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Table 4 Detailed results of samples containing multiple bacterial isolates for pneumococcal identifications and/or serotype assignment

From: Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

Sample ID Sample composition (ratio of serotypes) Total mapped reads per sample Total reads mapped against serotype sequences % reads mapped against serotype 19F* % reads mapped against serotype 3* % reads mapped against other serotype* Number of reads mapped against lytA sequences % reads mapped for S. pneumoniae(typical lytA) % reads mapped for other viridans streptococci (atypical lytA)
(a) Samples with two serotypes tested with PCR 1
49 1:1, 3:19F 16,318 16,318 77.8 22.1 0 NA NA NA
50 1:10, 19F:3 17,473 17,473 80.8 18.9 0.1 NA NA NA
51 1:10, 3:19F 19,239 19,239 85.0 14.8 0 NA NA NA
52 1:50, 19F:3 11,986 11,986 80.2 19.6 0 NA NA NA
53 1:50, 3:19F 4,853 4,853 82.3 17.5 0.1 NA NA NA
54 1:100, 19F:3 7,447 7,447 77.4 22.2 0.1 NA NA NA
55 1:100, 3:19F 4,251 4,251 85.5 13.7 0.2 NA NA NA
(b) Samples with two serotypes tested with PCR 2
56 1:1, 3:19F 9,700 6,631 76.2 22.8 1.0 3,069 99.7 0.3
57 1:10, 19F:3 17,282 12,952 79.8 19.9 0.2 4,330 99.7 0.3
58 1:10, 3:19F 10,644 7,690 84.1 15.8 0.2 2,954 99.7 0.3
59 1:50, 19F:3 11,623 8,666 79.2 20.7 0.2 2,957 99.6 0.4
60 1:50, 3:19F 6,378 4,392 85.2 14.6 0.3 1,986 99.4 0.6
61 1:100, 19F:3 8,673 6,385 79.9 19.8 0.3 2,288 99.4 0.6
62 1:100, 3:19F 5,740 4,023 85.8 13.9 0.4 1,717 99.0 1.0
(c) Samples with proportionately mixed Streptococcus pneumoniae and NCTC 11189 Streptococcus sp. viridans type. tested with PCR 2
63 1:1, NCTC 11189:19F 10,408 7,621 99.9 NA 0 2,787 46.6 53.4
64 1:10, 19F:NCTC 11189 3,459 2,112 99.9 NA 0.1 1,347 32.5 67.5
65 1:10, NCTC11189:19F 1,252 842 97.7 NA 1.8 410 86.1 13.9
66 1:50, 19F:NCTC 11189 18,079 10,467 100 NA 0 7,612 10.2 89.8
67 1:50, NCTC 11189:19F 16,336 10,172 99.8 NA 0 6,164 81.4 18.6
68 1:100,19F:NCTC 11189 18,259 8,612 100 NA 0 9,647 7.6 92.4
69 1:100, NCTC 11189:19F 8,694 3,559 100 NA 0 5,135 64.4 35.6
  1. *Denominator – total number of reads mapped against serotype/group specific sequences.
  2. NA = Not applicable.
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