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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.
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Group A Streptococcus (GAS) is a very important pathogen, especially for children.On a global scale, GAS is an important cause of morbidity and mortality.But the burden of disease caused by GAS is still unknown in China and also has not obtained enough attention.For this purpose, the expert consensus is comprehensively described in diagnosis, treatment and prevention of GAS diseases in children, covering related aspects of pneumology, infectiology, immunology, microbiology, cardiology, nephrology, critical care medicine and preventive medicine.Accordingly, the consensus document was intended to improve management strategies of GAS disease in Chinese children.
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Scarlet fever is a respiratory disease caused by Group A Streptococcus (GAS). It commonly attacks school children and has no available vaccine currently.The human history, especially European Industrial Revolution and Victorian Era, has witnessed large scale scarlet fever epidemics.Before antibiotics were invented, scarlet fever was once a highly transmissible disease with high mortality about 30%-50%.With the wide use of antibiotics after World War Ⅱ, the incidence and mortality of scarlet fever decrease significantly.Invasive streptococcal infections resurge in Europe and America in 1980s.In the past ten years, the incidence of scarlet fever kept increasing in several countries around the world.In this article, the latest research progress of scarlet fever epidemiology and pathogenesis was reviewed.Meanwhile, potential mechanisms and risk factors for the recently increasing incidence of scarlet fever in various regions were discussed.
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Objective To learn about the overall genomic characteristics and population structure of Helicobacterpylori isolated in China.Methods In this study,we used 10 public available genome sequences of H.pylori strains isolated in China,combined with other H.pylori sequences from GenBank,to analyzed the overall genomic characteristics of H.pylori isolated in China.Core genes and strain specific genes were determined for a further function definition.Results A total of 1 203 core genes were found among all sequenced China H.pylori isolates.The number of strain specific genes ranged from 19 to 32.These genes mainly encodes hypothetical proteins which might play an important role in adaption to different hosts.Genomic variation regions were mainly in genes encoding type four secretion systems and restriction modification systems.All the China isolates belong to hpEastAsia group,hspEAsia subgroup.Prophages sequences were found in three China H.pylori strains,carrying key elements required for phage assembly.Conclusion China H.pylori isolates belong to hpEastAsia group,hspEAsia subgroup,and some isolates contain prophages.
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Objective To learn about the overall genomic characteristics and population structure of Helicobacterpylori isolated in China.Methods In this study,we used 10 public available genome sequences of H.pylori strains isolated in China,combined with other H.pylori sequences from GenBank,to analyzed the overall genomic characteristics of H.pylori isolated in China.Core genes and strain specific genes were determined for a further function definition.Results A total of 1 203 core genes were found among all sequenced China H.pylori isolates.The number of strain specific genes ranged from 19 to 32.These genes mainly encodes hypothetical proteins which might play an important role in adaption to different hosts.Genomic variation regions were mainly in genes encoding type four secretion systems and restriction modification systems.All the China isolates belong to hpEastAsia group,hspEAsia subgroup.Prophages sequences were found in three China H.pylori strains,carrying key elements required for phage assembly.Conclusion China H.pylori isolates belong to hpEastAsia group,hspEAsia subgroup,and some isolates contain prophages.