Characterisation of emergent toxigenic M1_UKStreptococcus pyogenesand associated sublineages

Abstract

Emm1 Streptococcus pyogenes is a successful, globally-distributed epidemic clone that is regarded as inherently invasive. An emm1 sublineage, M1UK, that expresses increased SpeA toxin, was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterise M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and pts system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of the gldA gene in M1global 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 these four major 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, transcription and secretion of SpeA was upregulated ~10-fold in both M1_23SNPs and M1UK sublineages, compared with M1_13SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK 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 M1UK on an inherently successful emm1 streptococcal background.

Increase in invasive group A streptococcal infection notifications, England, 2022

“…Typing results have been reported for 13 child deaths, of which nine were emm 1, three were emm 12 and one was emm 77. Whole genome sequencing of all typed invasive and non-invasive isolates indicates that there has been no obvious expansion of a single clone for those emm types, however, the majority of the emm 1 isolates were part of the emm 1 M1UK clone, first detected in 2010, for which upregulation of SpeA expression, a virulence factor of Streptococcus pyogenes, has been demonstrated [7,8].…”

Tricontinental detection of Streptococcus pyogenes M1UK: A call for wider research and active surveillance

“…We recently reported that strains from the M113SNP intermediate sublineage produce negligible amounts of SpeA, similar to M1global (9). Phylogenetic analysis of Australian sequences (9) shows the M113SNP sublineage to be present in Australia too (Figure 1A).…”

“…We recently reported that strains from the M113SNP intermediate sublineage produce negligible amounts of SpeA, similar to M1global (9). Phylogenetic analysis of Australian sequences (9) shows the M113SNP sublineage to be present in Australia too (Figure 1A). Strains from the M123SNP sublineage, in contrast, produce SpeA at an increased level that is indistinguishable from M1UK isolates (9).…”

“…Phylogenetic analysis of Australian sequences (9) shows the M113SNP sublineage to be present in Australia too (Figure 1A). Strains from the M123SNP sublineage, in contrast, produce SpeA at an increased level that is indistinguishable from M1UK isolates (9). Despite increased SpeA production, by 2020, we were unable to detect M123SNP isolates when screening all emm1 isolates submitted to the reference laboratory in England (4).…”

“…intermediate sublineage appears to have been outcompeted by M1UK, suggesting an added fitness advantage in M1UK strains beyond production of SpeA alone. We postulate this further adaptation may be conferred by the additional 4 SNPs that distinguish M1UK from M123SNP isolates (3 nonsynonymous SNPs and an intergenic SNP 39bp upstream of glpF2, aquaporin, expression of which is significantly reduced in M1UK) (8,9). In this report we seek to further understand the mechanisms that differentiate SpeA-producers from non-producers among emm1 S. pyogenes strains that carry the phage that encodes speA.…”