Table 2.
partial and total genomic data, RTM analysis and bacteria genotyping.
| Samples | Run time | Identied pathogen | Specific reads at 20 min | Total reads at 2 h | Specific reads at 2 h | Specific reads (%) | Number of nucleotide | Genome coverage | Genotyping |
|---|---|---|---|---|---|---|---|---|---|
| Sample 1 | 2H | Streptococcus pneumoniae | 5897 | 174,156 | 33,465 | 19.22 | 1,940,109 | 95.17 | Serotype 16F |
| Sample 2 | 2H | Streptococcus pneumoniae | 7457 | 125,520 | 35,055 | 27.93 | 1,959,603 | 87.48 | Serotype 6B |
| Sample 3 | 2H | Neisseria meningitidis | 45 | 116 ,752 | 905 | 0.78 | 762,285 | 34.01 | Serotype B |
| Sample 4 | 2H | Streptococcus pneumoniae | 0 | 9137 | 6 | 0.065667068 | 4183 | 0.02 | Not realized |
| Sample 5 | 2H | Listeria monocytogenes | 0 | 480,000 | 21 | 0.00004375 | 14,597 | 0.5 | Not realized |
| Sample 6 | 2H | Streptococcus pneumoniae | 7 | 151,187 | 135 | 0.089293392 | 73,893 | 3.36 | Serotype 11A |
| Sample 7 | 2H | Haemophilus influenzae | 3471 | 180,169 | 26,014 | 14.43866592 | 1,751,169 | 88.37 | Serotype b |
| Sample 8 | 2H | Neisseria meningitidis | 0 | 3830 | 3 | 0.078328982 | 2687 | 0.1 | Not realized |
| Sample 9 | 2H | Streptococcus pneumoniae | 0 | 34,860 | 12 | 0.034423408 | 4578 | 0.22 | Not realized |
| Sample 10 | 2H | Streptococcus pneumoniae | 5 | 11,260 | 132 | 1.172291297 | 65,775 | 3 | Serotype A5 |
| Sample 11 | 2H | Streptococcus pneumoniae | 3451 | 30,015 | 17,074 | 56.88489089 | 1,994,683 | 93.65 | Serotype 3A |
| Sample 12 | 2H | Streptococcus pneumoniae | 245 | 131,943 | 1652 | 1.252055812 | 1,346,254 | 63.2 | Serotype 3A |
| Sample 13 | 2H | Streptococcus agalactiae | 123 | 206,130 | 1017 | 0.493377965 | 390,297 | 19.38 | Serotype V |
| Sample 14 | 2H | Neisseria meningitidis | 4513 | 60,134 | 18,965 | 31.53789869 | 2,023,530 | 93.96 | Serotype C |
| Sample 15 | 2H | Neisseria meningitidis | 411 | 57,227 | 3713 | 6.488196131 | 1,644,843 | 73.43 | Serotype A |
| Sample 16 | 2H | Streptococcus agalactiae | 341 | 125,815 | 2058 | 1.635735008 | 1,504,297 | 71.3 | Serotype V |
| Sample 17 | 2H | Streptococcus pneumoniae | 239 | 6501 | 1175 | 18.07414244 | 517,575 | 24.3 | Serotype 11A |
| Sample 18 | 2H | Haemophilus influenzae | 314 | 9283 | 1406 | 15.14596574 | 1,318,171 | 66.52 | Serotype b |
| Sample 19 | 2H | Negative | 0 | 39,810 | 0 | 0 | 0 | 0 | Not realised |
| Sample 20 | 2H | Negative | 0 | 8110 | 0 | 0 | 0 | 0 | Not realised |
| Sample 21 | 2H | Herpes Simplex Virus 1 | 0 | 4760 | 5 | 0.105042017 | 501 | 0.3 | Not realized |
| Sample 22 | 2H | Herpes Simplex Virus 1 | 0 | 14,110 | 2 | 0.014174344 | 271 | 0.2 | Not realized |
| Sample 23 | 2H | Herpes Simplex Virus 1 | 0 | 7082 | 9 | 0.127082745 | 1519 | 1 | Unkown |
| Sample 24 | 2H | Varicella Zoster Virus | 41 | 251,411 | 608 | 0.241835083 | 86,736 | 69.38 | Unkown |
