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

  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 – 1 849 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.