Streptococcus pyogenes strains associated with invasive and non-invasive infections present possible links with emm types and superantigens

Document Type: Short Communication


1 Department of Microbiology, University of Karachi, Karachi-75270, Pakistan

2 Liaquat National Hospital, Karachi-75270, Pakistan


Objective(s): Streptococcus pyogenes, a notorious human pathogen is responsible to cause a wide range of infections varies from superficial common clinical illness to severe and life threatening infections. To our knowledge this is the first report exploring the emm types and superantigen/exotoxin gene profile of S. pyogenes from Pakistan.
Materials and Methods: A total of 89 S. pyogenes strains were collected predominantly from throat swabs followed by pus, tissues and wound swabs. Profile of five superantigen genes speA, speB, speC, speF and ssa was screened for all the emm types.
Results: Extensive heterogeneity among S. pyogenes strains was indicated, revealing 34 different emm types/ subtypes. The most prevalent emm types were emm68 and emm104. Some of the emm types were exclusively isolated from invasive infections while others were isolated only from non-invasive infections indicating the possible link between emm types and invasive/ noninvasive infections. Similarly, erythromycin-resistant strains mainly belonged to three particular emm types. Multiplex PCR analysis indicated the presence of speB 100%, speF 76%, speC 20%, speA 18% and ssa 15%. Interestingly, superantigen genes speC and speA were mainly associated with invasive infections. Among the five superantigens tested, one strain of emm12 harbored all the analyzed exotoxin genes, while 4 strains carried 4 superantigen genes.
Conclusion: S. pyogenes clones associated with invasive and non-invasive infections in Pakistan present differences in emm types, superantigens and antimicrobial resistance. The present data indicates the possible link between particular genetic lineage of a bacterium with the manifestation of the infection.


1. Efstratiou A, Lamagni T. Epidemiology of Streptococcus pyogenes. Editors: Ferretti JJ, Stevens DL, Fischetti VA,. In:Streptococcus pyogenes: Basic Biology to Clinical Manifestations. Oklahoma City.
2. Sims Sanyahumbi A, Colquhoun S, Wyber R, Carapetis JR. Global disease burden of group A Streptococcus. editors. Ferretti JJ, Stevens DL, Fischetti VA. In: Streptococcus pyogenes : Basic Biology to Clinical Manifestations, Oklahoma City.
3. Strus M, Heczko PB, Golinska E. The virulence factors of group A Streptococcus strains isolated from invasive and noninvasive infections in Polish and German centre 2009-2011. Eur J Clin Microbiol Infect Dis 2017; 36:1643-1649.
4. Matsumoto M, Yamada K, Suzuki M, Adachi H, Kobayashi S, Yamashita T, et al. Description of the pathogenic features of Streptococcus pyogenes isolates from invasive and noninvasive diseases in Aichi, Japan. Jpn J Infect Dis 2016; 69:338-341.
5. Yoshizawa S, Matsumura T, Ikebe T, Ichibayashi R, Fukui Y, Satoh T, et al. Streptococcal toxic shock syndrome caused by beta-hemolytic streptococci: Clinical features and cytokine and chemokine analyses of 15 cases. J Infect Chemother 2019; 25:355-361.
6. Hua CZ, Yu H, Yang LH, Xu HM, Lyu Q, Lu HP, et al. Streptococcal toxic shock syndrome caused by Streptococcus pyogenes: a retrospective study of 15 pediatric cases. Zhonghua Er Ke Za Zhi  2018; 56:587-591.
7. Bartos H, Fabianova L, Dlouhy P. Streptococcal toxic shock syndrome - a life-threatening condition caused by various Streptococcal species. Epidemiol Mikrobiol Imunol 2018; 67:82-86.
8. Liu TJ, Tai HC, Chien KL, Cheng NC. Predisposing factors of necrotizing fasciitis with comparison to cellulitis in Taiwan: a nationwide population-based case-control study. J Formos Med Assoc 2019; 6646:1-8.
9. van Sambeek CHL, van Stigt SF, Brouwers L, Bemelman M. Necrotising fasciitis: a ticking time bomb? BMJ Case Rep 2017; 2017:221770-221784.
