Increase in bloodstream infections caused by emm1 group A Streptococcus correlates with emergence of toxigenic M1UK, Belgium, May 2022 to August 2023

Many European countries have recently reported upsurges in invasive group A Streptococcus (iGAS) infections, mainly caused by emm1 Streptococcus pyogenes, specifically the toxigenic M1UK lineage. We present the epidemiology of emm1 causing iGAS in Belgium during 2018–August 2023, and describe an emergence of the toxigenic M1UK lineage in Belgium in mid-2022 that was observed as an increase in bloodstream infections caused by emm1 S. pyogenes that continued into 2023.

Many European countries have recently reported upsurges in invasive group A Streptococcus (iGAS) infections, mainly caused by emm1 Streptococcus pyogenes, specifically the toxigenic M1 UK lineage.We present the epidemiology of emm1 causing iGAS in Belgium during 2018-August 2023, and describe an emergence of the toxigenic M1 UK lineage in Belgium in mid-2022 that was observed as an increase in bloodstream infections caused by emm1 S. pyogenes that continued into 2023.
Since mid-2022, invasive group A Streptococcus (iGAS) infections caused by Streptococcus pyogenes harbouring emm1, which encodes the M1 protein, have been increasingly reported across different European countries [1][2][3][4].Specifically, this increase seems to be related to an increase in the proportion of the toxigenic M1 UK lineage [5] compared to the original M1 global lineage [6,7].The M1 UK lineage differs from the original by 27 defining single nucleotide polymorphisms (SNPs), which leads to an increased expression of the superantigen gene speA [8].Since June 2023, another M1 sublineage was reported from Denmark (M1 DK ), which is characterised by the presence of speC and 15 defining SNPs [4].In Belgium, a remarkable increase in iGAS infections was also observed from mid-2022, mostly caused by emm1 S. pyogenes.Here, we present the epidemiology, genetic characteristics and associated lineages of emm1 S. pyogenes causing iGAS infections in Belgium.
The ratio of bloodstream infections (BSI) and non-BSI remained fairly constant, with BSI comprising 74−82% of the iGAS infections from 2018−23 (Figure 1B).However, the proportion of BSIs caused by emm1 S. pyogenes, which was 26−28% in 2018−19, dropped to 9%−14% during the COVID-19 pandemic (2020-21).In 2022, the proportion increased to 35%, and in 2023 constituted almost 50% of all BSIs in Belgium (p ≤ 0.0105 when comparing 2023 with the other years, Fisher's exact test, Figure 1C).Patients with BSIs included those where emm1 S. pyogenes was isolated from blood cultures, or those with a primary differential diagnosis of septicaemia or meningitis, with or without other conditions, where emm1 S. pyogenes was isolated from another sample type, e.g.cerebrospinal fluid, pleural fluid.
Remarkably, BSI isolates constituted 73% (109/149) of the sequenced emm1 S. pyogenes in this study.The emm1-associated BSIs were detected in patients of all ages, ranging from 0−92 years.Sequencing identified the rapid increase in the proportion of the M1 UK lineage among iGAS isolates in Belgium during 2022-23 (Figure 2B and C).This toxigenic lineage was already detected in Belgium in one BSI sample as    2B and C).This lineage also constituted 72% (78/109) of the BSI-associated emm1 isolates sequenced in this study.However, disease outcomes did not vary notably between patients developing infections caused by M1 UK or M1 global .Of the 13 of 149 patients who died, eight were infected with M1 UK and were aged 7, 40, 56, 65 and over 65 (n = 4) years.Five patients who died were infected with M1 global (ages 0, 1 (n = 2), 33 and 34 years).Of these 13 patients, twelve had been diagnosed with BSI (septicaemia, with or without pneumonia, fasciitis or STSS), while one presented with pneumonia.In our dataset, neither severity of disease nor disease presentation varied between the two lineages.
Within the M1 UK isolates studied here, we identified on average 41 whole genome SNPs, indicating higher genome stability, in comparison to the M1 global isolates, which were isolated during the same timeframe, and presented on average 85 whole genome SNPs within the lineage (Figure 3).However, one M1 UK isolate presented a remarkably higher number of SNPs compared to the rest of isolates (452 whole genome SNPs on average), despite showing the same emm type and ST, and will require further investigation.Remarkably, M1 UK isolates showed on average 105 whole genome SNPs when compared to the M1 global isolates.
Most of the isolates (139/149, 93%) belonged to sequence type (ST)28, one M1 global isolate was ST785 and seven M1 UK isolates were ST1357.Screening for antimicrobial resistance genes showed that mefE, which encodes a macrolide resistance-conferring efflux pump, was present in eight isolates (seven M1 UK and one M1 global ), tetracycline resistance-encoding genes tetU and tetM were identified in four isolates (three M1 UK and one M1 global ), and one isolate (M1 UK ) presented with the aminoglycoside resistance determinant, aad [6].Although prevalence of antimicrobial resistance genes in the M1 UK lineage was rather low, this was higher than among M1 global isolates.The most commonly observed gene was mefE, as also reported in the original description of the M1 UK lineage [5].

