Skip to main content
    • Aa
    • Aa

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.

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
2. AC Bowen , The global epidemiology of impetigo: a systematic review of the population prevalence of impetigo and pyoderma. PLoS ONE 2015; 10: e0136789.

4. BJ Currie , JR Carapetis . Skin infections and infestations in Aboriginal communities in northern Australia. Australasian Journal of Dermatology 2000; 41: 139143.

5. CS Marshall , 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.

8. M McDonald , BJ Currie , JR Carapetis . Acute rheumatic fever: a chink in the chain that links the heart to the throat? Lancet Infectious Diseases 2004; 4: 240245.

9. MG Parnaby , JR Carapetis . Rheumatic fever in indigenous Australian children. Journal of Paediatrics and Child Health 2010; 46: 527533.

11. MI McDonald , 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. RS Bailie , M Stevens , EL McDonald . 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.

14. JR Carapetis , Success of a scabies control program in an Australian aboriginal community. Pediatric Infectious Diseases Journal 1997; 16: 494499.

17. AC Bowen , 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.

19. DS Sarovich , EP Price . SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Research Notes 2014; 7: 618.

20. A Stamatakis . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30: 13121313.

21. I Letunic , P Bork . 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. M Inouye , SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine 2014; 6: 90.

24. T Carver , Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012; 28: 464469.

25. M Krzywinski , Circos: an information aesthetic for comparative genomics. Genome Research 2009; 19: 16391645.

26. LJ Richardson , 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. MI McDonald , 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. RJ Towers , Extensive diversity of Streptococcus pyogenes in a remote human population reflects global-scale transmission rather than localised diversification. PLoS ONE 2013; 8: e73851.

29. N Dey , 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. V Sagar , Molecular heterogeneity among north Indian isolates of group A Streptococcus . Letters in Applied Microbiology 2004; 39: 8488.

31. V Sakota , 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. AC Steer , 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. PR Smeesters , Differences between Belgian and Brazilian group A Streptococcus epidemiologic landscape. PLoS ONE 2006; 1: e10.

34. W Tewodros , G Kronvall . M protein gene (emm type) analysis of group A beta-hemolytic streptococci from Ethiopia reveals unique patterns. Journal of Clinical Microbiology 2005; 43: 43694376.

37. SY Tong , Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. Genome Research 2015; 25: 111118.

38. SR Harris , 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: 9
Total number of PDF views: 70 *
Loading metrics...

Abstract views

Total abstract views: 345 *
Loading metrics...

* Views captured on Cambridge Core between September 2016 - 19th October 2017. This data will be updated every 24 hours.