Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context
Summary: 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 M1UK has been particularl...
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Elsevier
2025-02-01
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| Series: | The Lancet Regional Health. Western Pacific |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666606525000045 |
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| author | Jacqueline M. Morris Jake A. Lacey Kerrie Stevens Lamali Sadeesh Kumar Mathilda Wilmot Janet Strachan Marion Easton Daneeta Hennessy Tony M. Korman Andrew J. Daley Katherine B. Gibney Adam W.J. Jenney Steven Y.C. Tong Benjamin P. Howden Norelle L. Sherry |
| author_facet | Jacqueline M. Morris Jake A. Lacey Kerrie Stevens Lamali Sadeesh Kumar Mathilda Wilmot Janet Strachan Marion Easton Daneeta Hennessy Tony M. Korman Andrew J. Daley Katherine B. Gibney Adam W.J. Jenney Steven Y.C. Tong Benjamin P. Howden Norelle L. Sherry |
| author_sort | Jacqueline M. Morris |
| collection | DOAJ |
| description | Summary: 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 M1UK 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 M1Aus, detected in Australia (Victoria and Queensland), Belgium and the United Kingdom. In Victoria, M1Aus was the dominant emm1 variant in 2017 and 2018, more recently replaced by the M1UK lineage as the dominant variant, further demonstrating the worldwide impact of M1UK. 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 M1Aus 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). |
| format | Article |
| id | doaj-art-6337023b988349d3866a1489adc5662f |
| institution | Kabale University |
| issn | 2666-6065 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | The Lancet Regional Health. Western Pacific |
| spelling | doaj-art-6337023b988349d3866a1489adc5662f2025-01-30T05:15:02ZengElsevierThe Lancet Regional Health. Western Pacific2666-60652025-02-0155101467Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in contextJacqueline M. Morris0Jake A. Lacey1Kerrie Stevens2Lamali Sadeesh Kumar3Mathilda Wilmot4Janet Strachan5Marion Easton6Daneeta Hennessy7Tony M. Korman8Andrew J. Daley9Katherine B. Gibney10Adam W.J. Jenney11Steven Y.C. Tong12Benjamin P. Howden13Norelle L. Sherry14Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; 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, AustraliaMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaCommunicable Diseases, Epidemiology and Surveillance, Health Protection Branch, Department of Health Victoria, AustraliaCommunicable Diseases, Epidemiology and Surveillance, Health Protection Branch, Department of Health Victoria, AustraliaCommunicable Diseases, Epidemiology and Surveillance, Health Protection Branch, Department of Health Victoria, AustraliaMonash Infectious Diseases, Monash University and Monash Health, Clayton, VIC, AustraliaDepartment of Laboratory Services, Royal Children's Hospital, Parkville, VIC, Australia; Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, AustraliaDepartment of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaMicrobiology Unit & Department of Infectious Diseases, Alfred Health, Melbourne, VIC, AustraliaDepartment of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Disease Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, AustraliaDepartment of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; 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; Department of Infectious Diseases & Immunology, Austin Health, Heidelberg, VIC, Australia; Centre for Pathogen Genomics, University of Melbourne, Melbourne, VIC, Australia; Corresponding author. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; 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; Department of Infectious Diseases & Immunology, Austin Health, Heidelberg, VIC, Australia; Corresponding author. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.Summary: 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 M1UK 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 M1Aus, detected in Australia (Victoria and Queensland), Belgium and the United Kingdom. In Victoria, M1Aus was the dominant emm1 variant in 2017 and 2018, more recently replaced by the M1UK lineage as the dominant variant, further demonstrating the worldwide impact of M1UK. 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 M1Aus 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).http://www.sciencedirect.com/science/article/pii/S2666606525000045Streptococcus pneumoniaeInvasive group A streptococcusGenomic epidemiologyStreptococcal typing |
| spellingShingle | Jacqueline M. Morris Jake A. Lacey Kerrie Stevens Lamali Sadeesh Kumar Mathilda Wilmot Janet Strachan Marion Easton Daneeta Hennessy Tony M. Korman Andrew J. Daley Katherine B. Gibney Adam W.J. Jenney Steven Y.C. Tong Benjamin P. Howden Norelle L. Sherry Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context The Lancet Regional Health. Western Pacific Streptococcus pneumoniae Invasive group A streptococcus Genomic epidemiology Streptococcal typing |
| title | Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context |
| title_full | Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context |
| title_fullStr | Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context |
| title_full_unstemmed | Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context |
| title_short | Genomic interrogation of invasive group A Streptococcus (iGAS) epidemiology and COVID-19 impacts in Victoria, Australia: a 6-year retrospective studyResearch in context |
| title_sort | genomic interrogation of invasive group a streptococcus igas epidemiology and covid 19 impacts in victoria australia a 6 year retrospective studyresearch in context |
| topic | Streptococcus pneumoniae Invasive group A streptococcus Genomic epidemiology Streptococcal typing |
| url | http://www.sciencedirect.com/science/article/pii/S2666606525000045 |
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