Table 4.
Performance of cross-sectional estimation of vaccine efficacy under imperfect detection of double colonisation. The simulated complete data were the same as used in Table 3. Consequently, all doubly-colonised states were recorded as singly-colonised, with 50% chance of either of the colonising strains being detected.
| Strain | True efficacy (VEi) | No. of colonised samples† (% of all samples) | Estimates of vaccine efficacy (SE log(OR); 90% cov. prob.)†† | ||
|---|---|---|---|---|---|
| Vaccinees | Controls | VEW|V̄0 | HRK | ||
| 1 | 0.7 | 75(7.5) | 196(19.6) | 0.70(0.15; 0.90) | 0.66(0.14; 0.78) |
| 2 | 0.4 | 61(6.1) | 82(8.2) | 0.42(0.18; 0.90) | 0.27(0.18; 0.72) |
| 3 | 0.7 | 21(2.1) | 55(5.5) | 0.71(0.27; 0.89) | 0.64(0.27; 0.84) |
| 4 | 0.4 | 20(2.0) | 28(2.8) | 0.40(0.30; 0.90) | 0.24(0.30; 0.83) |
| 5 | 0 | 163(16.3) | 133(13.3) | 0.07(0.14; 0.85)* | −0.28(0.13; 0.40) |
| 6 | 0 | 100(10.0) | 81(8.1) | 0.07(0.16; 0.86)* | −0.27(0.16; 0.59) |
| 7 | 0 | 31(3.1) | 25(2.5) | 0.05(0.28; 0.88)* | −0.27(0.28; 0.82) |
| 8 | 0 | 17(1.7) | 14(1.4) | 0.00(0.38; 0.91)* | −0.34(0.38; 0.86) |
| 9 | 0 | 10(1.0) | 8(0.8) | −.06(0.50; 0.91)* | −0.42(0.49; 0.88) |
|
| |||||
| Vaccine strains | 0.61 | 177(17.7) | 361(36.1) | 0.62(0.11; 0.88) | 0.62(0.11; 0.88) |
| Non-vaccine strains | 0 | 321(32.1) | 261(26.1) | 0.08(0.11; 0.80)* | −0.33(0.10; 0.11) |
| 0 | 502(50.2) | 378(37.8) | |||
*
For efficacy against non-vaccine strains, the reference state is 0 and estimator (5) was used.
†
The mean number of samples in the 1000 simulated data sets.
††
The average standard error for the log odds ratio, based on the 1000 simulated data sets. The coverage probability of a 90% confidence interval, based on the 1000 simulated data sets.