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

Characteristics of Streptococcus pyogenes causing invasive infections among adults in Portugal, 2016-2019: Pre-COVID-19 expansion of the M1UK sublineage

BACKGROUND

Genome-based epidemiological surveillance of Streptococcus pyogenes (Lancefield Group A Streptococcus, GAS) infections facilitated the detection of emergent successful lineages, such as the M1UK sublineage. This sublineage dominated the post-COVID-19 upsurge of invasive GAS infections (iGAS) in multiple countries, including Portugal. Here, we characterized the genetic lineages causing iGAS in Portugal during 2016-2019 to evaluate possible temporal trends and compare them with internationally circulating lineages.

METHODS

Whole-genome sequencing and antimicrobial susceptibility testing were performed for 273 iGAS isolates.

RESULTS

The dominant emm types were emm1 (n = 87), emm3 (n = 37), and emm89 (n = 26), collectively comprising 55 % of all isolates (n = 273). Throughout the study, the M1UK sublineage increased in prevalence, accounting for 48 % of all emm1 isolates. Core-genome multilocus sequence typing supports multiple introductions of M1UK in Portugal pre-COVID-19, and a limited relatedness to the M1UK isolates recovered during the post-COVID-19 surge in pediatric iGAS. Several internationally disseminated lineages expressing various emm types were identified. Mutations inactivating key regulators of virulence (CovRS and RopB) and in the capsule locus were found in a significant fraction of isolates. Macrolide resistance was primarily associated with the erm(A) and erm(B) genes and remained low (4 %), highlighting differences between Europe and North America.

CONCLUSIONS

Despite adult iGAS in Portugal being caused by geographically widespread, successful GAS lineages that may be repeatedly introduced in the country, including M1UK, there was no apparent increase in disease. This is consistent with upsurges of iGAS post-COVID-19 not being driven primarily by the emergence or introduction of novel GAS clones.

Changes in Epidemiology in Pediatric Invasive Group A Streptococcal Infections in Ireland During the 2022-2023 Outbreak

BACKGROUND

From October 2022 to June 2023, there was a 4-fold increase in pediatric invasive group A streptococcus cases (iGAS) in the Republic of Ireland. This project aimed to better understand the clinical characteristics and disease course of iGAS in children in Ireland to inform Public Health interventions and messaging for carers, clinicians and the public.

METHODS

All cases of iGAS notified to Public Health under 16 years from October 2022 to June 2023 inclusive were collated. A clinical case review of every death and hospitalization was performed under the auspices of the National Incident Management team using an online questionnaire. Analysis was performed using a 2-sided Fischer's exact test and 1-way analysis of variance.

RESULTS

Of 180 cases of iGAS in children, 167 had clinical data collected; 33 of 49 with skin and soft tissue infection had active varicella, and 69 of 167 had at least 1 respiratory viral coinfection. Seventy-four of 167 required therapeutic procedural intervention, and 34 of 167 required pediatric intensive care unit admission. Ten of 12 patients who died had necrotizing pneumonia, and 8 had an out-of-hospital cardiac arrest. Compared with historical data, significant changes in iGAS epidemiology in children were seen, with an increase in respiratory diagnoses, a decrease in musculoskeletal disease and an increased need for procedural intervention.

CONCLUSIONS

The rapidity and severity of secondary deterioration and death in children with iGAS highlight the importance of sepsis awareness in primary and secondary care. The high prevalence of viral coinfection emphasizes the importance of current vaccine uptake and expansion of the national schedule to include varicella zoster virus.

National 10-year Cohort Study of Life-threatening Invasive Group A Streptococcal Infection in Children, 2013-2023

BACKGROUND

Invasive group A streptococcal disease (iGAS) is an important cause of pediatric morbidity and mortality. We aimed to describe severe, life-threatening, iGAS cases to inform critical care services planning and identify potential opportunities for early intervention to prevent progression to death.

METHODS

Retrospective, multicenter, national cohort study in Scotland investigating critically unwell iGAS cases ≤15 years old from October 01, 2013 to September 30, 2023. We included children and young people (CYP) who required advanced intensive care or died with iGAS as the primary cause of death. Information collected included demographics, Streptococcus pyogenes emm types, viral coinfections and clinical outcomes.

RESULTS

Eighty-two cases of severe, life-threatening iGAS were identified, with 20 resulting in death. The annual iGAS pediatric intensive care unit (PICU) admission rate was 0.69/100,000 CYP, with a mean annual mortality rate of 0.22/100,000. iGAS PICU admissions dropped during 2020-2021, returned to baseline in 2021-2022, and then increased sharply in 2022-2023 without an increase in death rates. Across the cohort, the predominant emm type was type 1. In 9.8% of cases, GAS was identified using a nonculture molecular method (specific polymerase chain reaction or 16S rRNA sequencing). Prior primary or secondary care contact was sought by 9/20 (45%) of CYP who died; there was no significant association between time-to-care to PICU and illness severity or risk of death. Viral coinfections were common and associated with higher severity scores.

CONCLUSION

We demonstrate a significant annual burden of severe, life-threatening iGAS at the national level. High rates of viral coinfections and care-seeking before PICU admission or death, suggest potential opportunities for intervention.

Low GAS Carriage in School-Aged Children in Western China during the National Atypical Scarlet Fever Resurgence: Insights from Two Cross-Sectional Studies

INTRODUCTION

This study examined group A streptococcus(GAS) carriage, emm types, and antibiotic susceptibility in children (6-13 years) in Aral, China, during the post-COVID-19 scarlet fever resurgence, providing regional insights.

METHODS

The prevalence of GAS carriage was assessed in 1,835 children aged 6-13 years across two surveys at an Aral school in China during the post-COVID-19 resurgence of scarlet fever. GAS isolates were analyzed for emm types, M1UK lineage, and antimicrobial susceptibility using culture, PCR, sequencing, and automated methods.

RESULTS

The first survey (885 children) showed a 1.9% isolation rate, highest in 9-year-olds (4.8%) and slightly higher in boys (2.3% vs. 1.5%, P > 0.05). The second survey (950 children) reported a 3.1% rate, peaking at 10 years (6.7%) and also higher in boys (3.5% vs. 2.6%, P > 0.05). Colonization rates were similar overall (P > 0.05), but increased significantly in children aged ≥10 years (1.1% to 3.3%, P = 0.038). No children tested positive for GAS in both sampling rounds, which meant that the two surveys identified distinct host populations colonized by the bacteria. Emm12 prevalence decreased from 76.5% to 55.2% (P > 0.05), while emm1 increased from 11.8% to 31.0% (P > 0.05), with no M1UK lineage detected. All isolates were sensitive to penicillin, linezolid, vancomycin, and levofloxacin. Among 33 co-resistant isolates, emm12 accounted for 84.8% and emm1 for 15.2%.

CONCLUSION

Despite low GAS carriage rates, variations in age distribution and emm types suggest increased bacterial activity, warranting ongoing monitoring for GAS-related diseases.

Post-pandemic upsurge in Group A Streptococcus infections at an Italian tertiary university hospital

Streptococcus pyogenes (Group A Streptococcus; GAS) is a pathogen of global significance. In the pre-antibiotic era, GAS was a major cause of childhood morbidity and mortality, but its spread rapidly declined until the mid-2010s. The continuing increase in GAS infections, associated with the expansion of the M1UK lineage, was observed first in the United Kingdom (UK) and, later, globally. Here, we endeavor to assess the various determinants underlying the post-pandemic GAS upsurge, with a focus on microbial genomic features. We performed an epidemiological analysis of all laboratory-confirmed GAS infections identified between June 2018 and June 2024 at a tertiary University Hospital located in Northern Italy, dividing them into three levels of severity: mild, moderate, and invasive GAS infections. A subset of 34 representative GAS isolates identified in the post-pandemic period were subjected to short- and long-read whole genome sequencing (WGS). Of the 531 GAS cases analyzed during this period, the majority (415, 78.2%) occurred in the last two years. This increase in GAS cases correlated with a significant shift in infection severity: among the 118 GAS cases identified in the June 2018-May 2022 period, only one resulted in an invasive infection (1/118, 0.8%). In contrast, among the 531 GAS cases identified in the June 2022-May 2024 period, 32 caused invasive infections (32/531, 7.9%). WGS of 34 isolates (including 15 invasive isolates) identified 11 different emm types, the most frequent being emm1 (9 isolates) followed by emm12 (7 isolates), then emm89 and emm28 (4 isolates each). Among the emm1 isolates, the M1UK sublineage was the most represented (8 out of 9 isolates), with the remaining "singleton" belonging to the M113SNP sublineage.

