Comparative genome analysis of Mycoplasma pneumoniae.
Comparative genome analysis of Mycoplasma pneumoniae.
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DOI：
10.1186/s12864-015-1801-0
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发表时间：
2015-08-16
期刊：
影响因子：
4.4
通讯作者：
Dybvig K
中科院分区：
文献类型：
--
作者：
Xiao L;Ptacek T;Osborne JD;Crabb DM;Simmons WL;Lefkowitz EJ;Waites KB;Atkinson TP;Dybvig K
肺炎支原体是一种常见病原体，可引起各年龄段人群的上呼吸道和下呼吸道感染，导致高达 40% 的社区获得性肺炎。它还引起多种肺外感染和自身免疫现象。该生物体的系统发育研究通常仅限于特定基因或基因组区域，因为仅完成了 4 个菌株的全基因组测序。为了更好地了解这种重要人类病原体的生理学和致病性，我们对 15 种肺炎支原体菌株进行了比较基因组分析，这些肺炎支原体菌株是在 2009 年至 2009 年间从来自美国、中国和英国的呼吸道标本和脑脊液中分离出来的。对15株菌株进行Illumina MiSeq全基因组测序，完成所有基因组测序。比较基因组分析的结果表明，虽然 1 型和 2 型菌株之间存在约 1500 个 SNP 和插入缺失变异，但菌株之间总体上存在高度的序列相似性（彼此相同 > 99%）。在这两种亚型中，观察到大多数基因的保守性，包括 CARDS 毒素基因和精氨酸脱亚胺酶基因。主要变异发生在与粘附素复合物相关的 P1 和 ORF6 基因中。在所有 15 个基因组中都发现了多个具有可变串联重复拷贝数的 hsdS 基因（编码 I 型限制性酶的 S 亚基）。这些数据表明，尽管从 16S rRNA 序列得出的结论表明进化速度很快，但肺炎支原体基因组随着时间和全球地理距离的变化而异常稳定，并且明显缺乏水平基因转移的证据。本文的在线版本 (doi:10.1186/s12864-015-1801-0) 包含补充材料，可供授权用户使用。
Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England. Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99 % identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes. These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer. The online version of this article (doi:10.1186/s12864-015-1801-0) contains supplementary material, which is available to authorized users.