基于芯片的猪链球菌比较基因组学研究

发布时间：2018-10-17 08:51

【摘要】：猪链球菌是重要的人兽共患致病菌,可感染猪和人引起猪链球菌病并导致脑膜炎、败血症等严重临床表现。不同来源的猪链球菌致病力有明显差异,一些菌株具有更强的毒力。根据猪链球菌相关毒力相关因子的有无,猪链球菌病的流行病学,以及动物实验研究,致病性猪链球菌可分为中等致病株,高致病株,流行株。并且,通常认为能够引起人猪链球菌病散发和暴发流行的菌株具有高致病性。猪链球菌的多位点序列分型(MLST)方案可将猪链球菌至少分为181个序列型(ST),其中ST1序列群菌株的致病力明显强于其它ST型别,属高致病群。ST1克隆群中的ST7序列型菌株在1998年和2005年曾分别在中国的江苏省,四川省引起猪链球菌病暴发流行。然而,到目前为止,猪链球菌的致病机制及导致其致病力差异的遗传学基础尚不明确。木研究中,以ST1序列型菌株GZl的基因组序列为参考,我们使用NimbleGen公司的高密度原位合成基因组扫描芯片对31株(包括23个血清型,25个ST型)猪链球菌进行了比较基因组分析,并采用一个新的算法检测了菌株间基因组内容的差异。每个试验菌株相对GZ1缺失的基因数49至225不等；共632个基因至少在一个实验菌株中缺失,共1346个基因存在于所有试验菌株中,组成了猪链球菌的核心基因组(core genome),占GZ1基因组的68%。多数非核心基因呈簇状分布,其中在两株以上实验菌株中发生缺失的共有62个基因簇,定义为变异区(regions of difference,RDs);26个RD具有基因组岛(Genomic islands,GIs)的特征。聚类和统计分析确认8个RD与高致病性显著相关。其中3个RD编码已知的猪链球菌毒力相关因子,包括细胞外因子(EF),荚膜多糖(CPS)和SrtF菌毛。基于试验菌株多位点序列分型(MLST)数据的群体遗传学分析,31个试验菌株分为5个亚群(subpopulation/group);比较62个RD在各亚群的分布特点,显示RD片段在亚群进化过程中的演化过程。本研究从基因组学角度阐明了猪链球菌种群的多态性,发现了新的高致病相关基因和基因组岛。这些发现为进一步揭示猪链球菌的致病机制,深入认识其毒力进化过程提供了重要线索。
[Abstract]:Streptococcus suis is an important zoonotic pathogen which can infect pigs and humans and lead to severe clinical manifestations such as meningitis and septicemia. The pathogenicity of Streptococcus suis from different sources was significantly different, and some strains had stronger virulence. According to the factors related to the virulence of Streptococcus suis, the epidemiology of Streptococcus suis and the animal experiment, the pathogenic Streptococcus suis can be divided into moderate pathogenic strain, high pathogenic strain and epidemic strain. Moreover, strains that can cause sporadic and outbreak of human streptococcus suis are thought to be highly pathogenic. Streptococcus suis can be divided into at least 181 (ST), by multi-locus sequence typing (MLST). The virulence of ST1 sequence group strains is obviously stronger than that of other ST types. In 1998 and 2005, ST7 sequenced strains of ST1 clones caused outbreaks of Streptococcus suis in Jiangsu Province and Sichuan Province, respectively. However, the pathogenetic mechanism of Streptococcus suis and the genetic basis for its pathogenicity are unclear. Based on the genomic sequence of ST1 sequence strain GZl, 31 strains of Streptococcus suis (including 23 serotypes and 25 ST types) were analyzed by NimbleGen high-density in situ synthetic genomic scanning microarray. A new algorithm was used to detect the difference of genome content among strains. A total of 632 genes were deleted in at least one strain, and a total of 1346 genes were found in all the tested strains. The core genome (core genome), of Streptococcus suis was 68% of the GZ1 genome. Most of the non-core genes were clustered, of which 62 were found missing in more than two experimental strains, defined as (regions of difference,RDs), and 26 RD were characterized as genomic islands (Genomic islands,GIs). Cluster and statistical analysis confirmed that 8 RD were significantly associated with high pathogenicity. Three known virulence related factors of Streptococcus suis were encoded by RD, including extracellular factor (EF), capsule polysaccharide (CPS) and SrtF pili. Based on the (MLST) data of multilocus sequence typing, 31 strains were divided into 5 subpopulations (subpopulation/group), and the distribution characteristics of 62 RD in each subgroup were compared to show the evolution process of RD fragment in the evolution of subgroup. In this study, the polymorphisms of Streptococcus suis population were elucidated from the perspective of genomics, and a novel highly pathogenic gene and genomic island were found. These findings provide important clues for further understanding the pathogenic mechanism of Streptococcus suis and its virulence evolution.
【学位授予单位】：中国疾病预防控制中心
【学位级别】：博士
【学位授予年份】：2011
【分类号】：R378

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