In individual-randomised phase IV settings in which the aim is to estimate direct protective efficacy, however, interference from indirect effects may be problematic. In this case, the use of prevalence-based estimates of vaccine efficacy has been proposed based on a mathematical model for two competing types [22]. Because it is not possible to observe directly

the acquisition events, estimation of VEcol needs to be based on identification of prevalent cases (colonisation, 5-Fluoracil purchase i.e. the presence of current carrier state) instead of incident cases (acquisition events). Moreover, for practical reasons there is preference to collect only a single measurement per study subject. Therefore, the methods reviewed in this section focus on the statistical methodology for estimating serotype-specific and aggregate efficacy in a cross-sectional study, in which the study subjects are sampled only once to generate point prevalence and serotype distribution. The primary parameter then is VET. The discussion is largely based on a previous article, which provides an extensive justification of the estimation MEK inhibitor clinical trial method [11]. The estimation of VET from cross-sectional data necessitates the use of a quantitative relationship between the prevalence and incidence of colonisation. Such relationship holds if colonisation

is considered in its stationary phase, i.e. when the prevalence and serotype distribution of colonisation in the study population are stable over time [11]. The question of how quickly after vaccination this occurs

is discussed in the accompanying article in this volume [14]. A robust way to assess VET is to calculate 1 – OR where OR is the ratio of the odds of being vaccinated among those colonised with the (select) vaccine serotypes to the odds of those being colonised with the non-vaccine serotypes, including those not colonised by pneumococci at all [11]. The exact composition Thymidine kinase of these target and reference states of colonisation depends on the serotype(s) against which efficacy is considered. We define the target set of colonisation states as those in which the individual carries any of the target serotypes, either alone or simultaneously with any of the non-vaccine types. The target set is different for each individual vaccine type and is largest for all vaccine serotypes for the estimation of aggregate efficacy. We define the reference set of colonisation states as those in which the individual does not carry pneumococcus at all or carries non-vaccine serotypes. The strictest choice for a reference set is the ‘uncolonised’ state; however, choosing this reference leads to less efficient estimation of vaccine efficacy and larger sample sizes are thus required to compensate this.