Background: Routinely collected healthcare data such as administrative claims and electronic health records (EHR) can complement clinical trials and spontaneous reports when ensuring the safety of vaccines, but uncertainty remains about what epidemiological design to use. Methods: Using 3 claims and 1 EHR database, we evaluate several variants of the case-control, comparative cohort, historical comparator, and self-controlled designs against historical vaccinations with real negative control outcomes (outcomes with no evidence to suggest that they could be caused by the vaccines) and simulated positive controls. Results: Most methods show large type 1 error, often identifying false positive signals. The cohort method appears either positively or negatively biased, depending on the choice of comparator index date. Empirical calibration using effect-size estimates for negative control outcomes can restore type 1 error to close to nominal, often at the cost of increasing type 2 error. After calibration, the self-controlled case series (SCCS) design shows the shortest time to detection for small true effect sizes, while the historical comparator performs well for strong effects. Conclusions: When applying any method for vaccine safety surveillance we recommend considering the potential for systematic error, especially due to confounding, which for many designs appears to be substantial. Adjusting for age and sex alone is likely not sufficient to address the differences between vaccinated and unvaccinated, and for the cohort method the choice of index date plays an important role in the comparability of the groups Inclusion of negative control outcomes allows both quantification of the systematic error and, if so desired, subsequent empirical calibration to restore type 1 error to its nominal value. In order to detect weaker signals, one may have to accept a higher type 1 error.
Vaccine safety surveillance using routinely collected healthcare data - An empirical evaluation of epidemiological designs