| Objective:To identify the epidemic types of Group A Streptococcus(GAS)causing scarlet fever,to compare the gene structure and variability of GAS with different emm types,and to elucidate the epidemiological pattern of scarlet fever pathogens.Methods:176 GAS strains were collected and stored in the biological sample bank of Shenzhen Children’s Hospital from children with scarlet fever from January 1,2016 to May 31,2018.The GAS strains were preserved for emm genotyping analysis.The sex and age distribution of children with scarlet fever caused by GAS,and the prevalence of emm1 and emm12 strains were analyzed.The strains of representative emm types were selected for whole-genome sequencing.The genomic polymorphism of GAS strain was described by comparative genomic analysis.Moreover,a phylogenetic tree was constructed based on the whole genome core-gene Single Nucleotide Polymorphism(SNPs)to clarify the evolutionary relationship between strains.Data between groups were compared by Rank sum test.Results:Among 176 GAS isolates that caused scarlet fever in children,7 emm types were detected.The most common genotype was emm 12.0 and its subtype(107/176,60.8%),followed by emm 1.0 and its subtype(55/176,32.9%).These two genotypes accounted for 93.7% of all isolates collected.In children infected with emm12 in2018,there were more children under 6 years old than children over 6 years old(χ 2=7.138,P < 0.05),and the difference was statistically significant.Comparative genome analysis was made taking GCA-900984775 as a reference sequence and the results showed that the genomes of GAS strains had high levels of SNP and insretion or deletion(InDel)polymorphisms.There were more SNPs in emm12.0 strains [183(163,213)] than those in emm1.0 strains [63(54,75)],and the difference was statistically significant(P <0.05).As for InDel,more insertions [4(3,6)]and deletions [8(6,10)] were observed in emm12.0 strains than those[1(0,2),5(3,7)] in emm1.0 strains.According to the phylogenetic tree built by taking MAGS5005 as the reference sequence based on the whole genome core-gene SNPs,18 strains and reference strains formed two clades.Conclusions:The emm12 and emm1 types were the most common GAS strains leading to scarlet fever in children.There are differences in the genome composition of different GAS strains.The emm12 strains has higher genetic diversity. |
