Whole genome sequence of the <i>Treponema pallidum</i> subsp. <i>pallidum</i> strain Amoy: An Asian isolate highly similar to SS14

Treponema pallidum ssp. pallidum (T. pallidum), the causative agent of the sexually transmitted disease syphilis, is an uncultivatable human pathogen. The geographical differences in T. pallidum genomes leading to differences in pathogenicity are not yet understood. Presently, twelve T. pallidum genomes are available to the public, all of which are American in origin and often co-infect patients with human immunodeficiency virus (HIV). In this study, we examined the T. pallidum subsp. pallidum strain Amoy, a syphilis pathogen found in Xiamen, China. We sequenced its genome using Illumina next-generation sequencing technology and obtained a nearly (98.83%) complete genome of approximately 1.12 Mbps. The new genome shows good synteny with its five T. pallidum sibling strains (Nichols, SS14, Mexico A, DAL-1, and Chicago), among which SS14 is the strain closest to the Amoy strain. Compared with strain SS14, the Amoy strain possesses four uncharacterized strain-specific genes and is likely missing six genes, including a gene encoding the TPR domain protein, which may partially account for the comparatively low virulence and toxicity of the Amoy strain in animal infection. Notably, we did not detect the 23S rRNA A2058G/A2059G mutation in the Amoy strain, which likely explains the sensitivity of Amoy strain to macrolides. The results of this study will lead to a better understanding of the pathogenesis of syphilis and the geographical distribution of T. pallidum genotypes.梅毒螺旋体苍白亚种（Treponema pallidum ssp. pallidum, T. pallidum）是引起性传播疾病梅毒的病原体，同时也是一种无法体外培养的人类致病菌。目前学界尚未阐明梅毒螺旋体基因组的地理差异如何导致致病性差异的机制。当前公开可用的12株梅毒螺旋体基因组均源自美国，且多分离自合并感染人类免疫缺陷病毒（Human Immunodeficiency Virus, HIV）的患者体内。本研究针对中国厦门分离的梅毒致病菌——梅毒螺旋体苍白亚种Amoy株展开分析，采用Illumina二代测序技术对其基因组进行测序，获得了完整度达98.83%、长度约1.12 Mbp的近完整基因组。该新基因组与5株亲缘梅毒螺旋体菌株（Nichols、SS14、Mexico A、DAL-1及Chicago）具有良好的基因组共线性，其中SS14株与Amoy株的亲缘关系最为接近。与SS14株相比，Amoy株携带4个尚未注释的株特异性基因，且可能缺失6个基因，其中包含一个编码TPR结构域蛋白（Tetratricopeptide Repeat domain protein）的基因，这或许可以部分解释Amoy株在动物感染模型中相对较低的毒力与毒性。值得注意的是，本研究未在Amoy株中检测到23S rRNA的A2058G/A2059G突变，这一结果或可解释Amoy株对大环内酯类抗生素的敏感性。本研究结果将有助于进一步阐明梅毒的致病机制以及梅毒螺旋体基因型的地理分布特征。