Discussion
The increase in emm1 iGAS observed during mid-2022 until August 2023 in Belgium was primarily because of an upsurge in BSIs caused by emm1 S. pyogenes.
Remarkably, this coincided with the lifting of mandatory use of protective face masks in Belgium.Other countries have observed a similar increase in emm1 iGAS infections with different clinical presentations after the removal of COVID-19-related non-pharmaceutical protective measures.A rise in pleural empyema was reported in Scotland and England [1,13], meningitis in the Netherlands [6], and general infections in the Netherlands [2], France [3], Denmark [4] and England [7].
Our observations were similar to previous studies reporting that the M1 UK lineage does not lead to more severe infections, although the emm1 genotype itself has been linked to higher virulence and requirement for intensive care [3,4].In Belgium, the emm1-associated BSIs or those caused by the M1 UK lineage did not show a proclivity for any age group, in contrast to previous findings that M1 UK infections are more common among the paediatric population [7].The success of the M1 UK lineage has been hypothesised to be derived from the accumulation of SNPs in the genome that provide a fitness advantage in colonising the host [8], which caused this lineage to become predominant before the pandemic in the United Kingdom [5].Genome stability, measured by accumulation of new SNPs in a defined timeframe, was higher among the M1 UK isolates than the M1 global studied here.These data support the hypothesis that the SNPs accumulated by the M1 UK lineage are sufficient to provide a fitness advantage, which -coupled with a potentially lowered herd immunity to S. pyogenes because of decreased exposure during the pandemic and the increase in other respiratory viral infections -might explain the upsurge in iGAS infections reported in the 2022/23 winter season in many European countries.
Our investigation had some limitations.We studied a selection of the emm1 S. pyogenes that were all isolated from invasive infections, which did not allow a contextual analysis of other prevalent genotypes or of the prevalence of M1 UK among non-invasive GAS infections.Despite the limitations, analysis of emm1 iGAS from years both pre-and post-COVID-19 pandemic nonetheless facilitated a clear picture of emm1 iGAS dynamics in Belgium.

Conclusion
The toxigenic M1 UK lineage emerged in Belgium in mid-2022 and was observed as an increase in bloodstream infections caused by emm1 S. pyogenes that has continued until August 2023.These data call for increased vigilance and a sustained real-time monitoring of iGAS infections in Europe.

Ethical statement
Genomic and epidemiological data presented in this study were obtained as part of national surveillance efforts.

Funding statement
The Belgian Reference Centre for invasive β-haemolytic streptococci is supported by the Belgian Ministry of Social Affairs through a fund within the Health Insurance System.

License, supplementary material and copyright
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC BY 4.0) Licence.You may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made.
Any supplementary material referenced in the article can be found in the online version.This article is copyright of the authors or their affiliated institutions, 2023.

Figure 1
Figure 1 Overview of invasive group A Streptococcus infections caused by Streptococcus pyogenes, Belgium, 2018-August 2023

Figure 2
Figure 2 Distribution of emm1 invasive group A Streptococcus and bloodstream infections caused by the M1 UK lineage, Belgium, January 2018-August 2023

Figure 3
Figure 3Single nucleotide polymorphism (SNP) distance matrix representing number of whole genome SNPs between all included isolates, Belgium, Jan 2020-May 2023 (n = 149) early as January 2020.No isolate was identified that presented the 15 SNPs defining the recently described M1 DK lineage, although six (two M1 global and four M1 UK ) presented the speC superantigen gene.

Table
Number of emm1 invasive group A Streptococcus (iGAS) infections, 1 May 2022-14 August 2023 (n = 518), and number of M1 UK lineage among sequenced emm1 S. pyogenes causing iGAS infections, May 2022-May 2023 (n = 130) by age, Belgium For emm1 iGAS infections: % based on total isolates in that period.b For sex and sequenced isolates: % based on total number of isolates per age group.c Sex is unknown for one case in the > 65 age group.d For M1 isolates: % based on sequenced isolates.The dataset for lineage assignment is limited to the emm1 iGAS isolated during May 2022-May 2023 that underwent whole genome sequencing (n = 130).e For M1 UK causing BSI: % based on M1 UK causing iGAS. a