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.

肺炎链球菌（Streptococcus pneumoniae）是一种常见的鼻咽部共生细菌，亦是重要的人类致病菌。针对部分肺炎链球菌抗原多样性的疫苗可降低疾病发生率，且未改变无症状携带的频率，而是通过重塑细菌种群结构达成此效果。可借助全基因组测序对系统采集的携带型肺炎链球菌菌株集合进行表征，以此详细探究上述种群变化。本数据集包含616株已注释的肺炎链球菌草图基因组，这些菌株采集自2001年至2007年马萨诸塞州儿童的全科门诊常规就诊过程中，彼时距七价多糖结合疫苗引入仅短短数年。随数据集同步公开的还包括：用于描述整体种群结构的核心基因组比对文件与系统发育树、直系同源蛋白质序列簇、可从Illumina测序读段中推断血清型的分析软件，以及用于分析密切相关肺炎链球菌菌株集合的全基因组比对文件。上述数据可用于研究疫苗诱导免疫选择压力下的细菌进化过程与致病菌种群流行病学特征。