Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Ouli Xie, Jacqueline M. Morris, Andrew J. Hayes, Rebecca J. Towers, Magnus G. Jespersen, John A. Lees, Nouri L. Ben Zakour, Olga Berking, Sarah L. Baines, Glen P. Carter, Gerry Tonkin-Hill, Layla Schrieber, Liam McIntyre, Jake A. Lacey, Taylah B. James, Kadaba S. Sriprakash, Scott A. Beatson, Tadao Hasegawa, Phil Giffard, Andrew C. Steer, Michael R. Batzloff, Bernard W. Beall, Marcos D. Pinho, Mario Ramirez, Debra E. Bessen, Gordon Dougan, Stephen D. Bentley, Mark J. Walker, Bart J. Currie, Steven Y. C. Tong, David J. McMillan and Mark R. Davies ()
Additional contact information
Ouli Xie: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Jacqueline M. Morris: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Andrew J. Hayes: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Rebecca J. Towers: Charles Darwin University
Magnus G. Jespersen: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
John A. Lees: European Bioinformatics Institute EMBL-EBI
Nouri L. Ben Zakour: The University of Queensland
Olga Berking: The University of Queensland
Sarah L. Baines: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Glen P. Carter: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Gerry Tonkin-Hill: University of Oslo
Layla Schrieber: The University of Sydney
Liam McIntyre: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Jake A. Lacey: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Taylah B. James: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Kadaba S. Sriprakash: QIMR Berghofer Medical Research Institute
Scott A. Beatson: The University of Queensland
Tadao Hasegawa: Nagoya City University Graduate School of Medical Sciences
Phil Giffard: Charles Darwin University
Andrew C. Steer: Murdoch Children’s Research Institute
Michael R. Batzloff: QIMR Berghofer Medical Research Institute
Bernard W. Beall: Centers for Disease Control and Prevention
Marcos D. Pinho: Universidade de Lisboa
Mario Ramirez: Universidade de Lisboa
Debra E. Bessen: Valhalla
Gordon Dougan: Wellcome Sanger Institute
Stephen D. Bentley: Wellcome Sanger Institute
Mark J. Walker: The University of Queensland
Bart J. Currie: Charles Darwin University
Steven Y. C. Tong: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
David J. McMillan: University of the Sunshine Coast
Mark R. Davies: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.

Date: 2024
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DOI: 10.1038/s41467-024-46530-2

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