TABLE 3.
Detailed microbiological analysis of 11 OP samples using lytA qPCR, microarray, latex sweep agglutination, and multiplex PCR
| Sample ID | lytA qPCR result (CT)a | Microarray PathIDb | Microarray serotypingc | Latex sweep agglutination | mPCR cpsA resultd | mPCR serotypinge |
|---|---|---|---|---|---|---|
| FVEP-002-004 | Equivocal (39.52) | SP-3/5 | 9A-like* (34%) + 7F-like* (26%) + 36-like* (17%) + NT4b* (17%) + 27-like* (6%) | 4 + 9L + 36 + 15 | Positive | 7F/7A + 24F/24A/24B + 10F/10C/33C + 9N/9L |
| FVEP-002-418 | Equivocal (38.48) | SP-3/5 | NT4a* (53%) + 24A-like* (21%) + NT4b* (11%) + 43/39-like* (9%) + 16A-like* (3%) + 28A-like* (2%) + 4-like* (1%) | 24A | Negative | 33F/33A/37 + 35B + 24F/24A/24B + 4 + 10F/10C/33C + 35A/35C/42 + 9N/9L |
| FVEP-002-496 | Equivocal (37.93) | SP-3/5 | 10C/21-like* (41%) + NT4a* (20%) + 36-like* (12%) + 39-like* (8%) + 16A-like* (8%) + 48-like* (4%) + 24A-like* (4%) + 45-like* (2%) + 19B-like* (1%) | NSDf | Positive | 22F/22A + 24F/24A/24B + 10A + 10F/10C/33C + 20 + 13 |
| FVEP-002-460 | Equivocal (35.82) | SP-5/5 | NT4b* (35%) + 10C/21-like* (29%) + 48-like* (11%) + 41A (7%) + 20-like* (5%) + 23F (4%) + 35A-like* (4%) + 5-like* (3%) + 16A-like* (2%) | NSD | Positive | 6A/6B/6C/6D + 6C/6D + 22F/22A + 33F/33A/37 + 35B + 4 + 23F + 10A + 10F/10C/33C + 5 + 35A/35C/42 + 34 + 21 + 20 |
| FVEP-002-002 | Equivocal (37.79) | SP-3/5 | NT4b* (46%) + 33A-like* (40%) + 9V (5%) + 18F-like (4%) + 35A-like (4%) + 19B-like (1%) | 12 + 33 + 35B | Positive | 6A/6B/6C/6D + 19A + 33F/33A/37 + 38/25F/25A + 35B + 10A + 10F/10C/33C + 35A/35C/42 |
| FVEP-002-084 | Equivocal (37.57) | SP-3/5 | NT4b* (62%) + 36-like* (25%) + 5-like* (7%) + 19B-like* (5%) + 9N-like* (1%) | 19B | Positive | 4 + 5 + 9N/9L |
| FVEP-002-488 | Equivocal (39.82) | SP-3/5 | NT4b* (45%) + 48-like* (36%) + 19B-like* (11%) + 43/39-like* (8%) | NSD | Negative | 38/25F/25A + 4 + 23F + 39 + 10F/10C/33C + 34 + 21 + 20 + 6A/6B/6C/6D |
| FVEP-002-078 | Positive (28.44) | SP-3/5 | NT4b* (26%) + 10C/21-like* (26%) + 7F-like* (26%) + 16A-like* (11%) + 45-like* (6%) + 9L-like* (5%) | 35B | Positive | 15A/15F + 7F/7A + 24F/24A/24 + 4 + 10F/10C/33C + 9N/9L + 21 + 20 |
| FVEP-002-080 | Positive (34.41) | SP-5/5 | NT4b* (32%) + 48-like* (27%) + 24B (20%) + 19B-like* (13%) + 1 (8%) | 19B | Positive | 24F/24A/24B + 1 + 9N/9L + 13 |
| FVEP-002-422 | Positive (34.70) | SP-3/5 | NT4b* (42%) + 10C/21-like* (42%) + 19C-like* (12%) + 16A-like* (4%) | NSD | Positive | 15B/15C + 10F/10C/33C + 21 + 17F |
| FVEP-002-486 | Equivocal (35.29) | SP-3/5 | NT4b* (71%) + 10C/21-like* (17%) + 11B-like* (5%) + 16A-like* (5%) + 19C-like* (2%) | NSD | Positive | 15A/15F + 10F/10C/33C + 35A/35C/42 + 9N/9L + 31 + 20 |
CT, cycle threshold value for lytA qPCR (CT of < 35, positive; CT of 35 to 40, equivocal; no CT, negative).
SP-5/5 result for the PathID component on microarray indicates a sample positive for S. pneumoniae; SP-4/5 or less indicates that S. pneumoniae is not present.
Pseudoserotypes are marked by “*” indicating that the result is likely from a nonpneumococcal bacterial species and “-like” indicating a partial or divergent set of capsule genes.
cpsA in mPCR is used as a positive control for pneumococci.
Each sample also had additional mPCR products that did not correlate with an expected mPCR serotype product size that are not listed here.
NSD, no serotype detected.