IMPORTANCE

Streptococcus pyogenes (GAS) is a narrow-spectrum pathogen, circulating only in humans. Following the loosening of various public health measures implemented to face the challenge of the COVID-19 pandemic, a significant rise in GAS cases has been observed. Our study revealed a significant rise in GAS cases, particularly invasive infections, over the last two years. Genomic analysis identified multiple sequence types, including isolates belonging to an emerging lineage named M1UK. These findings underscore the importance of ongoing surveillance and genomic monitoring of GAS infections, especially considering their rising incidence and severity. Public health strategies should consider not only microbe-associated aspects but also host-associated and external factors to effectively address this resurgence and prevent future outbreaks.

Epidemiological and genomic characterisation of an outbreak of Streptococcus pyogenes emm5.23

OBJECTIVES

This retrospective cross-sectional study examined the epidemiology, clinical presentations, and genomics of Streptococcus pyogenes genotype emm5.23, linked to severe outcomes in Scotland.

METHODS

Between 2014 and 2022, 58 cases of invasive Group A Streptococcus (iGAS) disease associated with emm5.23 were reported in Scotland. Surveillance data from 45 cases were analysed for clinical characteristics and risk factors. Whole-genome sequencing (WGS) included all available emm5.23 strains from Scotland (n=58), a subset from England (n=29), and emm5 strains of non-5.23 subtypes from Scotland (n=10), England (n=2), and Canada (n=1).

RESULTS

Nearly all cases (96%, 43/45) were hospitalised, of whom 33% (15/45) required intensive care and 20% (9/45) died with iGAS. The most common presentations were bacteraemia (51%, 23/45) and pneumonia (24%, 11/45). WGS identified an emerging emm5.23 clade in Scotland, encompassing most isolates, which shared highly similar genomes and three non-synonymous polymorphisms.

CONCLUSIONS

Although genomic traits known to increase GAS virulence potential were not found, polymorphisms that may affect the emm5.23 phenotype were detected. This suggests this emm5.23 genotype was transiently successful rather than hypervirulent, with low population-level immunity contributing to its spread. This study emphasises the need for integration of real-time genomic data in public health surveillance to enhance source attribution and guide interventions.

GAS-J, a User-Friendly Browser Application for Genome Assembly, emm-Typing, MLST Typing, and Virulence Factor Gene Detection of Streptococcus pyogenes

Clinical isolates of Streptococcus pyogenes are usually classified using emm and multilocus sequence typing (MLST). Recently, whole genome sequencing (WGS) has been employed for emm typing and MLST analysis. WGS data provides additional information on the presence of virulence factor genes. To enable researchers unfamiliar with bioinformatics to analyze WGS data of S. pyogenes, we opened an online tool named GAS-J, which automatically outputs emm types, sequence types (STs), carriage of virulence factor genes, and phylogenetic trees. The tool accepts raw short-read data as inputs, since it includes the velvet assembler. In all isolates, the emm typing results from this tool were identical to those obtained by conventional PCR and Sanger sequencing, even in cases where isolates had pseudo-emm (emm-like) genes. STs are determined by performing a BLAST search using seven alleles as references. To detect S. pyogenes virulence factor genes, we prepared a new data set containing 620 related proteins. Users may choose which isolates to include in SNP-based phylogenetic tree from a pool of 406 isolates with epidemiological data. The data set includes isolates whose symptoms (STSS or non-STSS) were diagnosed based on the STSS criteria of the Japan Communicable Disease Prevention Law. GAS-J application is available at http://gasj.ncgm.go.jp. The data of isolates are going to be updated in the future.

Group A Streptococcus vaccine Development: An Indian public health imperative

BACKGROUND

Group A Streptococcus (GAS) is a significant pathogen responsible for a wide range of diseases, including severe complications such as Rheumatic Heart Disease (RHD), which predominantly affect low- and middle-income countries (LMICs) like India. GAS infections impact over 800 million individuals annually, resulting in approximately 639,000 deaths due to RHD complications. Despite significant advancements, developing an effective GAS vaccine has faced several challenges, including the complexity of GAS virulence mechanisms, the diversity of emm types, and the lack of suitable preclinical models. Recent vaccine research has focused on both M protein-based and non-M protein-based vaccines, with several candidates showing promising results. However, current vaccines only address 50 % of the prevalent emm types in India, highlighting the need for further research and development.

OBJECTIVE

This review aims to examine the historical and current progress in GAS vaccine development, identify key challenges, and explore future strategies, with a focus on the Indian public health context.

CONTENT

A comprehensive review of existing literature on GAS and its complications was conducted, focusing on the global and Indian burden of GAS infections, the resurgence of scarlet fever, and the emergence of virulent strains such as M1UK. The study also reviewed recent global initiatives like the Cairo Accord and the 71st World Health Assembly's resolution on RHD to emphasize the need for international collaboration in vaccine development. Continued global cooperation, intensified research efforts, and targeted public health initiatives are essential for overcoming the challenges in GAS vaccine development. Advocacy and investment in this area are crucial for reducing the global burden of GAS infections and their associated complications. This study aims to provide comprehensive genomic data on GAS isolates from India, enabling comparisons with global findings, highlighting regional differences, and contributing to a more comprehensive understanding of GAS epidemiology and pathogenicity.

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study

BACKGROUND

Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of S pyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity.

METHODS

In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive S pyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from five hospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream S pyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity.

FINDINGS

We identified 500 cases of invasive S pyogenes infection in patients in the Top End and 495 cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5·97 (95% CI 4·61-7·73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5·41, 4·28-6·89). The odds of in-hospital mortality (OR 0·43, 95% CI 0·26-0·70), 30-day mortality (0·38, 0·23-0·63), and ICU admission (0·42, 0·30-0·59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 S pyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hyperendemic Top End. Using a lower transmission rate, larger population size, and lower levels of migration similar to those of communities in urbanised southeast Australia, the transmission model qualitatively reproduced a pattern of dominant lineages that cycled in frequency. Despite distinct circulating lineages, the prevalence of accessory genes in the bacterial population was maintained across geographies and temporal periods.

INTERPRETATION

In a hyperendemic setting, the replacement of distinct S pyogenes lineages occurred in waves, which could be linked to the disproportionate burden of disease and sparse human population in this setting. The maintenance of bacterial gene frequency could be consistent with multilocus selection. These findings suggest that lineage-specific interventions-such as vaccines under development-should consider disease setting and, without broad cross-protection, might lead to lineage replacement.

FUNDING

National Health and Medical Research Council, and Leducq Foundation.

Comparison of pharyngeal and invasive isolates of Streptococcus pyogenes by whole-genome sequencing in Toronto, Canada

Invasive Group A streptococcal (iGAS) infections are rising in Canada and wordwide. The 2022-2023 Ontario iGAS season was among the highest recorded, a trend continuing in 2023-2024. We sequenced 38 invasive (blood) and 117 non-invasive (pharyngeal) Streptococcus pyogenes clinical isolates from Toronto (January-May 2023) to compare between the two cohorts and against published sequences to determine if any genomic changes accounted for the trend. Results demonstrated limited clustering with one small totally invasive cluster (emm49) with both invasive and non-invasive isolates represented across a diverse set of lineages. Non-invasive isolates were predominantly emm12 (70.1%), whereas invasive isolates included emm12 (26.32%), emm49 (23.68%), and emm1 (13.16%) with most emm1 strains containing the 27 SNPs that define the hypervirulent M1UK clone (58.33%). Although there were no differences in the presence of overall virulence factors/adhesin genes between cohorts, there were statistically more superantigen and DNase genes in non-invasive isolates and a rare phage gene was significantly associated with invasiveness across three emm-types. The prevalence of individual virulence factor/adhesin genes also differed between our cohorts, including a higher likelihood of speA, enn, mrp, ideS/Mac, fbaA, and fbaB in invasive isolates. There were also no significant differences across the 11 antimicrobial resistance genes identified. Finally, pharyngeal isolates had larger hydrolysis and hemolysis zones, and covS deletions were observed in only seven invasive strains. Despite there being no genetic signature that differentiated our isolates, we observed several features that were predominant in invasive strains which provides further insights into the factors that contribute to GAS invasiveness.IMPORTANCEIncreasing rates of invasive Group A streptococcal (iGAS) infections are being seen both in Canada and worldwide, which is leading to a greater disease burden caused by this pathogen. Leveraging whole-genome sequencing gives us an opportunity to better understand the underlying genetic mechanisms of streptococcal disease. By utilizing this technique, we shed light on the circulating invasive and non-invasive strains of Streptococcus pyogenes in the largest urban area in Canada from January to May 2023. GAS strains causing non-invasive disease were found to have a higher abundance of superantigen and DNase genes, whereas invasive isolates were more likely to contain M-like protein genes, the superantigen speA, the protease ideS/Mac, and/or the fibronectin-binding proteins fbaA and fbaB. This work provides valuable insights into iGAS disease which will help with surveillance, epidemiology as well as developing treatment and preventative modalities to help curb the disease burden caused by this globally important pathogen.