10. Plainvert C, Longo M, Seringe E, Saintpierre B, Sauvage E, Ma L, et al. A clone of the emergent Streptococcus pyogenes emm89 clade responsible for a large outbreak in a post-surgery oncology unit in France. Med Microbiol Immunol 2018; 207:287-296.
11. Wong SSY, Yuen KY. The comeback of scarlet fever. EBio Med 2018; 28:7-8.
12. Shannon BA, McCormick JK, Schlievert PM. Toxins and Superantigens of Group A Streptococci. Microbiol Spectr 2019; 7:1-7.
13. Bisno AL, Brito MO, Collins CM. Molecular basis of group A Streptococcal virulence. Lancet Infect Dis 2003; 3:191-200.
14. Courtney HS, Hasty DL, Dale JB. Anti-phagocytic mechanisms of Streptococcus pyogenes: binding of fibrinogen to M-related protein. Mol Microbiol 2006; 59:936-947.
15. De Oliveira DM, Hartley-Tassell L, Everest-Dass A, Day CJ, Dabbs RA, Ve T, et al. Blood group antigen recognition via the Group A Streptococcal m protein mediates host colonization. MBio 2017; 8:2237-2249.
16. DebRoy S, Li X, Kalia A, Galloway-Pena J, Shah BJ, Fowler VG, et al. Identification of a chimeric emm gene and novel emm pattern in currently circulating strains of emm4 Group A Streptococcus. Microbial Genom 2018; 4:1-6.
17. Olafsdottir LB, Erlendsdottir H, Melo-Cristino J, Weinberger DM, Ramirez M, Kristinsson KG, et al. Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012. Euro Surveill. 2014; 19:5-14.
18. Luca-Harari B, Darenberg J, Neal S, Siljander T, Strakova L, Tanna A, et al. Clinical and microbiological characteristics of severe Streptococcus pyogenes disease in Europe. J Clin Microbiol 2009; 47:1155-1165.
19. Dauby N, Miendje Deyi VY, Delforge V, Martiny D, Mekkaoui L, Hallin M, et al. Streptococcus pyogenes infections with limited emm-type diversity in the homeless population of Brussels, 2016-2018. Int J Infect Dis 2019; 81:52-56.
20. Meehan M, Murchan S, Gavin PJ, Drew RJ, Cunney R. Epidemiology of an upsurge of invasive group A Streptococcal infections in Ireland, 2012-2015. J Infect 2018; 77:183-190.
21. Tuffs SW, Haeryfar SMM, McCormick JK. Manipulation of innate and adaptive immunity by Staphylococcal superantigens. Pathogens 2018; 7:53-76.
22. Berman HF, Tartof SY, Reis JN, Reis MG, Riley LW. Distribution of superantigens in group A streptococcal isolates from Salvador, Brazil. BMC Infect Dis 2014; 14:294-300.
23. Commons R, Rogers S, Gooding T, Danchin M, Carapetis J, Robins-Browne R, et al. Superantigen genes in group A streptococcal isolates and their relationship with emm types. J Med Microbiol 2008; 57:1238-1246.
24. Proft T, Fraser JD. Bacterial superantigens. Clin Exp Immunol 2003; 133:299-306.
25. Reglinski M, Sriskandan S, Turner CE. Identification of two new core chromosome-encoded superantigens in Streptococcus pyogenes; speQ and speR. J Infect 2019; 78:358-363.
26. Lin JN, Chang LL, Lai CH, Lin HH, Chen YH. Emergence of Streptococcus pyogenes emm102 causing toxic shock syndrome in Southern Taiwan during 2005-2012. PloS One 2013; 8:81700-81709.
27. Lu B, Fang Y, Fan Y, Chen X, Wang J, Zeng J, et al. High prevalence of macrolide-resistance and molecular characterization of Streptococcus pyogenes isolates circulating in China from 2009 to 2016. Front Microbiol 2017; 8:1052-1062.
28. Zeppa JJ, Kasper KJ, Mohorovic I, Mazzuca DM, Haeryfar SMM. Nasopharyngeal infection by Streptococcus pyogenes requires superantigen-responsive vbeta-specific T cells. Proc Natl Acad Sci U S A 2017; 114:10226-10231.
