Overlapping transmission of group A and C/G Streptococcus facilitates inter-species mobile genetic element exchange

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. We conducted a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. From 4,547 person-consultations, 294 SDSE and 315 S. pyogenes isolates were sequenced. SDSE and S. pyogenes transmission intersected extensively among households and the observed co-occurrence and transmission links were consistent with independent transmission without inter-species interference. At least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes was found in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate extensive co-circulation of both pathogens and HGT and support a need to integrate SDSE and S. pyogenes surveillance and control efforts. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement We acknowledge the assistance of the sequencing and pathogen informatics core teams at the Wellcome Sanger Institute, UK where this work was supported by the Wellcome Trust core grants 206194 and 108413/A/15/D. OX was supported by the Australian Health and Medical Research Council (NHMRC) postgraduate scholarship (GNT2013831) and Avant Foundation Doctors in Training Research Scholarship (2021/000017). MRD was supported by a University of Melbourne CR Roper Fellowship. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/RB of the Northern Territory Department of Health and Menzies School of Health Research gave ethical approval for this work (approval 2015-2516). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Accessions for newly sequenced SDSE isolates are listed in Supplementary Table 1 under the BioProject identifier PRJEB35476.