Emerging Trends in Streptococcal Toxic Shock Syndrome, Japan

Japan experienced substantial increases in streptococcal toxic shock syndrome and group A Streptococcus pharyngitis after relaxing COVID-19 restrictions in May 2023. Increased detection of the M1UK lineage of Streptococcus pyogenes, especially in the vicinity of Tokyo, emphasizes the need to raise awareness of disease characteristics and epidemiologic trends.

Invasive Group A Streptococcal Infection in Children, 1992-2023

Importance

The resurgence of invasive group A streptococcal (iGAS) infections and progress in GAS vaccine development emphasize the importance of understanding current trends in the epidemiology of iGAS.

Objective

To describe the epidemiology of pediatric iGAS over a 32-year period.

Design, Setting, and Participants

This case series uses population-based surveillance data for iGAS in Toronto and Peel Region, Canada, including emm typing from Canada's National Microbiology Laboratory and population data from Statistics Canada. All children (age <18 years) with iGAS from January 1, 1992, to December 31, 2023, were included. Data were analyzed from July 15, 2023, to September 1, 2024.

Main Outcomes and Measures

Outcomes of interest were disease incidence over time and by age; variation in clinical presentation, disease severity, outcomes and infecting emm types; and antimicrobial resistance.

Results

Overall, 498 iGAS cases (300 [60.2%] male; median [IQR] age, 5.1 [2.7-8.6] years) occurred, including 151 (30.7%) in children with comorbidities. The most common presentations were soft tissue infection (140 cases [28.1%]) and bacteremia without focus (131 cases [26.3%]). iGAS incidence increased from 1.8 events per 100 000 population per year in 1992 to 2011 to 2.4 events per 100 000 population per year in 2012 to 2019 (incidence rate ratio, 1.3 [95% CI, 1.1-1.6]), with the increase occurring in GAS infections of the respiratory tract. Incidence declined to 1.2 events per 100 000 population per year in 2020 and 0.5 events per 100 000 population per year in 2021 before increasing to 6.0 events per 100 000 population per year in 2023. In 2022 to 2023, 18 of 56 children with iGAS (32.0%) had a viral respiratory coinfection. Varicella-associated iGAS cases declined from 23 of 137 children (16.8%) in 1992 to 2001 to 2 of 223 children (0.9%) in 2012 to 2023 (P < .001), after routine varicella vaccination implementation in 2004. Streptococcal toxic shock syndrome occurred in 29 children (5.8%), necrotizing fasciitis in 12 children (2.4%); 10 children (2.0%) died. The most common emm types were emm1 (182 of 471 isolates [38.6%]), emm12 (75 isolates [15.9%]), and emm4 (31 isolates [6.6%]). The M1UK subtype was first identified in 2019 and comprised 32 of 46 emm1 isolates (70.0%) from 2019 to 2023. Compared with other emm types, emm1 was more likely to be associated with pneumonia (odds ratio [OR], 1.99 [95% CI, 1.16-3.40]), bone and joint infections (OR, 1.70 [95% CI, 1.08-2.68]), and intensive care unit admission (OR, 1.67 [95% CI, 1.03-2.68]); emm4 was more likely to be associated with bacteremia without focus (OR, 6.10 [95% CI, 2.83-13.16]). Overall, 437 isolates (92.8%) were of emm types included in the 30-valent GAS vaccine.

Conclusions and Relevance

This case series found that pediatric iGAS incidence increased in south-central Ontario prior to and after the COVID-19 pandemic in association with increased iGAS infections of the respiratory tract. Respiratory viral coinfections were common. Different emm types were associated with differing presentations and severity.

Streptococcus pyogenes bloodstream infections in an Italian hospital: A ten-year genomic picture

BACKGROUND

During 2022 and 2023, a large upsurge of cases of Group A Streptococcus (GAS) infection has struck many countries worldwide. This large epidemic event was caused by a diminished level of immunity after COVID-19 social restrictions and was fostered mainly by the emm1 genotype of the bacterium.

METHODS

We characterized the genomes of the GAS isolates that caused bloodstream infections in the last ten years in a 900-bed hospital in Northern Italy. We obtained short-read genomes, which we used for emm typing and to analyze the antimicrobial resistance and virulence gene content. Moreover, we contextualized the isolates in an epidemiological point of view using both ortholog-based and SNP-based phylogeny.

RESULTS

In the last ten years, we registered two upsurges of GAS cases in the study hospital: one in 2023 (in line with the global epidemiological situation), and one in 2016 (local, but observed also in another recent Italian study). The genomic analysis of the bloodstream infection isolates showed the circulation of multiple emm types, of which emm1, emm12, and emm4 characterized the two large epidemic events. Notably, the 2016 peak was mainly fostered by the M1Global and emm4 genotypes, in contrast with the rise of M1UK observed in the UK in the pre-pandemic years. Phylogeny analysis showed the presence of multiple monophyla of local strains. Despite our genomes being obtained from blood-culture isolates, we did not observe any increased presence of virulence or antimicrobial resistance genes.

CONCLUSIONS

Our results further confirm the role of emm1 as the most prevalent genotype worldwide. However, we also unveiled the central role of genotype emm4 in the 2016 epidemic event, described in the study hospital. Finally, our results suggest the presence of multiple locally persistent strains. Among these, we underlined the presence of a multi-drug resistant strain of emm92.

A Striking Increase in Carriage Among Young Children in Iceland Paralleled the Unprecedented Increase of Invasive Group A Streptococcal Infection From 2022 to 2023

BACKGROUND

An unprecedented increase in pediatric invasive group A streptococcal (iGAS) infections was observed in most countries, including Iceland, in early 2023. The reasons for this rise are largely unknown. The aim of the study was to describe the parallel between nasopharyngeal (NP) carriage of group A streptococcal (GAS) in Icelandic children and the incidence of invasive disease.

METHODS

Electronic health records were used to identify children admitted to the Children's Hospital, Iceland, with iGAS. NP samples from asymptomatic children were collected for culture in February and March 2023 in 15 day-care centers in the greater Reykjavik area. Invasive and noninvasive isolates were characterized using whole genome sequencing. The results of the NP carriage were compared with data from 2009 to 2020.

RESULTS

Twenty-one children were diagnosed with iGAS from December 2022 to April 2023. Empyema, necrotizing fasciitis and septic or toxic shock were the most common clinical presentations. All the children were hospitalized; none died, but 9 needed intensive care. Pediatric iGAS infections increased 8-fold from a mean of 2.0/100.000 for 1975 to 2022 to 16.5/100.000 in early 2023. Asymptomatic NP GAS carriage among healthy children increased 3.5-fold from 8.0% from 2009 to 2020 to 28.5% in early 2023. Close genetic relatedness was found between carriage and invasive strains.

CONCLUSIONS

The significant rise of NP GAS carriage observed in early 2023 likely contributed to the simultaneous increased incidence of iGAS. With surveillance data, microbiological culture and molecular typing, genetic similarities between invasive disease isolates and NP isolates characteristics were confirmed.

A Rapid Molecular Detection Tool for Toxigenic M1UK Streptococcus pyogenes

BACKGROUND

The gradual replacement of the Streptococcus pyogenes M1global genotype by a newly emergent M1UK variant is a global public health threat warranting increased surveillance. M1UK differs from progenitor M1global genotype by 27 single-nucleotide polymorphisms and is characterized by increased speA superantigen expression in vitro.

METHODS

An allele-specific real-time polymerase chain reaction assay was developed for the rapid detection of M1UK strains. The assay was used in combination with whole genome sequencing to determine emm (sub)type distribution for 51 invasive (n = 9) and noninvasive (n = 42) S pyogenes clinical isolates.

