A clone of the emergent Streptococcus pyogenes emm89 clade responsible for a large outbreak in a post-surgery oncology unit in France

Presence of Group A streptococcus frequently assayed virulence genes in invasive disease: a systematic review and meta-analysis

Introduction

It is currently unclear what the role of Group A streptococcus (GAS) virulence factors (VFs) is in contributing to the invasive potential of GAS. This work investigated the evidence for the association of GAS VFs with invasive disease.

Methods

We employed a broad search strategy for studies reporting the presence of GAS VFs in invasive and non-invasive GAS disease. Data were independently extracted by two reviewers, quality assessed, and meta-analyzed using Stata®.

Results

A total of 32 studies reported on 45 putative virulence factors [invasive (n = 3,236); non-invasive (n = 5,218)], characterized by polymerase chain reaction (PCR) (n = 30) and whole-genome sequencing (WGS) (n = 2). The risk of bias was rated as low and moderate, in 23 and 9 studies, respectively. Meta-,analyses of high-quality studies (n = 23) revealed a significant association of speM [OR, 1.64 (95%CI, 1.06; 2.52)] with invasive infection. Meta-analysis of WGS studies demonstrated a significant association of hasA [OR, 1.91 (95%CI, 1.36; 2.67)] and speG [OR, 2.83 (95%CI, 1.63; 4.92)] with invasive GAS (iGAS). Meta-analysis of PCR studies indicated a significant association of speA [OR, 1.59 (95%CI, 1.10; 2.30)] and speK [OR, 2.95 (95%CI, 1.81; 4.80)] with invasive infection. A significant inverse association was observed between prtf1 [OR, 0.42 (95%CI, 0.20; 0.87)] and invasive infection.

Conclusion

This systematic review and genomic meta-analysis provides evidence of a statistically significant association with invasive infection for the hasA gene, while smeZ, ssa, pnga3, sda1, sic, and NaDase show statistically significantly inverse associations with invasive infection. SpeA, speK, and speG are associated with GAS virulence; however, it is unclear if they are markers of invasive infection. This work could possibly aid in developing preventative strategies.

Insights gained from sequencing Australian non-invasive and invasive Streptococcus pyogenes isolates

Epidemiological data have indicated that invasive infections caused by the Gram-positive cocci Streptococcus pyogenes (group A streptococcus, GAS) have increased in many Australian states over the past two decades. In July 2022, invasive GAS (iGAS) infections became nationally notifiable in Australia via public-health agencies. Surveillance for S. pyogenes infections has been sporadic within the state of New South Wales (NSW). This has led to a lack of genetic data on GAS strains in circulation, particularly for non-invasive infections, which are the leading cause of GAS's burden on the Australian healthcare system. To address this gap, we used whole-genome sequencing to analyse the genomes of 318 S. pyogenes isolates collected within two geographical regions of NSW. Invasive isolates were collected in 2007-2017, whilst non-invasive isolates were collected in 2019-2021. We found that at least 66 different emm-types were associated with clinical disease within NSW. There was no evidence of any Australian-specific clones in circulation. The M1UK variant of the emm1 global pandemic clone (M1global) has been detected in our isolates from 2013 onwards. We detected antimicrobial-resistance genes (mainly tetM, ermA or ermB genes) in less than 10 % of our 318 isolates, which were more commonly associated with non-invasive infections. Superantigen virulence gene carriage was reasonably proportionate between non-invasive and invasive infection isolates. Our study adds rich data on the genetic makeup of historical S. pyogenes infections within Australia. Ongoing surveillance of invasive and non-invasive GAS infections within NSW by whole-genome sequencing is warranted to inform on outbreaks, antimicrobial resistance and vaccine coverage.

Global genomic epidemiology of Streptococcus pyogenes

Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide causing a range of clinical manifestations in humans. Colonizing a range of ecological niches within its sole host, the human, is key to the ability of this opportunistic pathogen to cause direct and post-infectious manifestations. The expansion of genome sequencing capabilities and data availability over the last decade has led to an improved understanding of the evolutionary dynamics of this pathogen within a global framework where epidemiological relationships and evolutionary mechanisms may not be universal. This review uses the recent publication by Davies et al., 2019 as an updated global framework to address S. pyogenes population genomics, highlighting how genomics is being used to gain new insights into evolutionary processes, transmission pathways, and vaccine design.

Complete Genome Sequences of Two Strains of Streptococcus pyogenes Belonging to an Emergent Clade of the Genotype emm 89 in Brittany, France

The frequency of infections due to Streptococcus pyogenes M/emm89 strains is increasing, presumably due to the emergence of a genetically distinct clone. We sequenced two emm89 strains isolated in Brittany, France, in 2009 and 2010 from invasive and noninvasive infections, respectively. Both strains belong to a newly emerged emm89 clade 3 clone.

The frequency of infections due to Streptococcus pyogenes M/emm89 strains is increasing, presumably due to the emergence of a genetically distinct clone. We sequenced two emm89 strains isolated in Brittany, France, in 2009 and 2010 from invasive and noninvasive infections, respectively. Both strains belong to a newly emerged emm89 clade 3 clone.

Long-term, single-center surveillance of non-invasive group A streptococcal (GAS) infections, emm types and emm clusters

Group A streptococci (GAS) are among the most frequent pathogens in children. Many epidemiological studies focus on specific GAS infections (such as tonsillopharyngitis or invasive disease), on GAS carriers or on post-streptococcal sequelae. By comparison, reports on regional GAS characteristics, particularly circulating non-invasive GAS in Europe, are rare. In a monocentric study, all GAS isolated from pediatric patients at a tertiary care hospital over a 6-year period (2006-2012) were characterized. GAS emm types and clusters were determined. Associated patient data were analyzed. Five hundred sixty-six GAS strains were collected. GAS tonsillopharyngitis was most common (71.6%), followed by pyoderma (6.0%), otitis media (3.7%), perineal dermatitis (3.4%), and invasive infections (1.4%). Colonizing strains represented 13.6% of GAS. GAS emm12 was most prevalent among invasive and non-invasive isolates. Emm1, emm4, emm28, and emm89 were the most frequent non-invasive GAS strains. The emm E4 cluster was most common, followed by the A-C4, A-C3, and E1. Among the GAS infections, different emm types and clusters were identified, e.g., emm4 was more common among patients with scarlet fever. Three new emm subtypes were characterized: emm29.13, emm36.7, and emm75.5. This comprehensive review of a large, local GAS cohort points to the differences between and similarities among GAS genotypes and disease manifestations, while minimizing regional variations. Considerable deviation from previous epidemiological findings is described, especially regarding the frequent detection of emm1 and emm89 in non-invasive GAS infections. Periodic updates on molecular and epidemiological GAS characteristics are needed to track the multifaceted pathogenic potential of GAS.

A report on the first outbreak of emm89 group A streptococcus invasive infections in a burns unit in Tunisia

Four group A streptococcus (GAS) bacteraemia occurred in a small burn unit within 2 weeks. The GAS patient isolates, characterized as emm89, shared the same PFGE pulsotype with two other strains isolated 2 months later. The outbreak investigation revealed that a nurse was the most likely source of GAS transmission, as she was confirmed to carry the same outbreak strain in her throat and had direct and regular contact with the six outbreak patients in the unit. The outbreak was controlled after the nurse had undergone eradication treatment. This report highlights the emergence of the emm89 clone and its capacity to elicit invasive GAS outbreaks.