Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study

Abstract

Background: Since 2014, England has seen increased scarlet fever activity unprecedented in modern times. In 2016, England's scarlet fever seasonal rise coincided with an unexpected elevation in invasive Streptococcus pyogenes infections. We describe the molecular epidemiological investigation of these events.

Methods: We analysed changes in S pyogenes emm genotypes, and notifications of scarlet fever and invasive disease in 2014-16 using regional (northwest London) and national (England and Wales) data. Genomes of 135 non-invasive and 552 invasive emm1 isolates from 2009-16 were analysed and compared with 2800 global emm1 sequences. Transcript and protein expression of streptococcal pyrogenic exotoxin A (SpeA; also known as scarlet fever or erythrogenic toxin A) in sequenced, non-invasive emm1 isolates was quantified by real-time PCR and western blot analyses.

Findings: Coincident with national increases in scarlet fever and invasive disease notifications, emm1 S pyogenes upper respiratory tract isolates increased significantly in northwest London in the March to May period, from five (5%) of 96 isolates in 2014, to 28 (19%) of 147 isolates in 2015 (p=0·0021 vs 2014 values), to 47 (33%) of 144 in 2016 (p=0·0080 vs 2015 values). Similarly, invasive emm1 isolates collected nationally in the same period increased from 183 (31%) of 587 in 2015 to 267 (42%) of 637 in 2016 (p<0·0001). Sequences of emm1 isolates from 2009-16 showed emergence of a new emm1 lineage (designated M1_UK)-with overlap of pharyngitis, scarlet fever, and invasive M1_UK strains-which could be genotypically distinguished from pandemic emm1 isolates (M1_global) by 27 single-nucleotide polymorphisms. Median SpeA protein concentration in supernatant was nine-times higher among M1_UK isolates (190·2 ng/mL [IQR 168·9-200·4]; n=10) than M1_global isolates (20·9 ng/mL [0·0-27·3]; n=10; p<0·0001). M1_UK expanded nationally to represent 252 (84%) of all 299 emm1 genomes in 2016. Phylogenetic analysis of published datasets identified single M1_UK isolates in Denmark and the USA.

Interpretation: A dominant new emm1 S pyogenes lineage characterised by increased SpeA production has emerged during increased S pyogenes activity in England. The expanded reservoir of M1_UK and recognised invasive potential of emm1 S pyogenes provide plausible explanation for the increased incidence of invasive disease, and rationale for global surveillance.

Funding: UK Medical Research Council, UK National Institute for Health Research, Wellcome Trust, Rosetrees Trust, Stoneygate Trust.

Figure 1

2016 surge in scarlet fever associated with expansion of emm1 upper respiratory tract isolates of Streptococcus pyogenes (A) Monthly notifications of scarlet fever in northwest London (bars) in 2013–16 showing the surge in notifications between March and May, peaking in 2016. National scarlet fever notifications (dashed lines) are shown for comparison. (B) emm genotyping of all upper respiratory tract isolates of S pyogenes from northwest London between March and May each year during 2014–16. emm1 strains emerged as the dominant upper respiratory tract genotype by 2016.

Figure 2

Emergence of new emm1 lineage among non-invasive Streptococcus pyogenes isolates Maximum likelihood phylogenetic tree constructed from core single-nucleotide polymorphisms (excluding prophage regions) of emm1 non-invasive isolates collected in northwest London in 2009–16 (n=135). Background shading in grey indicates the emergent lineage M1_UK. 52 (85%) of 61 strains within the emergent lineage were isolated in either 2015 or 2016. The scale bar indicates the nucleotide substitutions per site. The black star indicates the reference strain MGAS5005. See appendix (p 3) for rooted tree with available metadata.

Figure 3

Expression of scarlet fever toxin SpeA in emergent M1_UK isolates and other emm1 isolates Phenotypic comparison of emergent M1_UK isolates with M1_global strains. (A) Quantification of absolute copy number of speA transcripts relative to house-keeping gene proS in all genome-sequenced non-invasive isolates from northwest London (n=135). Isolates were assigned to each lineage on the basis of SNPs (appendix pp 7–11). Quantification of speA transcript expression (B) and SpeA protein concentration in supernatant (C) from randomly selected M1_UK and M1_global strains lacking any mutations in covRS (n=10 per group). Median values are shown by horizontal lines in each graph. p values are from Mann-Whitney U tests. Grey squares denote strains that are intermediate members of the M1_UK lineage. SpeA=streptococcal pyrogenic exotoxin type A.

Figure 4

Prevalence of emm1 strains among invasive Streptococcus pyogenes infections nationally during scarlet fever seasons and emergence of M1_UK lineage over time (A) emm genotypes of invasive S pyogenes isolates referred to national reference laboratory per month during 2014–16. Increases in total invasive disease cases were observed locally and nationally during March to May 2016 (appendix p 2). (B) Maximum likelihood phylogenetic tree constructed from core single-nucleotide polymorphisms (excluding prophage regions) of genome-sequenced invasive emm1 S pyogenes isolates in England and Wales (n=552) between March and May each year during 2013–16. Shading in grey indicates the emergent lineage M1_UK. Clustering was not observed based on geographical origin, indicating emergence of the lineage on a national level. The black star indicates the reference strain MGAS5005. The scale bar represents the number of nucleotide substitutions per site.

Figure 5

Longitudinal (A) and geographical (B) comparison of M1_UK lineage with pandemic emm1 strains of Streptococcus pyogenes (A) Proportions of M1_UK and M1_global isolates among total sequenced invasive and non-invasive emm1 S pyogenes isolates (n=1240) annually in the UK between 2007 and 2016. (B) M1_UK lineage in a global context. Maximum likelihood phylogenetic tree constructed from core SNPs (excluding prophage regions) comparing all sequenced UK emm1 isolates with the global emm1 populations from North America, Nordic countries, and Asia (n=2800 isolates). Shading in grey indicates the emergent lineage M1_UK; orange arc indicates intermediate isolates that lie outside M1_UK but possess 13 or more of the 27 SNPs present in M1_UK, including three SNPs in rofA. UK and international emm1 isolates arise throughout the tree, but isolates within the M1_UK lineage are exclusively from the UK, except two single isolates from Denmark and the USA (arrows). The scale bar indicates the number of nucleotide substitutions per site. See appendix (p 6) for the unrooted tree. SNPs=single-nucleotide polymorphisms.