Overlapping transmission of group A and C/GStreptococcusfacilitates inter-species mobile genetic element exchange

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. 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.