Construction of a genomic database for Group A Streptococcus and the analysis of prophage distribution
10.3760/cma.j.cn101070-20230322-00240
- VernacularTitle:A族链球菌基因组数据库建设及前噬菌体分布分析
- Author:
Fanliang MENG
1
;
Caixin XIANG
;
Jianzhong ZHANG
;
Yuanhai YOU
Author Information
1. 传染病溯源预警与智能决策全国重点实验室，中国疾病预防控制中心传染病预防控制所，北京 102206
- Keywords:
Genome;
Group A Streptococcus;
Population structure;
Database;
Phage
- From:
Chinese Journal of Applied Clinical Pediatrics
2024;39(1):49-53
- CountryChina
- Language:Chinese
-
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.
