Fig. 2: Characteristics and dynamics of the extended pneumococcal strains.

a Frequency of serotypes; each episode was counted once and serotypes with frequency >0.2% are shown. b An example of a colonisation profile for infant ID: 65 showing different colonisation episodes. The sampling point marked with the cross (×) represents culture-negative pneumococcal samples (uncolonised). Different types of episodes are shown in (b) namely transient colonisation whereby an episode consisted of a serotype was detected at a single time point, extended colonisation which refers to an episode where the serotype was detected at multiple time points and multiple colonisation where there was co-occurrence of overlapping episodes of different serotypes at certain time points. c Schematic representation of the three-state multistate model showing colonised and uncolonised carriage states and the estimated transition intensities (rates) between the states. d, e Observed and expected prevalence of each colonisation state. f The inferred sojourn time (duration) in each colonisation state. The error bars represent the 95% confidence interval for the estimated mean values.