29. Chalker V, Jironkin A, Coelho J, Al-Shahib A, Platt S, Kapatai G, et al. Genome analysis following a national increase in scarlet fever in England 2014. BMC genomics 2017; 18:224-234.
30. Commons R, Rogers S, Gooding T, Danchin M, Carapetis J, Robins-Browne R, et al. Superantigen genes in group A streptococcal isolates and their relationship with emm types. J med microbiol 2008; 57:1238-1246.
31. Lintges M, van der Linden M, Hilgers RD, Arlt S, Al-Lahham A, Reinert RR, et al. Superantigen genes are more important than the emm type for the invasiveness of group A Streptococcus infection. J Infect Dis 2010; 202:20-28.
32. Paveenkittiporn W, Nozawa T, Dejsirilert S, Nakagawa I, Hamada S. Prevalent emm types and superantigen gene patterns of group A Streptococcus in Thailand. Epidemiol Infect 2016; 144:864-869.
33. Balaji K, Thenmozhi R, Prajna L, Dhananjeyan G, Pandian SK. Comparative analysis of emm types, superantigen gene profiles and antibiotic resistance genes among Streptococcus pyogenes isolates from ocular infections, pharyngitis and asymptomatic children in South India. Infect Genet Evol 2013; 19:105-112.
34. Liu X, Shen X, Chang H, Huang G, Fu Z, Zheng Y, et al. High macrolide resistance in Streptococcus pyogenes strains isolated from children with pharyngitis in China. Pediatr Pulmonol 2009; 44:436-441.
35. Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144-156.
36. Sayyahfar S, Fahimzad A. Antibiotic susceptibility evaluation of group A streptococcus isolated from children with pharyngitis: a study from Iran. Infect Chemother 2015; 47:225-230.
37. Jose JJM, Brahmadathan KN, Abraham VJ, Huang CY, Morens D, Hoe NP, et al. Streptococcal group A, C and G pharyngitis in school children: a prospective cohort study in Southern India. Epidemiol Infect 2018; 146:848-853.
38. Zafar A, Hasan R, Nizamuddin S, Mahmood N, Mukhtar S, Ali F, et al. Antibiotic susceptibility in Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes in Pakistan: a review of results from the survey of antibiotic resistance (SOAR) 2002-15. J Antimicrob Chemother 2016; 71:103-109.
39. Masud S, Mirza S, Abbasi S, Usman M, Khan M, Waqar A. Incidence of erythromycin resistance in clinical isolates of Streptococcus pyogenes at AFIP, Rawalpindi. Pak J Pathol 2005; 16:86-89.
40. Memon BA. Erythromycin resistance in Streptococcus Pyogenes group a throat isolates in Sukkurcity. Rawal Med J 2007; 32:11-3.
41. Rizwan M, Bakht J, Bacha N, Ahmad B. In vitro activity of antimicrobial agents against streptococcus pyogenes isolated from different regions of Khyber Pakhtun Khwa Pakistan. Pak J Pharm Sci 2016; 29:59-64.
42. Richter SS, Heilmann KP, Dohrn CL, Beekmann SE, Riahi F, Garcia-de-Lomas J, et al. Increasing telithromycin resistance among Streptococcus pyogenes in Europe. J Antimicrob Chemother 2008; 61:603-611.
43. Alfaresi MS. Group A streptococcal genotypes from throat and skin isolates in the United Arab Emirates. BMC Res Notes 2010; 3:94-99.
44. Mihaila-Amrouche L, Bouvet A, Loubinoux J. Clonal spread of emm type 28 isolates of Streptococcus pyogenes that are multiresistant to antibiotics. J Clin Microbiol 2004; 42:3844-3846.
45. Abraham T, Sistla S. Identification of Streptococcus pyogenes - phenotypic tests vs molecular assay (spy1258PCR): a comparative study. J Clin Diag Res 2016; 10:1-3.