RESULTS

Emm1 was the most prevalent S pyogenes emm serotype (n = 11) in this set of clinical isolates, with M1UK being the dominant emm1 genotype (4/5 invasive, 3/6 noninvasive isolates). The assay accurately detected M1UK strains. Whole genome sequencing revealed continued presence of Australian M1UK sublineages associated with epidemic scarlet fever-causing S pyogenes in Asia.

CONCLUSIONS

Our study establishes a suitable target for detection of the toxigenic M1UK and confirms the maintenance of M1UK strains in Queensland, Australia. This assay can be deployed in laboratories and provides a valuable, cost-effective tool to enhance surveillance of the expanding M1UK clone.

Characterization of a novel covS SNP identified in Australian group A Streptococcus isolates derived from the M1UK lineage

Group A Streptococcus (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1UK lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections. However, the basis for its evolutionary success is not yet fully understood. During the transition to systemic disease, the M1 serotype is known to give rise to spontaneous mutations in the control of virulence two-component regulatory system (CovRS) that confer a fitness advantage during invasive infections. Mutations that inactivate CovS function result in the de-repression of key GAS virulence factors such as streptolysin O (SLO), a pore-forming toxin and major trigger of inflammasome/interleukin-1β-dependent inflammation. Conversely, expression of the streptococcal cysteine protease SpeB, which is required during initial stages of colonization and onset of invasive disease, is typically lost in such mutants. In this study, we identified and characterized a novel covS single nucleotide polymorphism detected in three separate invasive M1UK isolates. The resulting CovSAla318Val mutation caused a significant upregulation of SLO resulting in increased inflammasome activation in human THP-1 macrophages, indicating an enhanced inflammatory potential. Surprisingly, SpeB production was unaffected. Site-directed mutagenesis was performed to assess the impact of this mutation on virulence and global gene expression. We found that the CovSAla318Val mutation led to subtle, virulence-specific changes of the CovRS regulon compared to previously characterized covS mutations, highlighting an unappreciated level of complexity in CovRS-dependent gene regulation. Continued longitudinal surveillance is warranted to determine whether this novel covS mutation will expand in the M1UK lineage.IMPORTANCEThe M1UK lineage of GAS has contributed to a recent global upsurge in scarlet fever and invasive infections. Understanding how GAS can become more virulent is critical for infection control and identifying new treatment approaches. The two-component CovRS system, comprising the sensor kinase CovS and transcription factor CovR, is a central regulator of GAS virulence genes. In the M1 serotype, covRS mutations are associated with an invasive phenotype. Such mutations have not been fully characterized in the M1UK lineage. This study identified a novel covS mutation in invasive Australian M1UK isolates that resulted in a more nuanced virulence gene regulation compared to previously characterized covS mutations. A representative isolate displayed upregulated SLO production and triggered amplified interleukin-1β secretion in infected human macrophages, indicating an enhanced inflammatory potential. These findings underscore the need for comprehensive analyses of covRS mutants to fully elucidate their contribution to M1UK virulence and persistence.

Streptococcus pyogenes emm Type 3.93 Emergence, the Netherlands and England

A global increase in the incidence of invasive group A Streptococcus (iGAS) infections was observed after lifting of COVID-19 related restrictions in 2022, and type M1UK dominated in many countries. After seasonal declines in iGAS incidence during the summer of 2023, simultaneous, rapid expansion of a previously rare emm type 3.93 was seen beginning in November, increasing to 20% of all cases in England and 60% of all cases in the Netherlands within 4 months. emm3.93 was associated with iGAS in children 6-17 years of age and with increased risk for pneumonia or pleural empyema and meningitis in both countries. No excess risk of death was identified for emm3.93 compared with other types. Genomic analysis of historic and contemporary emm3.93 isolates revealed the emergence of 3 new clades with a potentially advantageous genomic configuration. Our findings demonstrate the value of molecular surveillance, including long-read sequencing, in identifying clinical and public health threats.

Trends in the growing impact of group A Streptococcus infection on public health after COVID-19 pandemic: a multicentral observational study in Okayama, Japan

PURPOSE

Following the COVID-19 pandemic, group A Streptococcus (GAS) infection has been surging worldwide. We aimed to compare the disease burden between notified cases of streptococcal toxic shock syndrome (STSS) and unreported GAS infections.

METHODS

This is a multicentral observational study, retrospectively performed at seven hospitals in Okayama prefecture in Japan from January 2022, to June 2024. Clinical and microbiological data of patients with positive cultures of GAS were collected from the medical records. Primary outcomes were defined as rates of surgical procedures, intensive care unit (ICU) admission, and in-hospital mortality, which were compared among patients with locally-defined STSS, invasive GAS (iGAS), and non-iGAS infection.

RESULTS

GAS was detected in 181 patients, with 154 active cases of GAS infection. The number of patients with GAS infection surged in late 2023. The most common source of infection was skin and soft tissue infections, accounting for 83 cases, including 15 cases of necrotizing fasciitis, and 12 cases (7.8%) were notified to public health authorities as STSS. Among the 25 unreported iGAS cases, 9 (36.0%) underwent surgical intervention, and 4 patients (16.0%) required ICU admission. The mortality rates in the unreported iGAS cases were comparable to those observed in the notified STSS.

CONCLUSIONS

We highlighted that the number of iGAS infections was twofold higher than that of notified STSS, with comparable mortality rate between these groups, indicating substantial underestimation of the true burden of iGAS. This epidemiological investigation has significant implications for enhancing infectious disease surveillance frameworks and public health policy development.

Clinical and microbiological characterization of invasive group a Streptococcus infection in children in Japan: A single-center experience

BACKGROUND

Invasive group A Streptococcus (iGAS) infections are rare but potentially fatal. Although the number of invasive group A Streptococcus (iGAS) infections decreased during the coronavirus disease (COVID-19) pandemic, it sharply increased worldwide following the pandemic due to the emergence of M1UK strains. In Japan, non-fluminant iGAS infections have not been included in the national survey notification system. Therefore, the clinical and microbiological characteristics of iGAS infection are unknown. In this study, we aimed to clarify the clinical and microbiological characteristics of pediatric iGAS infections.

METHODS

We conducted a case-series analysis of children aged 0-15 years with positive Streptococcus pyogenes cultures from otherwise sterile sites, diagnosed between July 2018 and June 2024. Clinical data were extracted from the electronic medical records. Samples of clinical isolates were sent to the Public Health Research Institute for further analysis.

RESULTS

We identified 11 patients (median age, 5 years [interquartile range 1-8.5 years]; 6 girls). The incidence rate of the iGAS infections was highest in 2024, with 3 cases in 6 months. Primary bacteremia without focal infection was the predominant diagnosis, followed by skin and soft tissue infections with bacteremia. Among the 11 iGAS infections, 9 isolates were available for additional microbiological tests. M12 and M1 strains were predominant (four cases each). Three of the four M1 isolates were M1UK strains.

CONCLUSIONS

In the present study, the increasing incidence of iGAS infection and clinical diagnoses are similar to those reported in other countries; however, M12 strains as well as M1 strains are predominant.

Recombinant production platform for Group A Streptococcus glycoconjugate vaccines

Group A Streptococcus (Strep A) is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydrate biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins within Escherichia coli cells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.

Characterization of Streptococcus pyogenes Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023-FIRST Detection of M1UK in Bulgaria

Recently a resurgence of Streptococcus pyogenes infections has arisen, with concerns around the highly virulent M1UK lineage. Our aim was to characterize S. pyogenes, the immune responses it causes, and to determine the presence of the M1UK lineage in Sofia, Bulgaria. In our study, the infections were confirmed by culture testing or rapid antigen test. Identification was performed by MALDI-TOF and was followed up by antibiotic susceptibility testing (EUCAST). Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. Out of 82 children, 38 had scarlet fever and the rest had streptococcal pharyngitis. Strains were susceptible to penicillin (β-lactams), macrolides, clindamycin, tetracyclines, co-trimoxazole, fluoroquinolones, and linezolid. Superantigen profiles were identified: SpeA + SpeJ (45%), SpeC, and SpeI + SpeH (27.5% each). A novel Multilocus sequence typing (MLST) haplotype in the mutS gene (d90b) was found in four strains. The M1UK lineage was detected for the first time in Bulgaria. We observed an increase in complement fractions C3 and C4 and a decrease in T lymphocytes. A significant increase in the levels of IFN-γ, IL-6, and IL-10 with corresponding reduction in IL-17A were revealed. In conclusion, the studied S. pyogenes strains were characterized by their susceptibility to antibiotics and the predominance of SpeA superantigen; for the first time in Bulgaria the presence of M1UK and a novel SNP variation in the mutS gene (d90b) were found. A mixed pattern of pro- and anti-inflammatory immune responses in patients was observed.

