Table 1. Serotype identification results.
|
A |
CDC sequential multiplex PCR (n = 130) | Sequetyping | WGS | ||
| NCBI online database (n = 124) | Curated cpsB database (n = 124) | Assembling strategy (n = 88) | PneumoCaT (n = 87)(1) | ||
| Serotype | 35% (45) | 49% (61) | 52% (65) | 60% (53) | 70% (61) |
| Serogroup | 32% (42) | 16% (20) | 16% (20) | 28% (25) | 0% (0) |
| Subset | 17% (22) | 11% (14) | 10% (12) | 7% (6) | 0% (0) |
| Misidentified | 1% (2) | 19% (23) | 17% (21) | 5% (4) | 30% (26) |
| N.D. | 15% (19) | 5% (6) | 5% (6) | 0% (0) | 0% (0) |
| B | CDC sequential multiplex PCR (n = 83) | Sequetyping | WGS | ||
| NCBI online database (n = 83) | Curated cpsB database (n = 83) | Assembling strategy (n = 53) | PneumoCaT (n = 52)(1) | ||
| Serotype | 27% (22) | 42% (35) | 46% (38) | 55% (29) | 59,5% (31) |
| Serogroup | 29% (24) | 14,5% (12) | 17% (14) | 24,5% (13) | 0% (0) |
| Subset | 20% (17) | 14,5% (12) | 14% (12) | 11% (6) | 0% (0) |
| Misidentified | 0% (0) | 17% (14) | 16% (13) | 5,5% (3) | 36,5% (19) |
| Inconsistent | 1% (1) | 6% (5) | 1% (1) | 4% (2) | 4% (2) |
| N.D. | 23% (19) | 6% (5) | 6% (5) | 0% | 0% (0) |
Results presented according to the 3 molecular methods tested and considering (A) isolates or (B) serotypes (number of isolates in brackets).
N.D. = not determinable (not detectable in CDC PCR protocol or cpsB not amplified).
(1) One sample analysis failed because of too low reads number