Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database.
Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database.
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DOI：
10.1371/journal.pone.0061003
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Donati C
中科院分区：
文献类型：
--
作者：
Moschioni M;Lo Sapio M;Crisafulli G;Torricelli G;Guidotti S;Muzzi A;Barocchi MA;Donati C
肺炎链球菌的多位点序列分型（MLST）是基于7个管家基因片段的序列。通过eBURST分析MLST等位基因谱，可以将遗传相关的菌株分组为克隆复合体（CC），包括具有来自预测祖先的共同血统的那些基因型。然而，越来越多地使用MLST来表征S。肺炎菌株的鉴定已经导致鉴定出大量新的序列类型（ST），导致以前不同的谱系合并成更大的CC。这方面的一个例子是CC 156，其表现出高水平的复杂性，并且包括在所有七个MLST基因座、荚膜类型和菌毛胰岛-1（PI-1）的存在方面具有不同等位基因谱的菌株。对CC 156的详细分析表明，新ST（如ST 4945）的鉴定诱导了以前不同克隆复合物的合并。为了区分CC 156内的菌株多样性，最近开发的分型模式，96-MLST，用于分析代表41个不同ST的66株。通过层次聚类和最小生成树分析等位基因谱确定了10个遗传上不同的进化谱系。用不同的方法对串联序列进行系统发育分析，得到了相似的结果。鉴定的谱系在荚膜类型和PI-1存在方面是同质的。ST 4945菌株明确归属于其中一个谱系。总之，通过对来自不同实验室的肺炎球菌菌株进行详尽分析来识别新的ST，这突出表明，通过eBURST可以将潜在不相关的亚组分组为单个CC。分析额外的位点，如那些包括在96-MLST模式，将是必要的，以准确区分肺炎球菌种群的克隆进化。
Multi-Locus Sequence Typing (MLST) of Streptococcus pneumoniae is based on the sequence of seven housekeeping gene fragments. The analysis of MLST allelic profiles by eBURST allows the grouping of genetically related strains into Clonal Complexes (CCs) including those genotypes with a common descent from a predicted ancestor. However, the increasing use of MLST to characterize S. pneumoniae strains has led to the identification of a large number of new Sequence Types (STs) causing the merger of formerly distinct lineages into larger CCs. An example of this is the CC156, displaying a high level of complexity and including strains with allelic profiles differing in all seven of the MLST loci, capsular type and the presence of the Pilus Islet-1 (PI-1). Detailed analysis of the CC156 indicates that the identification of new STs, such as ST4945, induced the merging of formerly distinct clonal complexes. In order to discriminate the strain diversity within CC156, a recently developed typing schema, 96-MLST, was used to analyse 66 strains representative of 41 different STs. Analysis of allelic profiles by hierarchical clustering and a minimum spanning tree identified ten genetically distinct evolutionary lineages. Similar results were obtained by phylogenetic analysis on the concatenated sequences with different methods. The identified lineages are homogenous in capsular type and PI-1 presence. ST4945 strains were unequivocally assigned to one of the lineages. In conclusion, the identification of new STs through an exhaustive analysis of pneumococcal strains from various laboratories has highlighted that potentially unrelated subgroups can be grouped into a single CC by eBURST. The analysis of additional loci, such as those included in the 96-MLST schema, will be necessary to accurately discriminate the clonal evolution of the pneumococcal population.
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