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，可引起严重的性行为。 人类中的传染性疾病。尤其是衣原体的生物学和致病机制的研究。 因为缺乏插入或使目标基因失活的系统而具有挑战性。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的有价值的信息。 这个系统中的基因组方法特别可行，因为测序富含A+T的小的、非重复的衣原体基因组可以以相对较小的成本完成。这项建议描述了使用基因组测序来研究三种新的衣原体表型，这三种表型是在对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的实验室核心维护。要检查的表型如下。首先，某些血清型的分离株与同性恋者的直肠感染高度相关，因此表现出直肠嗜性。其次，某些沙眼衣原体分离株，特别是G血清型的分离株，在感染单个基本体的细胞内形成大量次生包涵体。最后，在组织培养中鉴定出一组形成非融合包涵体的沙眼衣原体分离物。这些表型的遗传基础将通过完成六个具有代表性的临床分离株的基因组序列来探索。 这一测序将允许在分离株中识别核苷酸多态(NP)，并与已公布的衣原体基因组进行比较。然后，将对这些NPs进行排序，并筛选出更大一组菌株，以在统计上将单个NPs与表型联系起来。这些定量研究将与STI-TM-CRC生物统计核心一起进行，并将利用从UWCR中挑选的最新临床分离株。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是否可能对表型有贡献。我们预计，这些研究将提供证据，将衣原体基因与三种表型差异联系起来，并将确定衣原体基因在衣原体生物学和致病机制中的重要作用。 这些基因组序列的完成也将是研究衣原体进化和多样性的重要工具。

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.