Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study

doi:10.1016/j.lanwpc.2025.101467

. 2025 Jan 29:55:101467.

doi: 10.1016/j.lanwpc.2025.101467. eCollection 2025 Feb.

Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study

Jacqueline M Morris¹, Jake A Lacey², Kerrie Stevens², Lamali Sadeesh Kumar^{1

2}, Mathilda Wilmot², Janet Strachan³, Marion Easton³, Daneeta Hennessy³, Tony M Korman⁴, Andrew J Daley^{5

6

7}, Katherine B Gibney^{8

9}, Adam W J Jenney¹⁰, Steven Y C Tong^{8

9}, Benjamin P Howden^{1

2

11

12}, Norelle L Sherry^{1

2

11}

Affiliations

¹ Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
² Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
³ Communicable Diseases, Epidemiology and Surveillance, Health Protection Branch, Department of Health Victoria, Australia.
⁴ Monash Infectious Diseases, Monash University and Monash Health, Clayton, VIC, Australia.
⁵ Department of Laboratory Services, Royal Children's Hospital, Parkville, VIC, Australia.
⁶ Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁷ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
⁸ Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
⁹ Victorian Infectious Disease Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
¹⁰ Microbiology Unit & Department of Infectious Diseases, Alfred Health, Melbourne, VIC, Australia.
¹¹ Department of Infectious Diseases & Immunology, Austin Health, Heidelberg, VIC, Australia.
¹² Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia.

PMID: 39944419
PMCID: PMC11814704
DOI: 10.1016/j.lanwpc.2025.101467

Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study

Jacqueline M Morris et al. Lancet Reg Health West Pac. 2025.

. 2025 Jan 29:55:101467.

doi: 10.1016/j.lanwpc.2025.101467. eCollection 2025 Feb.

Authors

Affiliations

¹ Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
² Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
³ Communicable Diseases, Epidemiology and Surveillance, Health Protection Branch, Department of Health Victoria, Australia.
⁴ Monash Infectious Diseases, Monash University and Monash Health, Clayton, VIC, Australia.
⁵ Department of Laboratory Services, Royal Children's Hospital, Parkville, VIC, Australia.
⁶ Murdoch Children's Research Institute, Parkville, VIC, Australia.
⁷ Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.
⁸ Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
⁹ Victorian Infectious Disease Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
¹⁰ Microbiology Unit & Department of Infectious Diseases, Alfred Health, Melbourne, VIC, Australia.
¹¹ Department of Infectious Diseases & Immunology, Austin Health, Heidelberg, VIC, Australia.
¹² Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia.

PMID: 39944419
PMCID: PMC11814704
DOI: 10.1016/j.lanwpc.2025.101467

Abstract

Background: Invasive group A Streptococcus (iGAS) cases have increased globally in 2022-2023, raising concerns within the medical and public health communities, including in Australia, while this impact is polyclonal in nature the worldwide spread and dominance of M1_UK has been particularly concerning.

Methods: To investigate these changes and prepare to implement routine genomic surveillance of iGAS for public health purposes, we performed whole genome sequencing (WGS) on iGAS isolates from Victoria, Australia between 2017 and 2022. Genomic analyses were conducted to determine the epidemiology, genetic diversity, and population dynamics of iGAS.

Findings: Analysis of 955 confirmed iGAS cases over a 6-year period revealed a polyclonal population. Fewer iGAS cases were noted between 2020 and 2021 in addition to genetic bottlenecks, likely reflecting the implementation of strict public health measures during the COVID pandemic, followed by a resurgence in cases post-COVID. Low levels of antimicrobial resistance were observed, primarily to macrolides and tetracyclines. Phylogenetic analysis identified a previously undescribed emm1 sub-lineage, designated M1_Aus, detected in Australia (Victoria and Queensland), Belgium and the United Kingdom. In Victoria, M1_Aus was the dominant emm1 variant in 2017 and 2018, more recently replaced by the M1_UK lineage as the dominant variant, further demonstrating the worldwide impact of M1_UK.

Interpretation: This comprehensive genomic study of iGAS in Victoria, Australia provides valuable insights into the population dynamics, genetic diversity, and impact of pandemic public health measures on iGAS epidemiology. The identification of the M1_Aus sub-lineage emphasises the need for continued genomic surveillance and monitoring of iGAS strains, particularly in the context of emerging global sub-lineages and shifts in population structure.

Funding: MDU PHL-Department of Health, Victoria. NHMRC (GNT1196103 to BPH; Partnership Grant GNT1149991).

Keywords: Genomic epidemiology; Invasive group A streptococcus; Streptococcal typing; Streptococcus pneumoniae.

