Skip to main content Accessibility help

Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities

  • A. C. BOWEN (a1) (a2) (a3), T. HARRIS (a1), D. C. HOLT (a1), P. M. GIFFARD (a1), J. R. CARAPETIS (a2) (a3), P. T. CAMPBELL (a4), J. McVERNON (a4) and S. Y. C. TONG (a1) (a5)...

Impetigo is common in remote Indigenous children of northern Australia, with the primary driver in this context being Streptococcus pyogenes [or group A Streptococcus (GAS)]. To reduce the high burden of impetigo, the transmission dynamics of GAS must be more clearly elucidated. We performed whole genome sequencing on 31 GAS isolates collected in a single community from children in 11 households with ⩾2 GAS-infected children. We aimed to determine whether transmission was occurring principally within households or across the community. The 31 isolates were represented by nine multilocus sequence types and isolates within each sequence type differed from one another by only 0–3 single nucleotide polymorphisms. There was evidence of extensive transmission both within households and across the community. Our findings suggest that strategies to reduce the burden of impetigo in this setting will need to extend beyond individual households, and incorporate multi-faceted, community-wide approaches.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the or variations. ‘’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities
      Available formats
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities
      Available formats
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Whole genome sequencing reveals extensive community-level transmission of group A Streptococcus in remote communities
      Available formats
Corresponding author
* Author for correspondence: A/Professor S. Y. C. Tong, Menzies School of Health Research, PO Box 41096, Casuarina, NT 0811, Australia. (Email:
Hide All
1. Koning, S, et al. Interventions for impetigo. Cochrane Database of Systematic Reviews 2012; 1: CD003261.
2. Bowen, AC, et al. The global epidemiology of impetigo: a systematic review of the population prevalence of impetigo and pyoderma. PLoS ONE 2015; 10: e0136789.
3. Carapetis, JR, et al. The global burden of group A streptococcal diseases. Lancet Infectious Diseases 2005; 5: 685694.
4. Currie, BJ, Carapetis, JR. Skin infections and infestations in Aboriginal communities in northern Australia. Australasian Journal of Dermatology 2000; 41: 139143.
5. Marshall, CS, et al. Acute post-streptococcal glomerulonephritis in the Northern Territory of Australia: a review of 16 years data and comparison with the literature. American Journal of Tropical Medicine and Hygiene 2011; 85: 703710.
6. White, AV, Hoy, WE, McCredie, DA. Childhood post-streptococcal glomerulonephritis as a risk factor for chronic renal disease in later life. Medical Journal of Australia 2001; 174: 492496.
7. Hoy, WE, et al. Post-streptococcal glomerulonephritis is a strong risk factor for chronic kidney disease in later life. Kidney International 2012; 81: 10261032.
8. McDonald, M, Currie, BJ, Carapetis, JR. Acute rheumatic fever: a chink in the chain that links the heart to the throat? Lancet Infectious Diseases 2004; 4: 240245.
9. Parnaby, MG, Carapetis, JR. Rheumatic fever in indigenous Australian children. Journal of Paediatrics and Child Health 2010; 46: 527533.
10. Bowen, AC, et al. Short-course oral co-trimoxazole versus intramuscular benzathine benzylpenicillin for impetigo in a highly endemic region: an open-label, randomised, controlled, non-inferiority trial. Lancet 2014; 384: 21322140.
11. McDonald, MI, et al. Low rates of streptococcal pharyngitis and high rates of pyoderma in Australian aboriginal communities where acute rheumatic fever is hyperendemic. Clinical Infectious Diseases 2006; 43: 683689.
12. Bailie, RS, Stevens, M, McDonald, EL. The impact of housing improvement and socio-environmental factors on common childhood illnesses: a cohort study in Indigenous Australian communities. Journal of Epidemiology and Community Health 2012; 66: 821831.
13. McDonald, EL, Bailie, RS, Morris, PS. Participatory systems approach to health improvement in Australian Aboriginal children. Health Promotion International. Published online: 4 February 2014. doi:10.1093/heapro/dau003.
