Construction of a genomic database for Group A Streptococcus and the analysis of prophage distribution / 中华实用儿科临床杂志

ABSTRACT

Objective:To illustrate the characteristics of the distribution of prophages among the Group A Streptococcus(GAS) by mining the existing whole genome sequencing of the GAS, performing bioinformatic analyses, extracting data about prophages, and analyzing the state of prophages in the genome and genetic composition of some prophages. Methods:It was a retrospective study.Genome assembly sequences of GAS reported in GenBank till May 2020 were collected, and the important background information of these strains was sorted out to create a local genomic database.A phylogenetic tree of the whole genome of GAS was conducted using the bioinformatics software.The core genome was analyzed, and potential prophages and their integrity in the genome were predicted to obtain the characteristics of the distribution of prophages.Genotype types, number of core genes, and number, length and carrying rate of prophages in the database for GAS were analyzed.Results:A database containing the genome sequence of 2 529 GAS strains was established, involving 140 emm genotypes.These strains were isolated from 19 countries from East Asia, Europe, America and Oceania.Stratified by the disease background, these strains were mainly divided into invasive infection, non-invasive infection and immune sequelae.Prophage analysis of 1 798 genomes showed that at least one complete prophage was detected in 1 366 (76.0%) genomes.The number of complete prophages of each strain ranged from 0 to 6, and the length ranged from 32.8 to 62.6 kb, which was mainly 30-40 kb in length.The phiHKUssa, phiHKUvir and phiHKU488 were the most common prophages present in dominant clones circulated in China in recent years, which mainly carried virulence genes like the speC, spd1 and ssa. Conclusions:Prophages are widely distributed in the genome of GAS, which are of great significance in the evolution and expansion of dominating clones and thus reshape the population structure within the emm genotype.The establishment of a local genome database provides important baseline data for molecular epidemiological surveillance.