10株A族链球菌标准菌株全基因组序列分析

Whole genome sequence analysis of 10 standard strains of group A Streptococcus

目的分析A族链球菌(GAS)不同标准菌株的基因组特征,为进一步探讨GAS致病性、耐药机制和分子进化规律提供参考依据。方法采用高通量测序技术对中国医学细菌保藏管理中心保藏的10株GAS标准菌株进行全基因组测序,分析菌株的M蛋白(emm)基因及多位点序列分型(MLST);采用velvet 1.2.03和glimmer 3.02等生物信息学软件对测序数据进行基因组装、基因预测及功能注释,并以此分析基因组中所含耐药基因、毒力基因及插入序列(IS)种类;应用Blast比对分析不同菌株基因组中的特定致热外毒素B基因和系列超抗原基因序列,通过比较基因组学分析拟合泛基因组和核心基因组积累曲线,筛选核心基因SNP,构建系统发育分子进化树。结果10株GAS标准菌株的染色体全基因组序列大小约为1.8 Mbp,在不同菌株基因组鉴定出1682~1849个基因;通过对基因组毒力基因注释分析发现,10株GAS标准菌株基因组中含有16~22种数量不等的毒力因子,其中部分是在GAS基因组保守存在的,包括细菌致病相关的层粘连蛋白基因(lmb)、致热外毒素B基因(speB)、纤维基因结合蛋白(Fbp);基因组耐药基因注释分析发现,每株GAS标准菌株仅携带1种耐药基因,除CMCC(B)32308菌株基因组携带抗大环内脂抗生素相关的lmrP基因外,在其他9株GAS基因组中均发现与氟喹诺酮抗性相关的patB耐药基因;10株GAS标准菌株中共含有IS1562、IS1239、ISSpy1、IS1548和ISSag5等5种IS元件,不同菌株之间IS种类略有差别;比较基因组学分析结果显示,随着GAS基因组测序数量的增加,泛基因组随之增加,而核心基因组则随着不同GAS菌株数量的增加而逐渐趋于稳定;本研究10株GAS标准菌株与已发表的S10394、SF370、A20、NZ131和s6180等5株GAS代表性菌株系统发育树进化分析结果显示,15株不同GAS菌株可分成4个进化分支,其中CMCC(B)32067和CMCC(B)32301分别形成2个独立进化分支,与其他GAS标准菌株进化距离较远。结论10株GAS标准菌株的基因组结构高度相似,GAS的核心基因组为相对稳定型,泛基因组为开放型。

Objective To analyze genomic characteristics of different standard strains of group A Streptococcus(GAS)for providing a reference to researches on the pathogenicity,drug resistance mechanisms and molecular evolution of GAS.Methods Totally 10 standard strains of GAS were derived from National Center for Medical Culture Collections(CMCC).The strains′whole genome sequence(WGS)were obtained with high-throughput sequencing and analyzed with multilocus sequence typing(MLST).Gene assembly,prediction and function annotation for WGS of the strains were performed using bioinformatics softwares including Velvet 1.2.03 and Glimmer 3.02.The drug resistance genes,virulence genes and insertion sequence(IS)elements in those genomes of the strains were analyzed.Blast was used to compare and analyze pyrogenic exotoxin B gene and series of superantigen gene in the genomes of different strains,and the pan-genome and core genome accumulation curves were fitted using comparative genomics analysis.The single-nucleotide polymorphisms(SNPs)of core genes were screened and the phylogenetic tree was constructed.Results The size of chromosome sequence for the 10 GAS standard strains were about 1.8 Mbp,and 1682–1849 genes were identified among the 10 strains.Totally 16–22 virulence factors were found in annotation analysis on virulence genes in the 10 GAS genomes,and some of which were conserved in the GAS genomes,including bacterial disease-related laminin gene(lmb),thermal exotoxin B gene(speB)and fiber gene binding protein(Fbp).Annotation analysis on genome resistance genes revealed that each of the GAS strains only carried one drug resistance gene.Except for the CMCC(B)32308 strain carrying the lmrP gene related to macrolide antibiotic resistance,the genome of the other 9 GAS strains were found to carry patB gene associated with quinolone resistance.There were 5 IS elements(IS1562,IS1239,ISSpy1,IS1548 and ISSag5)were found in the 10 GAS strains,which were slightly different among the strains.Comparative genetic analysis found that as the number of GAS genome sequencing increases,the pan-genome increases accordingly,while the core genome stabilizes gradually with the increasing number of different GAS strains.Phylogenetic analysis showed that 10 different GAS strains and the 5 published representative GAS strains including S10394,SF370,A20,NZ131 and s6180 were divided into 4 evolutionary branches,among which CMCC(B)32067 and CMCC(B)32301 were far away from other GAS strains and formed two independent evolutionary branches.Conclusion The genome structure of the 10 GAS standard strains is highly similar,with the core genome of GAS strains being relatively stable and the pan-genome being open.