Table 4.
Detailed results of samples containing multiple bacterial isolates for pneumococcal identifications and/or serotype assignment
| 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 |
*Denominator – total number of reads mapped against serotype/group specific sequences.
NA = Not applicable.