Comparing Genomic Characteristics of Streptococcus pyogenes Associated with Invasiveness over a 20-year Period in Korea

Abstract

Background: Few studies have investigated the invasiveness of Streptococcus pyogenes based on whole-genome sequencing (WGS). Using WGS, we determined the genomic features associated with invasiveness of S. pyogenes strains in Korea.Methods: Forty-five S. pyogenes strains from 1997, 2006, and 2017, including common emm types, were selected from the repository at Gyeongsang National University Hospital in Korea. In addition, 48 S. pyogenes strains were randomly selected depending on their invasiveness between 1997 and 2017 to evaluate the genetic evolution and the associations between invasiveness and genetic profiles. Using WGS datasets, we conducted virulence-associated DNA sequence determination, emm genotyping, multi-locus sequence typing (MLST), and superantigen gene profiling.Results: In total, 87 strains were included in this study. There were no significant differences in the genomic features throughout the study periods. Four genes, csn1, ispE, nisK, and citC, were detected only in invasive strains. There was a significant association between invasiveness and emm cluster type A-C3, including, emm1.0, emm1.18, emm1.3, and emm1.76 (P < 0.05). The predominant emm1 lineage belonged to ST28. There were no associations between invasiveness and superantigen gene profiles.Conclusions: This is the first study using WGS datasets of S. pyogenes strains collected between 1997 and 2017 in Korea. Streptococcal invasiveness is associated with the presence of csn1, ispE, nisK, and citC. The emm1 lineage and ST28 clone are explicitly associated with invasiveness, whereas genomic features remained stable over the 20-year period.

Biotypic and genotypic diversity in <i>Pasteurella canis</i> isolated from host animals and humans: differences in trehalose fermentation and nucleotide sequences encoding trehalose-6-phosphate hydrolase (<i>treC</i>)

“…The specificity of the primer sequences was examined by inserting them into the nucleotide basic local alignment search tool on the NCBI website (https://blast.ncbi.nlm.nih.gov/Blast.cgi). To assess the accuracy of the primer sequences within the genome sequences encoding the enzyme, we conducted simulation PCR analysis using Serial Cloner 2.6 (http://serialbasics.free.fr/Serial_Cloner.html) using WGSs, as previously described [ 21 , 25 ].…”

Successful treatment of streptococcal toxic shock syndrome complicated by primary peritonitis and bilateral empyema in a healthy young woman: Identification of uncommon clone emm103 and novel sequence type 1363

“…Phenotypic analyses included hemolysis, Lancefield carbohydrate antigen, pyrrolidonyl arylamidase production reaction, and antimicrobial susceptibility testing. Genotypic analyses included sagA (111-bp fragment) and slo (548-bp fragment) encoding hemolysin amplification, emm type/subtype based on the hyper-variable region of 180 base [6] , emm sequence, superantigen gene profile [7] , sequence type (ST) (allelic profile; gki - g tr - murI - mutS - recP - xpt - yqiL ) by multilocus sequence typing [6] , and antimicrobial resistance (AMR) gene profile [6] , [8] , [9] . The emm genotyping was based on the Centers for Disease Control and Prevention database ( https://www2.cdc.gov/vaccines/biotech/strepblast.asp ).…”

Virulence-associated Genome Sequences of Pasteurella canis and Unique Toxin Gene Prevalence of P. canis and Pasteurella multocida Isolated from Humans and Companion Animals

“…The specificity of the primer sequences was examined by inserting them into NCBI BLASTn. To assess the accuracy of the primer sequences, we conducted simulated PCR assays using Serial Cloner 2.6 (http://serialbasics.free.fr/Serial_Cloner.html) based on the obtained WGSs [16,17].…”