Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange

Ouli Xie, Cameron Zachreson, Gerry Tonkin-Hill, David J. Price, Jake A. Lacey, Jacqueline M. Morris, Malcolm I. McDonald, Asha C. Bowen, Philip M. Giffard, Bart J. Currie, Jonathan R. Carapetis, Deborah C. Holt, Stephen D. Bentley, Mark R. Davies and Steven Y. C. Tong ()
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Ouli Xie: University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Cameron Zachreson: University of Melbourne
Gerry Tonkin-Hill: University of Oslo
David J. Price: University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Jake A. Lacey: University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Jacqueline M. Morris: University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Malcolm I. McDonald: James Cook University
Asha C. Bowen: University of Western Australia and Perth Children’s Hospital
Philip M. Giffard: Charles Darwin University
Bart J. Currie: Charles Darwin University
Jonathan R. Carapetis: University of Western Australia and Perth Children’s Hospital
Deborah C. Holt: Charles Darwin University
Stephen D. Bentley: Wellcome Genome Campus
Mark R. Davies: University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Steven Y. C. Tong: University of Melbourne at the Peter Doherty Institute for Infection and Immunity

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.

Date: 2024
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DOI: 10.1038/s41467-024-47816-1

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