Genomic epidemiology of invasive Group A Streptococcus infections in Argentina, 2023: high prevalence of emm1-global and detection of emm1 hypervirulent lineages

The aim of this study is to describe the genomic epidemiology of invasive Group A Streptococcus (iGAS) in Argentina during 2023. A total of 476 invasive GAS isolates were subtyped and analyzed by whole-genome sequencing. A high prevalence of the emm1-type strain was observed. Among the emm1 strains, two highly virulent international variants, emm1-UK and emm1-DK, were identified. Additionally, a local variant, called emm1-ST1319, was detected. This seminal study provides initial insights into the genomic landscape of iGAS, contributing to active surveillance to monitor emerging virulent emm1 lineages and cross-border transmission in South America.IMPORTANCEAmid the increase in invasive Streptococcus pyogenes infections in Argentina in 2023, the implementation of genomic analysis of isolates allowed us to detect at the national level the prevalence of the emm1 type and within the M1 type, emerging national and international hypervirulent lineages. These findings from our report shed light on the distribution of invasive Group A Streptococcus, laying the foundation for genomic surveillance of this pathogen.

Streptococcal Toxic Shock Syndrome Due to Invasive Group A Streptococcal M1UK Strain Infection in a Previously Healthy Child

Invasive group A streptococcal (iGAS) infections are known to be potentially life-threatening. Few detailed pediatric cases of streptococcal toxic shock syndrome (STSS) caused by iGAS with the M1UK strain have been reported. This report describes the case of a child with STSS due to M1UK strain, with detailed documentation of the treatment progress. A 10-year-old female patient without predisposing factors associated with iGAS, initially presented with pneumonia and developed progressive multi-organ failure. A precise diagnosis by the primary hospital's attending physician and effective critical care in the pediatric intensive care unit (PICU) at a tertiary children's hospital led to lifesaving and favorable functional outcomes. The clinical course highlights the importance of recognizing the common presentation of iGAS and prompt medical coordination between general hospitals and PICU. Furthermore, public health measures against iGAS infection are just as important as early diagnosis and treatment to prevent deaths in the community after rapid deterioration.

Group A streptococcal infections in Alberta, Canada 2018-2023

Group A streptococcal or Streptococcus pyogenes infections have been increasing post-COVID-19 pandemic. We describe the epidemiology of S. pyogenes pharyngitis and invasive disease in Alberta, Canada 2018-2023. Positive pharyngitis specimens were identified from throat swabs collected from pharyngitis patients. Invasive S. pyogenes was defined as the isolation of S. pyogenes from a normally sterile site or severe skin infection. S. pyogenes isolates were emm typed. Pharyngitis and invasive disease displayed seasonal trends preceding the COVID-19 pandemic followed by a sharp decrease during COVID-19 intervention measures. After the lifting of interventions, rates of pharyngitis and invasive disease rose. There were 182 983 positive pharyngitis specimens between 2018 and 2023 for a positivity rate of 17.6%. The highest rates occurred in the 0-9 age group in 2023 (41.5%). Invasive disease increased in 2022-2023 driven by emm1 and 12 types. M1UK strain was the most frequent M1 type associated with invasive disease (59% of M1 isolates sequenced). Notably, out of 182 983 pharyngitis cases, there were 111 cases of invasive S. pyogenes detected for an invasive disease rate of 0.06%. This descriptive epidemiology of S. pyogenes pharyngitis and invasive S. pyogenes disease highlights the rapid increase in cases of S. pyogenes occurring in western Canada and illustrates the critical need for a vaccine.

The intricate pathogenicity of Group A Streptococcus: A comprehensive update

Group A Streptococcus (GAS) is a versatile pathogen that targets human lymphoid, decidual, skin, and soft tissues. Recent advancements have shed light on its airborne transmission, lymphatic spread, and interactions with neuronal systems. GAS promotes severe inflammation through mechanisms involving inflammasomes, IL-1β, and T-cell hyperactivation. Additionally, it secretes factors that directly induce skin necrosis via Gasdermin activation and sustains survival and replication in human blood through sophisticated immune evasion strategies. These include lysis of erythrocytes, using red cell membranes for camouflage, resisting antimicrobial peptides, evading phagocytosis, escaping from neutrophil extracellular traps (NETs), inactivating chemokines, and cleaving targeted antibodies. GAS also employs molecular mimicry to traverse connective tissues undetected and exploits the host's fibrinolytic system, which contributes to its stealth and potential for causing autoimmune conditions after repeated infections. Secreted toxins disrupt host cell membranes, enhancing intracellular survival and directly activating nociceptor neurons to induce pain. Remarkably, GAS possesses mechanisms for precise genome editing to defend against phages, and its fibrinolytic capabilities have found applications in medicine. Immune responses to GAS are paradoxical: robust responses to its virulence factors correlate with more severe disease, whereas recurrent infections often show diminished immune reactions. This review focuses on the multifaceted virulence of GAS and introduces novel concepts in understanding its pathogenicity.

Chains of misery: surging invasive group A streptococcal disease

PURPOSE OF REVIEW

We describe the epidemiology of the recent global surge in invasive group A streptococcal (GAS) disease and consider its proximate and distal causes. We highlight important knowledge gaps regarding clinical management and discuss potential strategies for prevention.

RECENT FINDINGS

Rates of invasive GAS (iGAS) disease were increasing globally prior to the COVID-19 pandemic. Since mid-2022, following the worst years of the pandemic in 2020 and 2021, many countries with systems to monitor GAS syndromes have reported surges in cases of iGAS concurrent with increased scarlet fever, pharyngitis, and viral co-infections. The emergence of the hypervirulent M1 UK strain as a cause of iGAS, particularly in high income countries, is concerning. New data are emerging on the transmission dynamics of GAS. GAS remains universally susceptible to penicillin but there are increasing reports of macrolide and lincosamide resistance, particularly in invasive isolates, with uncertain clinical consequences. Intravenous immunoglobulin is used widely for streptococcal toxic shock syndrome and necrotizing soft tissue infections, although there is limited clinical evidence, and none from a completed randomized controlled trial. Intensive and expensive efforts at population-level control of GAS infections and postinfectious autoimmune complications have been only partially successful. The great hope for control of GAS diseases remains vaccine development. However, all modern vaccine candidates remain in the early development stage.

SUMMARY

In many countries, iGAS rates surged from mid-2022 in the aftermath of pandemic control measures and physical distancing. The emergence of a dominant hypervirulent strain is an important but incomplete explanation for this phenomenon. Clinical management of iGAS remains highly empirical and new data has not emerged. A vaccine remains the most likely means of achieving a sustainable reduction in the burden of iGAS.

Streptococcus pyogenes M1UK Variant-Associated Sartorius Muscle Necrotizing Soft Tissue Infection: A Case Report and Literature Review

Necrotizing soft tissue infections (NTSIs) represent a concept of necrotizing infections involving the skin, subcutaneous tissue, fascia, and muscle, and it is a potentially fatal disease. Early exploratory incision is strongly recommended for both the diagnosis and treatment of necrotizing soft tissue infections. Treatment of necrotizing soft tissue infections requires the administration of appropriate antimicrobial agents and adequate surgical debridement. The emergence of M1UK-lineage Streptococcus pyogenes (S. pyogenes) is recently reported in the UK, Canada, the USA, and the Netherlands. We report a Japanese case of sartorius muscle (SM) NTSI caused by M1UK-lineage S. pyogenes. A 34-year-old man developed redness and swelling of his right thigh anterior compartment with fever in October 2024. The closed and deep effusions by active exploratory incision/debridement on hospital days one to three yielded the presence of Gram-positive cocci, although two sets of blood cultures upon admission revealed no bacterial growth; its species identification results indicated S. pyogenes. Clinical and pathological diagnosis was streptococcal SM NTSI (without toxic shock syndrome (TSS)). Negative pressure wound therapy with instillation and dwelling (NPWTi-d) to promote his soft tissue cure was performed along with antimicrobial regimens. The patient recovered and received micrografting (carrier: artificial dermis made from collagen sponge and silicon film, Pelnac Gplus® (Gunze Limited, Osaka, Japan) using the Rigenera® system (Rignera HBW, Candiolo, Italy). Thereafter, he developed bronchitis: the sputum yielded S. pyogenes growth: he recovered uneventfully. Split-thickness skin grafting (STG) was performed. Split-thickness skin grafting was fully engrafted, and the wounds achieved complete healing. The patient could walk by himself. Microbiological genetic analyses using both DNAs from effusion/sputum-origin strains revealed the emm1.0 and speA-speB-smeZ profiles. rofA-gldA-pstB sequencing results indicated M1UK-specific single-nucleotide polymorphisms. The streptococcal inhibitor of the complement-mediated lysis gene allele was the streptococcal inhibitor of the complement-mediated lysis-1.02 allele. Micrografting using the Rigenera® system and STG following NPWTi-d can be beneficial approaches. Clinicians should perform cultures using sterile specimens (deep effusions/tissues) from infection foci through exploratory incision/debridement, along with two sets of blood cultures, when examining patients with/without underlying medical conditions.

