Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Overlapping transmission of group A and C/G Streptococcus facilitates inter-species mobile genetic element exchange (93488)

Ouli Xie 1 2 , Cameron Zachreson 3 , David J Price 1 4 , Gerry Tonkin-Hill 5 , Jake A Lacey 1 6 , Jacqueline M Morris 6 , Malcolm I McDonald 7 , Asha C Bowen 8 , Philip M Giffard 9 10 , Bart J Currie 9 , Jonathan R Carapetis 8 , Ross M Andrews 9 11 , Deborah C Holt 9 , Stephen D Bentley 12 , Mark R Davies 6 , Steven YC Tong 1 13
  1. Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
  2. Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia
  3. School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
  4. Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia
  5. Department of Biostatistics, University of Oslo, Blindern, Norway
  6. Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
  7. Division of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
  8. Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
  9. Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia
  10. College of Health and Human Services, Charles Darwin University, Darwin, NT, Australia
  11. Research School of Population Health, Australian National University, Canberra, ACT, Australia
  12. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
  13. Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia

Background

Streptococcus dysgalactiae subspecies equisimilis (group C/G Streptococcus, SDSE) is closely related to S. pyogenes (group A Streptococcus). They share the same ecological niche on the skin and throat. While both pathogens can transmit via respiratory droplets, it is unknown if transmission of one interferes with the other. We examined household transmission of SDSE and its interaction with S. pyogenes using whole genome sequencing (WGS) level resolution of isolates in two remote communities in the Northern Territory (NT).

Methods

SDSE and S. pyogenes isolates were collected from throat and skin sore swabs during a monthly surveillance study between 2003 to 2005.1 SDSE transmission clusters were defined using single linkage clustering with a threshold of <8 single nucleotide polymorphisms (SNPs) and >99% shared gene content. Intra- and inter-household transmission networks were inferred from genomic clusters and epidemiological metadata. The SDSE transmission network and co-occurrence of the two species at the household level was compared to a previously published analysis of the S. pyogenes isolates.2
To capture putative horizontal gene transfer between SDSE and S. pyogenes, mobile genetic elements (MGEs) were systemically compared for near-identical elements across species.

Results

From 4,547 person-consultations, 294 SDSE isolates (286 throat, 8 impetigo) and 315 S. pyogenes (200 throat, 115 impetigo) were recovered for WGS. 37 SDSE genomic transmission clusters (237 isolates) were defined.
SDSE and S. pyogenes co-occurred in a household on 100/486 (21%) of household-visits. 137 SDSE and 173 S. pyogenes transmission links were inferred by network analysis with 11 overlapping edges. The observed frequency of co-occurrence and shared transmission edges were consistent with null models of independent transmission (i.e., no evidence of inter-species interference).
Three near-identical MGEs carrying macrolide resistance, tetracycline resistance, or streptodornase virulence genes were found across species and at least one of these MGEs was present in 55/294 (19%) of SDSE and 23/315 (7%) of S. pyogenes isolates.

Conclusion

SDSE and S. pyogenes largely transmit independently of each other at the household level without interference. In the setting of extensive transmission and co-occurrence in households, MGEs carrying antimicrobial resistance genes and virulence factors were found across species suggestive of interspecies horizontal gene transfer.

  1. McDonald M, Towers RJ, Andrews RM et al. Epidemiology of Streptococcus dysgalactiae subsp. equisimilis in tropical communities, Northern Australia. Emerg Infect Dis 2007; 13: 1694-700.
  2. Lacey JA, Marcato AJ, Chisholm RH et al. Widespread Streptococcus pyogenes Transmission between Impetigo Lesions and Asymptomatic Throat Carriage in a Longitudinal Cohort from Remote Communities. Available at SSRN: https://ssrn.com/abstract=4244747.