% of reads for pneumococcal lytA but >500 reads for serotype 11B	−	NA	−	NA	+	11B
1	Oral flora	<10% of reads for pneumococcal lytA but >500 reads for serotypes, with 39, 9N/9L, and 19B/19C	<10% of reads for pneumococcal lytA but >500 reads for serotypes, with 39, 9N/9L, and 19B/19C	+	9N/9L	+	9N/9L, 39	+	9N/9L, 39

^aSg, serogroup.

^bNA, not applicable.