First Evidence of Streptococcus pyogenes M1 UK Clone in Pediatric Invasive Infections in Italy by Molecular Surveillance

Invasive group A streptococci infections are increasing worldwide, mainly due to the emm1 lineage M1 UK emergence. Although this variant has recently been described in adult Italian patients, its circulation in children has not yet been established. Characterizing by whole genome sequencing 6 invasive group A streptococci strains isolated between 2022 and 2023, we highlighted M1 UK lineage circulation in pediatric patients in Italy.

COVID-19 complicated with severe M1UK-lineage Streptococcus pyogenes infection in elderly patients: A report of two cases

Case 1: A 71-year-old man was admitted to our hospital with progressive fever and dyspnea, which had developed three days after the onset of COVID-19. Initial chest computed tomography (CT) revealed a pulmonary lesion consistent with a secondary bacterial infection. Streptococcus pyogenes was isolated from cultures of primary sputum collected from the endotracheal tube, and identified as the causative microorganism. Case 2: A 91-year-old man was transferred to our hospital with severe hypotension, which had developed nine days after the onset of COVID-19. A chest CT revealed pericardial effusion and pericardiocentesis yielded purulent fluid. S. pyogenes was isolated from the fluid specimens and was identified as the causative microorganism of the secondary bacterial pericarditis. Isolates from both patients were subsequently identified as M1UK-lineage S. pyogenes via genetic analysis. This report implicates COVID-19 as a potential risk factor for severe M1UK infection via the respiratory tract.

Invasive Group A Streptococcus Hypervirulent M1UK Clone, Canada, 2018-2023

To determine invasive group A Streptococcus trends in Canada, we characterized emm1 isolates collected during 2018-2023. The percentage of hypervirulent M1UK lineage isolates increased significantly, from 22.1% in 2018 to 60.2% in 2023. Genomic analysis identified geographically and temporally associated clusters and genes associated with virulent bacteriophage acquisition.

Nosocomial Transmission of Necrotizing Fasciitis: A Molecular Characterization of Group A Streptococcal DNases in Clinical Virulence

Streptococcus pyogenes, or Group A Streptococcus (GAS), is responsible for over 500,000 deaths per year. Approximately 15% of these deaths are caused by necrotizing soft-tissue infections. In 2008, we isolated an M5 GAS, named the LO1 strain, responsible for the nosocomial transmission of necrotizing fasciitis between a baby and a nurse in Belgium. To understand this unusual transmission route, the LO1 strain was sequenced. A comparison of the LO1 genome and transcriptome with the reference M5 Manfredo strain was conducted. We found that the major differences were the presence of an additional DNase and a Tn916-like transposon in the LO1 and other invasive M5 genomes. RNA-seq analysis showed that genes present on the transposon were barely expressed. In contrast, the DNases presented different expression profiles depending on the tested conditions. We generated knock-out mutants in the LO1 background and characterized their virulence phenotype. We also determined their nuclease activity on different substrates. We found that DNases are dispensable for biofilm formation and adhesion to both keratinocytes and pharyngeal cells. Three of these were found to be essential for blood survival; Spd4 and Sdn are implicated in phagocytosis resistance, and Spd1 is responsible for neutrophil extracellular trap (NET) degradation.

Post-COVID-19-pandemic changes and clinical characteristics of invasive group a streptococcal infections from 2015 to 2023

PURPOSE

Since winter 2022, invasive GAS (iGAS) infections have re-emerged in Europe, causing severe diseases in children and adults. We aimed to examine whether this reported post-pandemic increase was associated with an increased disease severity and/or a shift in clinical disease phenotypes.

METHODS

We performed detailed clinical phenotyping of patients hospitalized with iGAS infections at a 1410-bed tertiary German Medical Center from 01/2015 to 09/2023.

RESULTS

One hundred seventy-eight patients were included: 50 children (28.1%) and 128 adults (71.9%). IGAS infections of Q1/2023 exceeded the pre-pandemic average by 551% (1200% for children). The mean age of affected patients shifted significantly post-pandemically (49.5 ± 26.5 to 32.4 ± 28.2 years of age, p < 0.05), mainly due to the higher percentage of children affected with iGAS infections (15.2% pre-pandemic, 44.2% post-pandemic). CFR was significantly lower for children (2%) compared to adults (11.7%) (p < 0.05) and decreased from 13% to 6.5% post-pandemically (p = 0.148). Duration of antibiotic therapy (13.5 (10 to 21) to 10 (9 to 14) days), length of hospital (10 (4 to 25) to 7 (5 to 15) days), and ICU stay (7.0 (2.5 to 18.0) to 5.0 (3.0 to 8.5) days) were shorter post-pandemically. Despite the higher post-pandemic percentage of affected children, PICU admissions (57% before to 32% after), use of catecholamines (28.6% to 11.8%), invasive ventilation (35.7% to 17.6%) and CFR (7% to 0%) were all lower after the pandemic.

CONCLUSION

Children were at higher risk for iGAS infections post-pandemically. The surge of post-pandemic iGAS infections was not accompanied by increased iGAS-associated morbidity and mortality.

Nationwide upsurge in invasive disease in the context of longitudinal surveillance of carriage and invasive Streptococcus pyogenes 2009-2023, the Netherlands: a molecular epidemiological study

Since 2022, many countries have reported an upsurge in invasive group A streptococcal (iGAS) infections. We explored whether changes in Streptococcus pyogenes carriage rates or emergence of strains with potentially altered virulence, such as emm1 variants M1UK and M1DK, contributed to the 2022/2023 surge in the Netherlands. We determined emm (sub)type distribution for 2,698 invasive and 351 S. pyogenes carriage isolates collected between January 2009 and March 2023. Genetic evolution of emm1 was analyzed by whole-genome sequencing of 497 emm1 isolates. The nationwide iGAS upsurge coincided with a sharp increase of emm1.0 from 18% (18/100) of invasive isolates in Q1 2022 to 58% (388/670) in Q1 2023 (Fisher's exact test, P < 0.0001). M1UK became dominant among invasive emm1 isolates in 2016 and further expanded from 72% in Q1 2022 to 96% in Q1 2023. Phylogenetic comparison revealed evolution and clonal expansion of four new M1UK clades in 2022/2023. DNase Spd1 and superantigen SpeC were acquired in 9% (46/497) of emm1 isolates. S. pyogenes carriage rates and emm1 proportions in carriage isolates remained stable during this surge, and the expansion of M1UK in iGAS was not reflected in carriage isolates. During the 2022/2023 iGAS surge in the Netherlands, expansion of four new M1UK clades was observed among invasive isolates, but not carriage isolates, suggesting increased virulence and fitness of M1UK compared to contemporary M1 strains. The emergence of more virulent clades has important implications for public health strategies such as antibiotic prophylaxis for close contacts of iGAS patients.IMPORTANCEThis study describes the molecular epidemiology of invasive group A streptococcal (iGAS) infections in the Netherlands based on >3,000 Streptococcus pyogenes isolates from both asymptomatic carriers and iGAS patients collected before, during, and after the COVID-19 pandemic period (2009-2023) and is the first to assess whether changes in carriage rates or carried emm types contributed to the alarming post-COVID-19 upsurge in iGAS infections. We show that the 2022/2023 iGAS surge coincided with a sharp increase of emm1, particularly the toxicogenic M1UK variant, in invasive isolates, but not in carriage isolates. These findings suggest that increased virulence and fitness of M1UK likely contributes to an increased dissemination between hosts. The emergence of a more virulent and fit lineage has important implications for iGAS control interventions such as antibiotic prophylaxis for close contacts of iGAS patients and calls for a reappraisal of iGAS control interventions and guidelines.

