Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae
Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae
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DOI：
10.1128/mbio.01286-19
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发表时间：
2019-05-01
期刊：
影响因子：
6.4
通讯作者：
Henriques-Normark, Birgitta
中科院分区：
文献类型：
--
作者：
Garriss, Genevieve;Nannapaneni, Priyanka;Henriques-Normark, Birgitta
假性肺炎链球菌是人类主要病原体肺炎链球菌的近亲。它越来越多地与下呼吸道感染（LRTI）和高流行的抗微生物药物耐药性（AMR）相关。假性肺炎链球菌由于与肺炎链球菌和其他mitis组（SMG）成员的相似性，很难用传统的分型方法识别。利用LRTI分离株的全基因组测序和比较基因组方法，我们发现假肺炎链球菌核心基因组中存在大量肺炎球菌毒力和定植基因。我们还揭示了该物种基因组编码的大量新的表面暴露蛋白。此外，我们提出了一种新的、完全特异的分子标记物，可用于鉴定假肺炎链球菌。假性肺炎链球菌的系统发育分析表明，特定进化支与核心蛋白的等位基因变异有关。对四环素和大环内酯这两种最常见的耐药类型的耐药性被发现是由tn916样整合共轭元件和Mega-2编码的。总的来说，我们发现AMR的基因型决定因素和表型AMR与假肺炎链球菌的特定谱系密切相关。综上所述，我们的研究结果揭示了在侵袭性疾病和定植过程中已知重要基因在假肺炎链球菌中的分布，并提供了对可能有助于毒力，定植和适应的特征的见解。假性肺炎链球菌是一种被忽视的病原体，作为下呼吸道感染的病原体出现，并与慢性阻塞性肺疾病（COPD）和COPD恶化有关。然而，其临床重要性和流行病学仍然未知，主要是由于缺乏特异性标记物将其与肺炎链球菌区分开来。在这里，我们提供了一个完全特异的假肺炎链球菌的新分子标记，并提供了在该物种中发现的毒力和定植基因的全面视图。最后，我们的研究结果为进一步了解假性肺炎链球菌的发病机制和流行病学奠定了基础。
Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.IMPORTANCE S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae.