Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
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DOI：
10.1186/1471-2164-10-239
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发表时间：
2009-05-21
期刊：
影响因子：
4.4
通讯作者：
Clarke, Ian N.
中科院分区：
文献类型：
--
作者：
Seth-Smith, Helena M. B.;Harris, Simon R.;Clarke, Ian N.
背景资料：沙眼衣原体是全球性传播感染的最常见原因，也是发展中国家可预防失明的主要原因。沙眼衣原体有两种生物变体：引起眼部和生殖道感染的“沙眼”和侵袭性的“性病淋巴肉芽肿”菌株。最近，在瑞典出现了一种新的生殖道沙眼衣原体变种。这种变体逃过了常规诊断测试，因为它携带一个缺失的质粒。未能检测到这种菌株意味着它已在全国范围内迅速传播，引发了全球警报。除了作为一个关键的诊断目标，质粒已被链接到衣原体的毒力。衣原体质粒及其同源染色体的分析进行染色体和质粒之间的进化关系的见解。这是必不可少的知识，如果质粒是继续依赖于作为一个关键的诊断标志物，并了解沙眼衣原体的演变。结果：两个新的沙眼衣原体菌株的基因组进行了测序，连同质粒从6个沙眼衣原体分离株，包括来自瑞典的新变异株。来自新瑞典变异体的质粒在第一个预测编码序列中缺失了377 bp，消除了用于PCR检测的位点，导致阴性诊断。此外，变体质粒在缺失下游具有44 bp重复。含有第二个预测编码序列的区域是所研究质粒中最高度保守的区域。质粒和染色体的系统发育分析是完全一致的。结论：沙眼衣原体基因组和质粒的进化路径表明，质粒的遗传与其同源染色体紧密连锁。这些数据表明，质粒不是一个高度移动的遗传元件，不容易在分离株之间转移。质粒序列的比较分析揭示了最保守的区域，这些区域应该用于设计未来的基于质粒的核酸扩增测试，以避免诊断失败。
Background: Chlamydia trachomatis is the most common cause of sexually transmitted infections globally and the leading cause of preventable blindness in the developing world. There are two biovariants of C trachomatis: 'trachoma', causing ocular and genital tract infections, and the invasive 'lymphogranuloma venereum' strains. Recently, a new variant of the genital tract C trachomatis emerged in Sweden. This variant escaped routine diagnostic tests because it carries a plasmid with a deletion. Failure to detect this strain has meant it has spread rapidly across the country provoking a worldwide alert. In addition to being a key diagnostic target, the plasmid has been linked to chlamydial virulence. Analysis of chlamydial plasmids and their cognate chromosomes was undertaken to provide insights into the evolutionary relationship between chromosome and plasmid. This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis.Results: The genomes of two new C trachomatis strains were sequenced, together with plasmids from six C trachomatis isolates, including the new variant strain from Sweden. The plasmid from the new Swedish variant has a 377 bp deletion in the first predicted coding sequence, abolishing the site used for PCR detection, resulting in negative diagnosis. In addition, the variant plasmid has a 44 bp duplication downstream of the deletion. The region containing the second predicted coding sequence is the most highly conserved region of the plasmids investigated. Phylogenetic analysis of the plasmids and chromosomes are fully congruent. Moreover this analysis also shows that ocular and genital strains diverged from a common C trachomatis progenitor.Conclusion: The evolutionary pathways of the chlamydial genome and plasmid imply that inheritance of the plasmid is tightly linked with its cognate chromosome. These data suggest that the plasmid is not a highly mobile genetic element and does not transfer readily between isolates. Comparative analysis of the plasmid sequences has revealed the most conserved regions that should be used to design future plasmid based nucleic acid amplification tests, to avoid diagnostic failures.