SeroBA
These results should not be used for clinical purposes or to inform vaccine programmes. Since the result is based on inference from the DNA sequence rather than a Quellung reaction (gold standard for serotyping) the result may in some cases not match the phenotypic result. However the methodology used by Pathogenwatch based on SeroBA has been shown to have a sensitivity and specificity of 0.98 and 1, respectively (Epping et al 2018).
SeroBA predicts a phenotype starting directly from short read data. Pathogenwatch uses assemblies as the starting genomic data, from which reads are simulated for the purposes of SeroBA. Because of this small difference in methodology 0.14% (28/20049) mismatches are observed between results direct from reads and those from assemblies. These are reported below and a result that may be subject to these differences is flagged with a 'Guidance' link.
Pathogenwatch Serotype | SeroBA Serotype | No. Mismatches (%) [a] | BLAST cps loci Nucleotide Similarity | BLAST cps loci Nucleotide Coverage | Distinguishing Genetic Features [b] |
untypable [c] | 19A | 9 (0.6) | - | - | - |
32F | 32A | 3 (100) [d] | 99 | 99 | 5 bp gap at the intergenic region between wcrN and the HG272/3 pseudogene |
32F | untypable | 2 (NA) | - | - | - |
33A/33F | 33F | 2 (1.1) | 99.9 | 92.0 | Frameshift mutation insT 433 in 33F wcjE gene |
possible 6A | 6A | 2 (0.2) | - | - | - |
11E | 11A | 1 (0.2) | - [e] | - | Disruption in wcjE |
19F | untypable | 1 (NA) | - | - | - |
32A | 32F | 1 (14) | 99 | 99 | 5 bp gap at the intergenic region between wcrN and the HG272/3 pseudogene |
32A | untypable | 1 (NA) | - | - | - |
35A | 35C | 1 (6.7) | 98.9 | 90 | Frameshift mutation insA 248 in wcrK encodes for a GT—consistent with differences in 35A wcrK |
6A | possible 6E | 1 (NA) | - | - | - |
possible 6C | 6B | 1 (0.09) | 99 | 92 | wciNα in 6B / wciNβ in 6C |
possible 6D | 6C | 1 (0.25) | 98.6 | 84 | A > G 583 in wciP |
possible 6E | 6B | 1 (0.09) | - | - | - |
untypable | 23F | 1 (0.08) | - | - | - |
[a] Percentage is calculated by the number of isolates that mismatched between Pathogenwatch and SeroBA over the total number of isolates for each serotype indicated on the same row typed by SeroBA.
[c] See https://github.com/sanger-pathogens/seroba#troubleshooting. The samples tested here were QC-passed, therefore the untypable results are likely due to low coverage of the cps region.
[d] Only serological analyses can reliably differentiate serotype 32A and 32F. In silico serotype within serogroup 32 is subject to improvement due to the small number of isolates for analysis (Kapatai et al 2016).
[e] Complete sequence of cps loci for 6E and 11E are not available for comparison.
NA = not available
Last modified 3yr ago