14. Carapetis, JR, et al. Success of a scabies control program in an Australian aboriginal community. Pediatric Infectious Diseases Journal 1997; 16: 494499.
15. Andrews, RM, et al. A regional initiative to reduce skin infections amongst aboriginal children living in remote communities of the Northern Territory, Australia. PLoS Neglected Tropical Diseases 2009; 3: e554.
16. Bowen, AC, et al. The microbiology of impetigo in Indigenous children: associations between Streptococcus pyogenes, Staphylococcus aureus, scabies, and nasal carriage. BMC Infectious Diseases 2014; 14: 727.
17. Bowen, AC, et al. Comparison of three methods for the recovery of skin pathogens from impetigo swabs collected in a remote community of Northern Territory, Australia. Transactions of the Royal Society of Tropical Medicine and Hygiene 2013; 107: 384389.
18. Ferretti, JJ, et al. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proceedings of the National Academy of Sciences USA 2001; 98: 46584663.
19. Sarovich, DS, Price, EP. SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Research Notes 2014; 7: 618.
20. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30: 13121313.
21. Letunic, I, Bork, P. Interactive Tree Of Life v. 2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 2011; 39 (Web Server issue): W475478.
22. Inouye, M, et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine 2014; 6: 90.
23. Zerbino, DR, Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 2008; 18: 821829.
24. Carver, T, et al. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012; 28: 464469.
25. Krzywinski, M, et al. Circos: an information aesthetic for comparative genomics. Genome Research 2009; 19: 16391645.
26. Richardson, LJ, et al. Diversity of emm sequence types in group A beta-haemolytic streptococci in two remote Northern Territory Indigenous communities: implications for vaccine development. Vaccine 2010; 28: 53015305.
27. McDonald, MI, et al. The dynamic nature of group A streptococcal epidemiology in tropical communities with high rates of rheumatic heart disease. Epidemiology and Infection 2008; 136: 529539.
28. Towers, RJ, et al. Extensive diversity of Streptococcus pyogenes in a remote human population reflects global-scale transmission rather than localised diversification. PLoS ONE 2013; 8: e73851.
29. Dey, N, et al. High diversity of group A Streptococcal emm types in an Indian community: the need to tailor multivalent vaccines. Clinical Infectious Diseases 2005; 40: 4651.
30. Sagar, V, et al. Molecular heterogeneity among north Indian isolates of group A Streptococcus . Letters in Applied Microbiology 2004; 39: 8488.
31. Sakota, V, et al. Genetically diverse group A streptococci from children in far-western Nepal share high genetic relatedness with isolates from other countries. Journal of Clinical Microbiology 2006; 44: 21602166.
32. Steer, AC, et al. emm and C-repeat region molecular typing of beta-hemolytic Streptococci in a tropical country: implications for vaccine development. Journal of Clinical Microbiology 2009; 47: 25022509.
33. Smeesters, PR, et al. Differences between Belgian and Brazilian group A Streptococcus epidemiologic landscape. PLoS ONE 2006; 1: e10.
34. Tewodros, W, Kronvall, G. M protein gene (emm type) analysis of group A beta-hemolytic streptococci from Ethiopia reveals unique patterns. Journal of Clinical Microbiology 2005; 43: 43694376.
35. Bessen, DE, et al. Molecular epidemiology and genomics of group A Streptococcus . Infection and Genetic Evolution 2015; 33: 393418.
36. Steer, AC, et al. Global emm type distribution of group A streptococci: systematic review and implications for vaccine development. Lancet Infectious Diseases 2009; 9: 611616.
37. Tong, SY, et al. Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. Genome Research 2015; 25: 111118.
38. Harris, SR, et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infectious Diseases 2013; 13: 130136.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Epidemiology & Infection
  • ISSN: 0950-2688
  • EISSN: 1469-4409
  • URL: /core/journals/epidemiology-and-infection
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Type Description Title
Supplementary materials

Bowen supplementary material
Table S2

 Word (28 KB)
28 KB
Supplementary materials

Bowen supplementary material
Table S1

 Excel (37 KB)
37 KB


Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed