Data from: Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and
important human pathogen. Vaccines against a subset of pneumococcal
antigenic diversity have reduced rates of disease, without changing the
frequency of asymptomatic carriage, through altering the bacterial
population structure. These changes can be studied in detail through using
genome sequencing to characterise systematically-sampled collections of
carried S. pneumoniae. This dataset consists of 616 annotated draft
genomes of isolates collected from children during routine visits to
primary care physicians in Massachusetts between 2001, shortly after the
seven valent polysaccharide conjugate vaccine was introduced, and 2007.
Also made available are a core genome alignment and phylogeny describing
the overall population structure, clusters of orthologous protein
sequences, software for inferring serotype from Illumina reads, and whole
genome alignments for the analysis of closely-related sets of pneumococci.
These data can be used to study both bacterial evolution and the
epidemiology of a pathogen population under selection from vaccine-induced
immunity.