Demography and vaccine type composition of pneumococcal sequence clusters.

For each sequence cluster (SC) or sub-cluster, the number of isolates, proportion of PCV7 and PCV13 vaccine types, and recombination rate (r/m) are listed. The best fit demographic and molecular clock model as determined through comparison of marginal likelihood estimates using BEAST are specified. The Ne directionality (constant, exponentially increasing or decreasing) were determined by assessing the slope of the Ne during the study period (1998–2012) and 95% Highest Posterior Density (HPD).