Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.
Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.
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DOI：
10.1093/gbe/evu263
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发表时间：
2014-12-04
影响因子：
3.3
通讯作者：
Bentley SD
中科院分区：
文献类型：
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作者：
Hilty M;Wüthrich D;Salter SJ;Engel H;Campbell S;Sá-Leão R;de Lencastre H;Hermans P;Sadowy E;Turner P;Chewapreecha C;Diggle M;Pluschke G;McGee L;Eser ÖK;Low DE;Smith-Vaughan H;Endimiani A;Küffer M;Dupasquier M;Beaudoing E;Weber J;Bruggmann R;Hanage WP;Parkhill J;Hathaway LJ;Mühlemann K;Bentley SD
肺炎链球菌周围的荚膜已被确定为主要的毒力因子，并被肺炎球菌结合疫苗（PCV）靶向。然而，未封装的S.肺炎克雷伯氏菌（非Ec-Sp）也在全球范围内分离，主要是在携带研究中。目前尚不清楚非Ec-Sp是否零星进化，是否具有高抗生素非亲和率和独特的特定基因含量。在这里，对来自世界各地17个不同地点的131个非Ec-Sp分离株进行了全基因组测序。结果显示，一个深分支的经典血统，是从多个零星的血统不同。零星的谱系与先前测序的，全球收集的封装S。肺炎克雷伯氏菌（Ec-Sp）分离株，而经典谱系主要由频繁鉴定的多位点序列类型（ST）ST 344（n = 39）和ST 448（n = 40）组成。所有ST 344和9株ST 448分离株对β-内酰胺类和其他抗菌药物的非药敏率均较高。辅助基因组的分析表明，经典的非Ec-Sp包含的移动的元素的数量增加，比Ec-Sp和散发性的非Ec-Sp。执行粘附测定选择经典和散发性的非Ec-Sp的人上皮细胞显示，一个整合的接合元件（ICE）的存在下，结果增加粘附到人上皮细胞（P = 0.005）。相比之下，缺乏ICE的散发性非Ec-Sp在体外具有更大的生长，可能导致适应性改善。总之，来自经典谱系的非Ec-Sp分离株分别进化。它们已经在全球范围内传播，很好地适应了鼻咽携带，并且能够与Ec-Sp共存。由于PCV的持续使用，非Ec-Sp可能变得更加流行。
The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.