46. Luca-Harari B, Ekelund K, van der Linden M, Staum-Kaltoft M, Hammerum AM, Jasir A. Clinical and epidemiological aspects of invasive Streptococcus pyogenes infections in Denmark during 2003 and 2004. J Clin Microbiol 2008; 46:79-86.
47. Engel ME, Muhamed B, Whitelaw AC, Musvosvi M, Mayosi BM, Dale JB. Group A streptococcal emm type prevalence among symptomatic children in Cape Town and potential vaccine coverage. Pediat Infect Dis J 2014; 33:208-210.
48. Chochua S, Metcalf BJ, Li Z, Rivers J, Mathis S, Jackson D, et al. Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015. mBio. 2017;8(5).
49.Rudolph K, Bruce MG, Bruden D, Zulz T, Reasonover A, Hurlburt D, et al. Epidemiology of invasive group A streptococcal disease in Alaska, 2001 to 2013. J Clin Microbiol 2016; 54:134-141.
50. Eisner A, Leitner E, Feierl G, Kessler HH, Marth E. Prevalence of emm types and antibiotic resistance of group A streptococci in Austria. Diag Microbiol Infect Dis 2006; 55:347-350.
51. Mathur P, Bhardwaj N, Mathur K, Behera B, Gupta G, Kapil A, et al. Clinical and molecular epidemiology of beta-hemolytic streptococcal infections in India. J Infect Dev Ctries 2014; 8:297-303.
52. Bergmann R, Nerlich A, Chhatwal GS, Nitsche-Schmitz DP. Distribution of small native plasmids in Streptococcus pyogenes in India. Int J Med Microbiol 2014; 304:370-378.
53. Sagar V, Bergmann R, Nerlich A, McMillan DJ, Nitsche-Schmitz DP, Fulde M, et al. Differences in virulence repertoire and cell invasive potential of group A Streptococcus emm1-2 in comparison to emm1 genotype. Int J Med Microbiol 2014; 304:685-695.
54. Lamb LE, Siggins MK, Scudamore C, Macdonald W, Turner CE, Lynskey NN, et al. Impact of contusion injury on intramuscular emm1 group A Streptococcus infection and lymphatic spread. Virulence 2018; 9:1074-1084.
55. Ikebe T, Tominaga K, Shima T, Okuno R, Kubota H, Ogata K, et al. Increased prevalence of group A Streptococcus isolates in Streptococcal toxic shock syndrome cases in Japan from 2010 to 2012. Epidemiol Infect 2015; 143:864-872.
56. Michaelsen TE, Andreasson IK, Langerud BK, Caugant DA. Similar superantigen gene profiles and superantigen activity in norwegian isolates of invasive and noninvasive group A Streptococci. Scand J Immunol 2011; 74:423-429.
57. Vahakuopus S, Vuento R, Siljander T, Syrjanen J, Vuopio J. Distribution of emm types in invasive and noninvasive group A and G streptococci. Eur J Clin microbiol Infect Dis 2012; 31:1251-1256.
58. Reglinski M, Sriskandan S. The contribution of group A streptococcal virulence determinants to the pathogenesis of sepsis. Virulence 2014; 5:127-136.
59. Mathur P, Bhardwaj N, Mathur K, Behera B, Gupta G, Kapil A, et al. Clinical and molecular epidemiology of beta-hemolytic streptococcal infections in India. J Infect Dev Ctries 2014; 8:297-303.
60. Imohl M, Fitzner C, Perniciaro S, van der Linden M. Epidemiology and distribution of 10 superantigens among invasive Streptococcus pyogenes disease in Germany from 2009 to 2014. PloS One 2017; 12:180757-180772.
61. Davies MR, Holden MT, Coupland P, Chen JH. Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance. Nat Genet 2015; 47:84-87.
62. You Y, Davies MR, Protani M, McIntyre L, Walker MJ, Zhang J. Scarlet fever epidemic in china caused by Streptococcus pyogenes serotype M12: epidemiologic and molecular analysis. EBio Med 2018; 28:128-135.
63. Walker MJ, Brouwer S, Forde BM, Worthing KA, McIntyre L, Sundac L, et al. Detection of epidemic scarlet fever group A Streptococcus in Australia. Clin Infect Dis 2019; 69:1232-1234.