Invasive Group A Streptococcal Infections in Europe After the COVID-19 Pandemic

BACKGROUND

The incidence of airborne respiratory infections fell as a result of the protective measures taken during the COVID-19 pandemic and rose again when these were stopped. In 2022, there was a notable rise in invasive group A streptococcal (iGAS) infections in many countries, including Germany. This rise was also reflected in the data of the university otorhinolaryngology department in Ulm, Germany.

METHODS

This review is based on publications retrieved by a selective literature search on the rise of iGAS infections in Europe, with particular attention to the timing of disease onset, clinical presentation, pathogenic strains, and potential causes and risk factors.

RESULTS

The rise in infections after the pandemic was especially marked among children up to age 10 and in older adults; in Germany, it affected all age groups equally, but predominantly persons older than 65. Rising prevalence figures were seen in Germany and elsewhere as early as the fall of 2022, outside the usual season, and peaked mainly in the first and second quarters of 2023. The increased incidence of iGAS-associated pneumonia was paralleled by that of viral airway infections and led to greater use of intensivecare measures for children. The main bacterial strain identified was emm1; a new variant (M1DK) played a role in Denmark, and an emm4 variant (M4NL22) became increasingly important in the Netherlands. In Germany, initial evidence suggested the predominance of M1UK. Increased antibiotic resistance was not found.

CONCLUSION

The reduced confrontation of the immune system with pathogens during the pandemic, along with the increased incidence of viral airway infections immediately after it, apparently accounted for the exceptionally high post-pandemic rise in iGAS infections and the increase in invasive pulmonary diseases in Europe. Consistent vaccination programs against coincident respiratory viruses could reduce the burden of iGAS infections. The further extension of multinational surveillance programs with obligatory participation could aid in the detection of factors affecting the course of disease and the spread of new bacterial strains.

Epidemiology of scarlet fever in Victoria, Australia, 2007-2017

In the last 10-15 years, there has been a global resurgence of scarlet fever, an infection historically associated with significant morbidity and mortality. It is unknown whether scarlet fever incidence has increased in Australia. We aimed to examine the incidence, predictors and severity of scarlet fever in the state of Victoria, Australia from 2007 to 2017, analyzing scarlet fever emergency department (ED) presentations, hospitalizations and deaths. Of the 1 578 scarlet fever cases during the study period, most occurred in children aged <10 years (1 344, 85%), in males (882, 56%), and during winter and spring months (918, 57%). There were no deaths with scarlet fever, however, 374 cases (24%) were admitted to hospital. The annual incidence of scarlet fever was stable during the study period (mean, 2.5; range, 1.9-3.1 cases per 100 000). Annual incidence was highest in children aged <5 years (19.3 per 100 000), and was 21% higher in males than females, adjusting for age and year (incidence rate ratio, 1.21, 95%CI 1.09-1.34). Whilst scarlet fever ED presentations and hospitalizations were stable in Victoria from 2007 to 2017, the recent identification of a Streptococcus pyogenes variant in Australia associated with epidemic scarlet fever overseas highlights the risk of future outbreaks.

Complicated pneumonia caused by group A Streptococcus in children - 2022/2023 infectious season outbreak and update on clinical characteristics

BACKGROUND

An increased incidence of group A Streptococcus (GAS) infections has been observed in pediatric population post-COVID-19 pandemic. While the majority of reports refer to scarlet fever or invasive GAS disease, detailed data on pulmonary manifestations such as complicated community-acquired pneumonia (CAP) are scarce. The aim of this study was to assess the contribution of GAS to complicated CAP in children during the 2022/2023 infectious season.

METHODS

We retrospectively analyzed the etiology and clinical presentation of complicated CAP patients hospitalized in our tertiary care center in Warsaw, Poland, between August 2022 and May 2023.

RESULTS

Among 91 patients with complicated CAP, GAS was the dominant cause constituting 24.2% (22/91; 95% CI 15.8-34.3%) of the study group. 68.2% of GAS pneumonia patients presented symptoms of scarlet fever, and 27.3% had preceding or concurrent viral infection. GAS complicated CAP was associated with longer hospitalization, higher incidence of chest tube insertion, but shorter duration of chest tube drainage than complicated CAP of other etiology. Children with GAS complicated CAP had higher procalcitonin concentration (28.1 vs. 1.5 ng/dL; p<0.0001) and a lower platelets level (254.5 vs. 422 × 103/μL; p = 0.0031) than those with non-GAS infection.

CONCLUSIONS

GAS is currently the predominant pathogen of complicated CAP in children. Clinicians should be aware of the current epidemiological situation and a more severe course of GAS pneumonia in this age group, and should monitor patients presenting with symptoms of scarlet fever and preceding viral infection closely.

Attribution of invasive group A streptococcal infections (iGAS) to predisposing viral infections, the Netherlands, 2010 to 2023

BackgroundAfter most COVID-19 pandemic control measures were lifted in 2022, many infectious diseases re-emerged. An increase in invasive group A streptococcal (iGAS) infections among adults and young children was reported by several countries. Viral infections including influenza and varicella, known risk factors for iGAS infection, also increased.AimTo estimate the proportion of GAS skin and soft tissue infections (SSTI) and pneumonia/sepsis in children (≤ 5 years) attributable to varicella, and the proportion of GAS pneumonia/sepsis in children and adults attributable to potentially predisposing respiratory viruses influenza A and B, RSV, hMPV and SARS-CoV-2 in the Netherlands.MethodsWe performed time series regression using weekly data on respiratory viruses, varicella and non-invasive GAS infections and GAS isolates cultured from blood, lower airways, skin, pus and wounds, from January 2010 to March 2023.ResultsIn 2010-19, 50% (95% CI: 36-64) of GAS SSTI in children were attributable to varicella. Between January 2022 and March 2023, 34% (95% CI: 24-43) of GAS SSTI cases were attributable to varicella. Of iGAS pneumonia/sepsis between January 2022 and March 2023, 34% (95% CI: 20-49) and 25% (95% CI: 18-32) was attributable to respiratory virus infections in children and adults, respectively, with the largest contributor (17%) being influenza A.ConclusionsPredisposing viral infections likely contributed to, but cannot fully explain, the observed iGAS increase among children and adults in 2022-23 in the Netherlands. Public health measures to control viral infections, such as vaccination against varicella or influenza, might reduce the iGAS disease burden.

Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes

SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.

Divergent effects of emm types 1 and 12 on invasive group A streptococcal infections-results of a retrospective cohort study, Germany 2023

As a potential side effect of the severe acute respiratory syndrome coronavirus type 2 pandemic, invasive group A Streptococcus (iGAS) infections in Europe have increased dramatically in both children and adults in the end of 2022. This epidemiological and molecular study describes the distributions of streptococcal genes encoding the M antigen (emm types) and superantigens in patients with invasive and non-invasive GAS infections. From December 2022 to December 2023, a total of 163 GAS isolates were collected from sterile and non-sterile sites of patients at five hospitals in Germany including two tertiary care centers. Genes encoding M protein and superantigens were determined following the guidelines of CDC Streptococcus laboratory. Patients' characteristics were reviewed retrospectively. Correlations of clinical factors, emm types, and superantigens with rates of invasive infections were analyzed. Of the 163 included GAS cases, 112 (69%) were considered as invasive. In total, 33 different emm types were observed, of which emm1.0 (n = 49; 30%), emm89.0 (n = 15; 9%), and emm12.0 (n = 14; 9%) were most prevalent. In total, 70% of emm1.0 isolates belonged to M1UK lineage. No difference in invasive infections was observed for the M1UK lineage compared with other emm1.0 isolates. However, the emm1.0 type, presence of speA1-3, speG, or speJ, as well as adulthood were significantly associated with invasive infections. In contrast, emm12.0 isolates were significantly less associated with invasive infections. Multivariable analysis confirmed a significant influence of speJ and adulthood on iGAS infections. This study underlines the importance of continuous monitoring of genomic trends and identification of emerging GAS variants. This may aid in delineating pathogenicity factors of Streptococcus pyogenes that propel invasive infections.

