Population genomics of post-vaccine changes in pneumococcal epidemiology

Nicholas Croucher and colleagues report whole-genome sequencing of 616 asymptomatically carried Streptococcus pneumoniae , a major cause of pneumonia, bacteremia and meningitis. They examine the impact of the introduction of the pneumococcal conjugate vaccine PCV7 on pneumococcal population dynamics. Whole-genome sequencing of 616 asymptomatically carried Streptococcus pneumoniae isolates was used to study the impact of the 7-valent pneumococcal conjugate vaccine. Comparison of closely related isolates showed the role of transformation in facilitating capsule switching to non-vaccine serotypes and the emergence of drug resistance. However, such recombination was found to occur at significantly different rates across the species, and the evolution of the population was primarily driven by changes in the frequency of distinct genotypes extant before the introduction of the vaccine. These alterations resulted in little overall effect on accessory genome composition at the population level, contrasting with the decrease in pneumococcal disease rates after the vaccine's introduction.