Comparative Genomics of Clinical C. trachomatis Strains

沙眼衣原体是一种专性细胞内细菌病原体， 传染给人类的疾病。衣原体生物学和致病机理的研究尤其重要， 由于缺乏插入或灭活靶基因的系统，这是一个挑战。在缺乏遗传系统的情况下，基因组序列分析提供了关于衣原体的独特有价值的信息。 该系统中的基因组方法是特别可行的，因为可以以相对较小的成本完成对小的、富含A + T的、非重复的衣原体基因组的测序。该提案描述了使用基因组测序来调查三种新的衣原体表型，这些表型是在对来自华盛顿大学衣原体储存库（UWCR）的分离株进行实验室和流行病学分析后确定的。UWCR包含超过12，000个临床分离株，由STD-CRC实验室核心维护。待检查的表型如下。首先，某些血清型中的分离株与同性恋男性的直肠感染高度相关，因此表现出直肠嗜性。第二，确定C.沙眼分离株，特别是血清型G的那些，在被单个原体感染的细胞内形成大量的次级包涵体。最后，一组C。已鉴定出沙眼分离株在组织培养中形成非融合性包涵体。将通过完成6株代表性临床分离株的基因组测序，探索这些表型的遗传基础。 这种测序将允许鉴定分离株之间的核苷酸多态性（NP），并与已发表的衣原体基因组进行比较。然后对这些NP进行排名，并筛选更大的菌株集，以在统计学上将单个NP与表型联系起来。这些定量研究将与STI-TM-CRC生物统计学核心联合进行，并将利用从UWCR中选择的最新临床分离株。然后将使用组织培养模型和其他体外方法来检查受影响的基因产物作为表型的可能贡献者。我们预计，这些研究将提供证据，衣原体基因型与三个表型的区别，并确定衣原体基因重要的衣原体生物学和发病机制，以前未知的方面。 完成这些基因组序列也将是重要的工具，衣原体的进化和多样性的研究。

Chlamydia trachomatis is an obligate intracellular bacterial pathogen that causes serious sexually transmitted diseases in humans. The study of chlamydial biology and pathogenesis is particularly challenging because of the lack of a system for inserting or inactivating target genes. In the absence of a genetic system, genome sequence analysis provides uniquely valuable information on the chlamydiae. Genomic approaches in this system are particularly feasible because sequencing the small, A + T rich, non-repetitive chlamydial genome can be completed at a comparatively small cost. This proposal describes the use of genome sequencing to investigate three novel chlamydial phenotypes that were identified following laboratory and epidemiologic analysis of isolates from the University of Washington Chlamydia Repository (UWCR). The UWCR contains over 12,000 clinical isolates and is maintained by the Laboratory Core of the STD-CRC. The phenotypes to be examined are the following. First, isolates within certain serovars are highly associated with rectal infection in homosexual men and, thus, demonstrate rectal tropism. Second, certain C. trachomatis isolates, particularly those of serovar G, form large numbers of secondary inclusions within cells infected with single elementary bodies. Finally, a group of C. trachomatis isolates has been identified that form non-fusogenic inclusions in tissue culture. The genetic basis for these phenotypes will be explored through the completion of the genome sequence for each of six representative clinical isolates. This sequencing will allow identification of nucleotide polymorphisms (NPs)among the isolates and in comparison to published chlamydial genomes. These NPs will then be ranked and a larger set of strains will be screened to statistically connect individual NPs with the phenotypes. These quantitative studies will be conducted in association with the STI-TM-CRC Biostatistics Core and will utilize recent clinical isolates selected from the UWCR. Tissue culture models and other in vitro approaches will then be used to examine the affected gene products as possible contributors to the phenotype. We anticipate that these studies will provide evidence linking chlamydial genotypes with the three phenotypic distinctions and will identify chlamydial genes important in previously uncharacterized aspects of chlamydial biology and pathogenesis. Completion of these genome sequences will be also important to tools for the study of chlamydial evolution and diversity.