PubMed Disclaimer

Conflict of interest statement

None.

Figures

**Fig. 1**
**The detection of Victorian iGAS isolates and impacts of public health measures implemented due to COVID-19**. Victorian iGAS isolates are plotted each month from 1st of January 2017 to the 31st of December 2022. The seventeen most common *emm* types (each with ≥10 occurrences) are coloured from most common (red) to less common (dark blue). Sixty-one less common *emm* types (with <10 occurrences), are grouped together as ‘Other’ (grey). Major public health measures implemented for both SARS-CoV-2 and iGAS are highlighted including Victorian staged restrictions (black lines), Australian border restrictions (blue lines), when iGAS became nationally notifiable (black star symbol) and when iGAS notifiable actions were implemented in Victoria (grey star symbol).

**Fig. 2**
**Victorian iGAS *emm1* diversity reveals a novel lineage M1**_Aus. A) The maximum likelihood phylogenetic relationship of the 263 Victorian iGAS isolates are compared with an additional 233 global representative isolates. Tree tips are coloured by sub-lineages; M1_UK (blue), M1_UK-inter (light blue) M1_Global (grey), M1_Aus (pink) and M1_interAus (light pink). The heat map shows the location within Australia (shades of green) vs global genomes (grey), followed by the presence of erythromycin resistance gene (*ermB*, red), superantigens *speA*, *speC* and *ssa* (orange), and streptodornase (DNAse) *spd1, spd3, spd4* and *sdaD* (purple). B) The distribution of each Victorian iGAS *emm*1 isolates is plotted, grouped by sub-lineage per month and year.

See this image and copyright information in PMC

References

1. Walker M.J., Barnett T.C., McArthur J.D., et al. Disease manifestations and pathogenic mechanisms of group A Streptococcus. Clin Microbiol Rev. 2014;27(2):264–301. - PMC - PubMed
1. Ikuta K.S., Swetschinski L.R., Robles Aguilar G., et al. Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2022;400(10369):2221–2248. - PMC - PubMed
1. Murray C.J., Ikuta K.S., Sharara F., et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629–655. - PMC - PubMed
1. Centre for Disease Control and Prevention Antibiotic resistance threats in the United States 2019. 2019. https://www.cdc.gov/DrugResistance/Biggest-Threats.html#groupa Available from:
1. Steer A.C., Lamagni T., Curtis N., Carapetis J.R. Invasive group A streptococcal disease: epidemiology, pathogenesis and management. Drugs. 2012;72(9):1213. - PMC - PubMed

LinkOut - more resources

Full Text Sources
- Elsevier Science
- PubMed Central

[1] Walker M.J., Barnett T.C., McArthur J.D., et al. Disease manifestations and pathogenic mechanisms of group A Streptococcus. Clin Microbiol Rev. 2014;27(2):264–301. - PMC - PubMed

[2] Walker M.J., Barnett T.C., McArthur J.D., et al. Disease manifestations and pathogenic mechanisms of group A Streptococcus. Clin Microbiol Rev. 2014;27(2):264–301. - PMC - PubMed

[3] Ikuta K.S., Swetschinski L.R., Robles Aguilar G., et al. Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2022;400(10369):2221–2248. - PMC - PubMed

[4] Ikuta K.S., Swetschinski L.R., Robles Aguilar G., et al. Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2022;400(10369):2221–2248. - PMC - PubMed

[5] Murray C.J., Ikuta K.S., Sharara F., et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629–655. - PMC - PubMed

[6] Murray C.J., Ikuta K.S., Sharara F., et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629–655. - PMC - PubMed

[7] Centre for Disease Control and Prevention Antibiotic resistance threats in the United States 2019. 2019. https://www.cdc.gov/DrugResistance/Biggest-Threats.html#groupa Available from:

[8] Centre for Disease Control and Prevention Antibiotic resistance threats in the United States 2019. 2019. https://www.cdc.gov/DrugResistance/Biggest-Threats.html#groupa Available from:

[9] Steer A.C., Lamagni T., Curtis N., Carapetis J.R. Invasive group A streptococcal disease: epidemiology, pathogenesis and management. Drugs. 2012;72(9):1213. - PMC - PubMed

[10] Steer A.C., Lamagni T., Curtis N., Carapetis J.R. Invasive group A streptococcal disease: epidemiology, pathogenesis and management. Drugs. 2012;72(9):1213. - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study

Affiliations

Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective study

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Similar articles

References

LinkOut - more resources

Full Text Sources

Abstract

Conflict of interest statement

Figures

Similar articles

References

Related information

LinkOut - more resources

Full Text Sources