ABSTRACT
Group A Streptococcus (GAS) is one of the most important pathogens leading to children deaths all over the world.Bacterial typing is the commonest approach to analyzing the epidemiological characteristics of pathogenic microorganisms.The emm typing is frequently adopted to study GAS.The emm cluster typing is a recently proposed typing method based on the amino acid sequence homology of M proteins and the ability to bind to the host serum protein.This typing system has been extensively used for epidemiological investigation, strain selection and vaccine deve-lopment in foreign countries.However, it has not been applied in China yet. emm typing is based on a small variable region of emm genes, while the emm cluster typing system defines GAS types according to nearly intact sequences of emm genes.Besides, the emm cluster grouping system is acquired directly by emm typing comparison, so it is simple and feasible.Furthermore, the emm cluster typing can provide more information regarding the functional and structural properties of M proteins in different emm types of GAS.In this review, the methods, principles and applications of the emm cluster typing system in GAS research were summarized, in order to promote its application in China.
ABSTRACT
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 in Shenzhen. Methods:Pharyngeal swab samples were collected and analyzed retrospectively from children diagnosed with scarlet fever in Shenzhen Children′s Hospital from January 1, 2016 to May 31, 2018.The GAS strains were preserved for emm genotyping analysis.The strains of representative emm types were selected for whole-genome sequencing.The genomic polymorphism of GAS strains was described by comparative genomic analysis.Moreover, a phylogenetic tree was constructed based on the whole genome core-gene single nucleotide polymorphisms(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, 8 emm types were detected.The most common genotype was emm12.0 and its subtype(108/176 strains, 61.4%), followed by emm1.0 and its subtype(53/176 strains, 30.1%). These two genotypes accounted for 91.5% of all isolates collected.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 insertion 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 and deletions [4(3, 6), 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 MGAS5005 as the reference sequence based on the whole genome core-gene SNPs, 18 strains and reference strains formed two clades. Conclusions:The emm12.0 and emm1.0 types are the most common GAS strains leading to scarlet fever in children.There are differences in the genome composition of different GAS strains.The emm12.0 strains have higher genetic diversity.
ABSTRACT
Objective:To explore the epidemiological characteristics of Streptococcus pyogenes, namely β-hemolytic Group A Streptococcus (GAS) in children in Shenzhen. Methods:Multilocus sequence typing (MLST) data on the epidemic clonal population of GAS infection in children in Shenzhen Children′s Hospital from January 2016 to December 2018 were retrospectively analyzed.In the present study, 32 GAS strains belonging to 7 different emm types were from 32 children′s with impetigo, cellulitis, scarlet fever, sepsis, pneumonia, obstructive sleep apnea hypopnea syndrome, bronchitis, allergy with rhinitis, buttock abscess, allergic purpura or pharyngeal tonsillitis, which were isolated from 23 throat swabs, 5 sputum samples, 3 pus and 1 blood.Using polymerase chain reaction technology, 7 pairs of allelic housekeeping genes ( gki, gtr, murI, mutS, recP, xpt and yqiL) of 32 GAS isolates were analyzed, and the target gene products were subjected to sequencing.Then the obtained gene sequences of each allele were submitted to the MLST database to obtain the allele profile.Finally, the allele profiles were introduced in the MLST database again to confirm the sequence typing (ST). Results:The GAS clone groups of emm 1.00 and its subtypes, emm 4.00, emm 12.00 and its subtypes, emm 22.00, emm 28.00, emm 75.00, and emm 89.00 belonged to the sequence typing ST28, ST39, ST36, ST46, ST52, ST49, and ST921, respectively. Conclusions:From 2016 to 2018, the MLST clone populations of GAS isolates causing infections in children in Shenzhen are classified as ST28, ST39, ST36, ST46, ST52, ST49 and ST921.
ABSTRACT
Objective To investigate and compare the molecular epidemiological characteristics of Streptococcus pyogenes isolates from Shanghai adult and pediatric patients in terms of antimicrobial susceptibility ,clone type ,emm type ,biofilm formation and virulence for better infection control and treatment .Methods Thirty‐nine nonduplicate clinical isolates of S . pyogenes from adult and pediatric patients were analyzed by determining the susceptibility to antimicrobial agents by Kirby‐Bauer method;clonal typing by multilocus sequence typing ( MLST ); genotyping by emm gene sequence analysis ,which encoding M protein;genomic characteristics of different emm type strains by pulsed field gel electrophoresis (PFGE );and biofilm formation by semi‐quantitative biofilm formation test . Twenty main virulence genes of S .pyogenes ,including 12 superantigen genes and 8 other key genes were detected by PCR and gel electrophoresis . Results A total of 39 nonduplicate S .pyogenes isolates were analyzed .The most common genotype was emm 12‐ST36 (64 .1% ) and emm 1‐ST28 (17 .9% ) .Isolates from adult and pediatric patients had the same dominant genotype , emm 12‐ST36 . The isolates from children showed significantly higher resistance rate to erythromycin and clindamycin than those from adult patients (P<0 .000 1) .Particular emm type and clone type were frequently identified in the same PFGE cluster .Statistical analysis showed that biofilm formation was significantly associated with emm type 1 (P=0 .005) and erythromycin/clindamycin resistance (P=0 .000 3) .The strains from children showed higher biofilm formation than those from adult patients (P<0 .000 1) .We found that virulence genes speA ,speJ and spd3 were significantly associated with emm type 1 (P<0 .000 1 ,P=0 .005 5 ,P<0 .000 1) ,while speI and sic were significantly associated with emm type 12 (both P<0 .000 1) .We also found that the prevalence of speC ,speH ,ssa , smeZ ,and sdaD genes was significantly different between emm type 12 and emm type 1 (P= 0 .023 8 , P< 0 .000 1 , P<0.0001,P= 0.0003,and P= 0.0068,respectively).TheprevalenceofvirulencegenesspeH,smeZandsdaDwas significantly different between the emm type 12 strains from children and those from adults (all P< 0 .000 1) .Conclusions There is a strong agreement between emm type ,clone type ,virulence genes and the clusters defined by PFGE profiling of S . pyogenes .S .pyogenes isolates from adult and pediatric patients are different in terms of antibiotic resistance and biofilm formation .Certain emm type is significantly associated with antibiotic resistance and virulence ,which is useful for infection control .Dominant virulence genes may be the potential target for developing new vaccine to reduce S .pyogenes infection in the future .