Molecular characterization of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022-2023 UK upsurge

At the end of 2022 into early 2023, the UK Health Security Agency reported unusually high levels of scarlet fever and invasive disease caused by Streptococcus pyogenes (StrepA or group A Streptococcus). During this time, we collected and genome-sequenced 341 non-invasive throat and skin S. pyogenes isolates identified during routine clinical diagnostic testing in Sheffield, a large UK city. We compared the data with that obtained from a similar collection of 165 isolates from 2016 to 2017. Numbers of throat-associated isolates collected peaked in early December 2022, reflecting the national scarlet fever upsurge, while skin infections peaked later in December. The most common emm-types in 2022-2023 were emm1 (28.7 %), emm12 (24.9 %) and emm22 (7.7 %) in throat and emm1 (22 %), emm12 (10 %), emm76 (18 %) and emm49 (7 %) in skin. While all emm1 isolates were the M1UK lineage, the comparison with 2016-2017 revealed diverse lineages in other emm-types, including emm12, and emergent lineages within other types including a new acapsular emm75 lineage, demonstrating that the upsurge was not completely driven by a single genotype. The analysis of the capsule locus predicted that only 51 % of throat isolates would produce capsule compared with 78% of skin isolates. Ninety per cent of throat isolates were also predicted to have high NADase and streptolysin O (SLO) expression, based on the promoter sequence, compared with only 56% of skin isolates. Our study has highlighted the value in analysis of non-invasive isolates to characterize tissue tropisms, as well as changing strain diversity and emerging genomic features which may have implications for spillover into invasive disease and future S. pyogenes upsurges.

The Emergence and Impact of the M1UK Lineage on Invasive Group A Streptococcus Disease in Aotearoa New Zealand

M1UK is associated with current surges in invasive infection globally, partly due to increased production of superantigen streptococcal pyrogenic exotoxin A. We show that M1UK is now the dominant invasive emm1 lineage in Aotearoa New Zealand and is genomically related to community infections, suggesting that measures that effectively prevent group A Streptococcus pharyngitis in children could reduce invasive disease.

Local Genomic Surveillance of Invasive Streptococcus pyogenes in Eastern North Carolina (ENC) in 2022-2023

The recent increase in Group A Streptococcus (GAS) incidences in several countries across Europe and some areas of the Unites States (U.S.) has raised concerns. To understand GAS diversity and prevalence, we conducted a local genomic surveillance in Eastern North Carolina (ENC) in 2022-2023 with 95 isolates and compared its results to those of the existing national genomic surveillance in the U.S. in 2015-2021 with 13,064 isolates. We observed their epidemiological changes before and during the COVID-19 pandemic and detected a unique sub-lineage in ENC among the most common invasive GAS strain, ST28/emm1. We further discovered a multiple-copy insertion sequence, ISLgar5, in ST399/emm77 and its single-copy variants in some other GAS strains. We discovered ISLgar5 was linked to a Tn5801-like tetM-carrying integrative and conjugative element, and its copy number was associated with an ermT-carrying pRW35-like plasmid. The dynamic insertions of ISLgar5 may play a vital role in genome fitness and adaptation, driving GAS evolution relevant to antimicrobial resistance and potentially GAS virulence.

Emergent emm4 group A Streptococcus evidences a survival strategy during interaction with immune effector cells

The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence among emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. By creating and analyzing isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates than the historic strains. Via the creation of isogenic mutant strains, we linked the emergent strain "survival" phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found a high ratio of mucosal (i.e., pharyngeal) relative to invasive infections among emm4 GAS. Since ever-increasing virulence is unlikely to be evolutionarily advantageous for a microbial pathogen, our data further understanding of the well-described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a "survival" strategy to outcompete previously circulating isolates.

Genomic epidemiology of Streptococcus pyogenes from pharyngeal and skin swabs in Gabon

The disease burden of Streptococcus pyogenes is particularly high in low- and middle-income countries. However, data on the molecular epidemiology of S. pyogenes in such regions, especially sub-Saharan Africa, are scarce. To address this, whole-genome sequencing (WGS) of S. pyogenes from Gabon was performed to identify transmission clusters and provide valuable genomic data for public repositories. A total of 76 S. pyogenes isolates from 73 patients, collected between September 2012 and January 2013, were characterized by short-read whole-genome sequencing. The predominant emm types were emm58.0, emm81.2 and emm223.0 with 9.2% (7 of 76), 7.9% (6 of 76), and 6.6% (5 of 76), respectively. Single-nucleotide polymorphism analysis revealed 16 putative transmission clusters. Four of these were household transmissions. Four antimicrobial genes (lmrP, tetM, tetL, and thfT) were found in the S. pyogenes isolates from this study. All strains carried lmrP. Of the 76 isolates, 64 (84.2%) carried at least one tetracycline resistance gene (tetM or tetL). Comparisons with other publicly available African genomic data revealed a significant correlation between geographical location and genetic diversity of S. pyogenes, with Gabonese strains showing similarities to those from Kenya and certain Oceanian regions. Our study showed that transmission of S. pyogenes can occur at the community/household level and that high-resolution molecular typing is needed to monitor changes in circulating clones and to detect community outbreaks. Advocacy for the adoption of WGS for comprehensive molecular characterization of S. pyogenes and data sharing through public repositories should be encouraged to understand the molecular epidemiology and evolutionary trajectory of S. pyogenes in sub-Saharan Africa.

IMPORTANCE

The study conducted in Gabon underscores the critical importance of addressing the limited knowledge of the molecular epidemiology of Streptococcus pyogenes in low- and middle-income countries, particularly sub-Saharan Africa. Our molecular analysis identified predominant emm types and unveiled 16 putative transmission clusters, four involving household transmissions. Furthermore, the study revealed a correlation between geographical location and genetic diversity, emphasizing the necessity for a comprehensive understanding of the molecular epidemiology and evolutionary trajectory of S. pyogenes in various regions. The call for advocacy in adopting whole-genome sequencing for molecular characterization and data sharing through public repositories is crucial for advancing our knowledge and implementing effective strategies to combat the spread of S. pyogenes in sub-Saharan Africa.

Novel insights into the immune response to bacterial T cell superantigens

Bacterial T cell superantigens (SAgs) are a family of microbial exotoxins that function to activate large numbers of T cells simultaneously. SAgs activate T cells by direct binding and crosslinking of the lateral regions of MHC class II molecules on antigen-presenting cells with T cell receptors (TCRs) on T cells; these interactions alter the normal TCR-peptide-MHC class II architecture to activate T cells in a manner that is independent of the antigen specificity of the TCR. SAgs have well-recognized, central roles in human diseases such as toxic shock syndrome and scarlet fever through their quantitative effects on the T cell response; in addition, numerous other consequences of SAg-driven T cell activation are now being recognized, including direct roles in the pathogenesis of endocarditis, bloodstream infections, skin disease and pharyngitis. In this Review, we summarize the expanding family of bacterial SAgs and how these toxins can engage highly diverse adaptive immune receptors. We highlight recent findings regarding how SAg-driven manipulation of the adaptive immune response may operate in multiple human diseases, as well as contributing to the biology and life cycle of SAg-producing bacterial pathogens.

M1UKStreptococcus pyogenes causing community-acquired pneumonia, pleural empyema and streptococcal toxic shock syndrome

OBJECTIVES

Streptococcus pyogenes causes superficial infections but can also cause deep-seated infections and toxin-mediated diseases. In the present study, phylogenetic and in silico prediction analyses were performed on an antimicrobial resistant M1UKS. pyogenes strain causing severe clinical manifestations during the current surge of invasive group A Streptococcus (iGAS) disease.

METHODS

A 40-year-old patient was admitted to the hospital with fever, chest pain and fatigue. Based on the clinical and laboratory findings, a diagnosis of sepsis with disseminated intravascular coagulation, community-acquired pneumonia, pleural empyema and streptococcal toxic shock syndrome was made. Microbial identification was performed by multiplex PCR and conventional culturing. Furthermore, antimicrobial susceptibility testing, whole genome sequencing, phylogenomic analysis and in silico prediction analysis of antimicrobial resistance genes and virulence factors were performed.

RESULTS

S. pyogenes isolates were detected in pleural fluid and sputum of the patient. Both isolates belonged to the M1UK lineage of the emm1/ST28 clone, being closely related with an M1UK GAS strain from Australia. They exhibited resistance to erythromycin and clindamycin and susceptibility-increased exposure to levofloxacin and carried genes encoding for protein homologues of antibiotic efflux pumps. Moreover, several virulence factors, and a previously described single-nucleotide polymorphism in the 5' transcriptional leader sequence of the ssrA gene, which enhances expression of SpeA, were detected.

CONCLUSIONS

The present antimicrobial-resistant M1UKS. pyogenes strain represents the first report of this emerging lineage associated with such manifestations of iGAS disease.