| Sample 25 | 2H | Haemophilus influenzae | 967 | 775,438 | 4352 | 0.005612312 | 1,555,463 | 83.8 | Serotype f |
| Sample 26 | 2H | Streptococcus pneumoniae | 2 | 74,278 | 31 | 0.000417351 | 18,086 | 0.8 | Not realized |
| Sample 27 | 2H | Haemophilus influenzae | 8 | 14,994 | 63 | 0.004201681 | 2,8751 | 1.45 | Serotype f |
| Sample 28 | 2H | Listeria monocytogenese | 0 | 511,274 | 6 | 1.17354E−05 | 9104 | 0.3 | Not realized |
| Sample 29 | 2H | Streptococcus pneumoniae | 29 | 305,696 | 2566 | 0.00839396 | 1,138,209 | 51.8 | Serotype 6B |
| Sample 30 | 2H | Streptococcus pneumoniae | 46 | 52,353 | 136 | 0.00259775 | 44,612 | 3 | Serotype 3A |
| Sample 31 | 2H | Negative | 0 | 52,000 | 0 | 0 | 0 | 0 | Not realised |
| Sample 32 | 2H | Neisseria meningitidis | 63 | 64,276 | 1107 | 0.017222603 | 1,918,857 | 85.6 | Serotype B |
| Sample 33 | 2H | Neisseria meningitidis | 51 | 92,000 | 591 | 0.006423913 | 796,395 | 37.12 | Serotype C |
| Sample 34 | 2H | Neisseria meningitidis | 4 | 228,118 | 238 | 0.00104332 | 359,034 | 16.73 | Serotype B |
| Sample 35 | 2H | Haemophilus influenzae | 192 | 84,000 | 2751 | 0.03275 | 1,869,540 | 99.06 | Non Typable |
| Sample 36 | 2H | Haemophilus influenzae | 23 | 287,552 | 561 | 0.001950951 | 378,275 | 20.66 | Serotype b |
| Sample 37 | 2H | Haemophilus influenzae | 0 | 69,418 | 5 | 7.20274E−05 | 1282 | 0.06 | Non Typable |
| Sample 38 | 2H | Staphylococcus aureus | 24 | 288,211 | 477 | 0.001655037 | 2,19,011 | 7.81 | Not realised |
| Sample 39 | 2H | Negative | 0 | 60,069 | 0 | 0 | 0 | 0 | Not realised |
| Sample 40 | 2H | Streptococcus pneumoniae | 97 | 88,376 | 1125 | 0.0127297 | 6,20,988 | 29.15 | Serotype 3A |
| Sample 41 | 2H | Neisseria meningitidis | 356 | 91,198 | 8726 | 0.095681923 | 2,054,566 | 91.29 | Serotype B |
| Sample 42 | 2H | Streptococcus agalactiae | 0 | 7409 | 5 | 0.000674855 | 573 | 0 | Serotype V |
| Sample 43 | 2H | Streptococcus pneumoniae | 0 | 74,260 | 8 | 0.00010773 | 27,083 | 1.3 | Serotype 12F |
| Sample 44 | 2H | Neisseria meningitidis | 0 | 7160 | 1638 | 0.22877095 | 1,161,716 | 51.16 | Serotype B |
| Sample 45 | 2H | Negative | Negative | 82,070 | 0 | 0 | 0 | 0 | Not realised |
| Sample 46 | 2H | Streptococcus pneumoniae | 562 | 199,270 | 6047 | 0.030345762 | 2,064,033 | 96.9 | Serotype 11A |
| Sample 47 | 2H | Streptococcus pneumoniae | 12 | 4238 | 456 | 0.107597924 | 1,011,157 | 47.5 | Serotype 3A |
| Sample 48 | 2H | Streptococcus pneumoniae | 4358 | 163,052 | 82,665 | 0.506985502 | 2,081,073 | 97.7 | Serotype 11A |
| Sample 49 | 2H | Escherichia coli | 0 | 2950 | 2 | 0.000677966 | / | / | Not realised |
| Sample 50 | 2H | Streptococcus pneumoniae | 2 | 12,370 | 14 | 0.00113177 | 4009 | 0.2 | Not realized |
| Sample 51 | 2H | Streptococcus pneumoniae | 0 | 3221 | 2,094 | 0.650108662 | 783,321 | 36.8 | Serotype 11A |
| Sample 52 | 2H | Streptococcus pneumoniae | 435 | 82,070 | 7632 | 0.092993786 | 2,028,482 | 95.23 | Serotype 3A |