Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
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DOI：
10.1099/mgen.0.000357
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发表时间：
2020-05-01
影响因子：
3.9
通讯作者：
Bentley, Stephen D.
中科院分区：
文献类型：
--
作者：
Gladstone, Rebecca A.;Lo, Stephanie W.;Bentley, Stephen D.
肺炎球菌谱系的知识，它们的地理分布和抗生素耐药性模式，可以提供对全球肺炎球菌疾病的见解。我们提供互动的生物信息学输出来探索这些主题，旨在增加基因组见解的传播到更广泛的社区，而不需要专家培训。我们准备了12个国家特定的系统发育快照，以及73个常见的全球肺炎球菌序列集群（GPSCs）的国际系统发育快照，之前使用PopPUNK定义，并在Microreact中展示。使用Roary定义的基因存在和缺失，以及来自Gubbins的重组谱在Phandango中呈现每个GPSC。使用BactDating评估每个GPSC的时间系统发育信号。我们提供了如何使用这些资源的示例。在我们使用国家特定系统发育快照的例子中，我们确定在南非的9个不相关的遗传背景中观察到血清型14。GPSC9的国际系统发育快照（其中大多数来自南非的14血清型分离株）突出显示有三个独立的亚群，以南非14血清型分离株为代表。我们从gpsc9年代树中估计，每个子集群都是在20世纪80年代在南非建立的。我们展示了重组图如何允许在GPSC97中识别横跨荚膜多糖位点的20 kb重组。这与据估计发生在20世纪90年代的从血清型6A到血清型19A的转变是一致的。抗性基因（tet, erm, cat）在GPSC23系统发育中的存在/缺失图与获得复合转座子一致。我们从gpsc23年代树中估计，采收发生在1953年至1975年之间。最后，我们通过Pathogenwatch证明了GPSC31对来自犹他州的17个外部产生的1型肺炎球菌组装体的分配。大多数犹他州分离株聚集在GPSC31内，属于美国特有的分支，其最近的共同祖先估计在1958年至1981年之间。我们提供的资源可以用来探索数据，检验假设，并产生新的假设。GPSCs的可访问分配允许其他人将他们自己的集合置于本文提供的数据之外。
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here.