Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011-23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study.

2025-10-07

Xie, Ouli

Featherstone, Leo

Nguyen, An N T

Hayes, Andrew

Pitt, Miranda

Spring, Stephanie

Liu, Alice

Tonkin-Hill, Gerry

Dotel, Ravindra

Joshi Rai, Neela

Rofe, Alexander

Duchêne, Sebastian

Holt, Deborah

Judd, Louise

Coin, Lachlan

Krause, Vicki

O'Sullivan, Matthew

Baird, Robert

Bond, Katherine

Howden, Benjamin

Korman, Tony

Currie, Bart

Davies, Mark

Tong, Steven

Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia.

Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia; Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia.

Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.

Department of Infectious Diseases, Blacktown Hospital, Sydney, NSW, Australia.

Department of Infectious Diseases, Westmead Hospital, Sydney, NSW, Australia.

Victorian Infectious Diseases Service, The Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology, The Royal Melbourne Hospital, Melbourne, VIC, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Computational Biology, Institut Pasteur, Paris, France.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Faculty of Health, Charles Darwin University, Darwin, NT, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Northern Territory Centre for Disease Control, Northern Territory Department of Health, Darwin, NT, Australia.

Department of Infectious Diseases, Westmead Hospital, Sydney, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; NSW Health Pathology, Westmead Hospital, Sydney, NSW, Australia.

Territory Pathology, Northern Territory Department of Health, Royal Darwin Hospital, Darwin, NT, Australia.

Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology, The Royal Melbourne Hospital, Melbourne, VIC, Australia.

Centre for Pathogen Genomics, The University of Melbourne, Melbourne, VIC, Australia; Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases & Immunology, Austin Health, Melbourne, VIC, Australia.

Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia; Centre for Inflammatory Diseases, Monash University, Melbourne, VIC, Australia.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia.

Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.

Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Service, The Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia. Electronic address: steven.tong@unimelb.edu.au.

Journal Article

Publication

Streptococcus dysgalactiae subspecies equisimilis (SDSE) is closely related to Streptococcus pyogenes, with overlapping disease manifestations. We compared the clinical and genomic epidemiology of invasive SDSE with invasive S pyogenes across different settings in Australia and phylogenetically contextualised the SDSE sequences within a global cohort of genomes.In this retrospective clinical and genomic epidemiology study, cases of invasive SDSE isolated from normally sterile sites were identified and whole-genome sequenced across five hospital networks in temperate southeast Australia (Melbourne and Sydney) and the tropical Top End of the Northern Territory. SDSE disease incidence, case demographics, clinical outcomes, and longitudinal lineage dynamics were compared between southeast Australia and the Top End and to co-collected invasive S pyogenes cases in each region. SDSE genomes and lineages were also contextualised within 1166 global SDSE sequences. Genomic transmission clusters (not necessarily direct transmission) were inferred between isolates from different individuals by single-linkage clustering at a single nucleotide polymorphism threshold of less than or equal to seven for SDSE and less than or equal to five for S pyogenes based on previous transmission analyses.Between Jan 1, 2011, and Feb 28, 2023, there were 693 invasive SDSE cases and 995 invasive S pyogenes cases. Invasive SDSE occurred almost exclusively in adults. The overall invasive SDSE incidence in southeast Australia was similar to invasive S pyogenes (incidence rate ratio [IRR] 1·15, 95% CI 0·91-1·46; p=0·26) and increased over the study period (IRR 1·06 per year, 95% CI 1·05-1·08; p<0·0001) from 1·30 cases per 10 000 admissions in 2011 to 3·72 cases per 10 000 admissions in the first 2 months of 2023 (95% CI 2·13-6·07). In southeast Australia, where stringent COVID-19 non-pharmaceutical interventions (NPIs) were implemented between 2020 and 2021, the SDSE incidence plateaued during 2020-21 but did not significantly decline (IRR 1·09 compared with 2017-19, 95% CI 0·88-1·35; p=0·47). By contrast, S pyogenes incidence substantially declined in 2020-21 in southeast Australia (IRR 0·35 compared to 2017-19, 95% CI 0·22-0·52; p=0·017). In the Top End, SDSE incidence was lower than S pyogenes (IRR 0·24, 95% CI 0·19-0·31; p<0·0001). However, crude incidence remained higher than southeast Australia (crude IRR 1·24, 95% CI 1·07-1·42; p=0·0037) and disproportionately affected First Nations Australians in the Top End compared with non-First Nations individuals (IRR 3·36, 95% CI 2·33-4·85; p<0·0001). Comparing 2020-21 with 2017-19, there was no decline in SDSE (IRR 1·27, 95% CI 0·73-2·24; p=0·45) or S pyogenes (IRR 0·97, 95% CI 0·80-1·18; p=0·81) incidence in the Top End, which did not implement prolonged stringent COVID-19 NPIs. Analysing the available genomes of invasive cases and in lineages for which more than or equal to five invasive cases occurred, only 24 (6%) of 384 SDSE cases were assigned to genomic transmission clusters, compared with 271 (52%) of 524 S pyogenes cases. An stG62647 lineage encompassed 113 (26%) of 436 sequenced SDSE genomes. Analysis of available SDSE sequences from Australia, western Europe, and North America inferred concurrent international expansion of the stG62647 lineage in all three regions between 1990 and 2005.We identified a substantial burden of invasive SDSE, dominated by the emergent stG62647 lineage. The contrasting epidemiology between species in the different Australian regions, during COVID-19 NPIs, and genomic infection patterns indicates transmission dynamic, pathogen population, and host-pathogen interaction differences between SDSE and S pyogenes and indicates implications for disease control measures.Australian National Health and Medical Research Council.

link

Lancet Microbe . 2025 Oct;6(10):101182. doi: 10.1016/j.lanmic.2025.101182. Epub 2025 Oct 7.

2666-5247

https://pubmed.ncbi.nlm.nih.gov/41072459/?otool=iaurydwlib