Sequence types (STs) were calculated according to the multilocus sequence typing (MLST) scheme of the Public databases for molecular typing and microbial genome diversity (https://pubmlst.org/organisms/streptococcus-pyogenes ) using Ariba v2.6.2 (22 (link)). Core genome MLST (cgMLST), consisting of 1,168 genes for S. pyogenes provided by SeqSphere+3.5.0 (Ridom, Münster, Germany), was performed. A simple diversity index (SDI) was applied to analyze population diversity (23 (link)).
Additionally, emm1 isolates from this study were analyzed as described by Linskey et al. (7 (link)) in comparison with a collection of 377 M1global and 247 M1UK hypervirulent S. pyogenes isolates reported in the previous reference. After removing all high single nucleotide polymorphisms (SNP) density regions (24 (link)), a core genome alignment with 6,411 SNPs was used to build a maximum-likelihood tree.
Additionally, emm1 isolates from this study were analyzed as described by Linskey et al. (7 (link)) in comparison with a collection of 377 M1global and 247 M1UK hypervirulent S. pyogenes isolates reported in the previous reference. After removing all high single nucleotide polymorphisms (SNP) density regions (24 (link)), a core genome alignment with 6,411 SNPs was used to build a maximum-likelihood tree.
