Colonisation endpoints in Streptococcus pneumoniae vaccine trials

Evaluating vaccine efficacy for protection against colonisation (VE_col) with bacterial pathogens is an area of growing interest. In this article, we consider estimation of VE_col for colonisation with Streptococcus pneumoniae (the pneumococcus). Colonisation is a common, recurrent and multi-type endpoint that requires both careful definition of the vaccine efficacy parameter and the corresponding method of estimation. We review recent developments in the area and provide practical guidelines for choosing the estimand and the estimation method in trials with a colonisation endpoint. We concentrate on methods that are based on a cross-sectional study design, in which only one nasopharyngeal sample is obtained per study subject.