Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae
Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae
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DOI：
10.1038/sdata.2015.58
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发表时间：
2015-01-01
期刊：
影响因子：
9.8
通讯作者：
Hanage, William P.
中科院分区：
文献类型：
--
作者：
Croucher, Nicholas J.;Finkelstein, Jonathan A.;Hanage, William P.
肺炎链球菌是鼻咽部常见的共生菌，也是人类重要的致病菌。针对肺炎球菌抗原多样性子集的疫苗通过改变细菌种群结构，在不改变无症状携带频率的情况下降低了发病率。这些变化可以通过使用基因组测序来描述系统采样的携带肺炎链球菌的集合来详细研究。这一数据集包括从2001年到2007年期间从马萨诸塞州初级保健医生常规就诊期间收集的616个带注释的分离株基因组草案，这些儿童是在引入七价多糖结合疫苗后不久收集的。还提供了描述整个种群结构的核心基因组比对和系统发育图，直系蛋白质序列的簇，从Illumina Reads推断血清型的软件，以及用于分析密切相关的肺炎球菌组的全基因组比对。这些数据既可用于研究细菌进化，也可用于研究疫苗诱导免疫中选择的病原体群体的流行病学。
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.