Characterization of emergent toxigenic M1_UK Streptococcus pyogenes and associated sublineages

Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1_UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1_UK is now dominant in England. To more fully characterize M1_UK, we undertook comparative transcriptomic and proteomic analyses of M1_UK and contemporary non-M1_UK emm1 strains (M1_global). Just seven genes were differentially expressed by M1_UK compared with contemporary M1_global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1_UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1_UK strains have a stop codon in gldA. Deletion of gldA in M1_global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M1_13SNPs) and 23/27 SNPs (M1_23SNPs), respectively, that had failed to expand in the population. Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M1_23SNPs and M1_UK sublineages, compared with M1_13SNPs and M1_global. We conclude that stepwise accumulation of SNPs led to the emergence of M1_UK. While increased expression of SpeA is a key indicator of M1_UK and undoubtedly important, M1_UK strains have outcompeted M1_23SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1_UK on an inherently successful emm1 streptococcal background.