Isolation ofStreptococcus pyogenesfrom children with pharyngitis andemmtype analysis : Journal of the Chinese Medical Association

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Original Article

Isolation ofStreptococcus pyogenesfrom children with pharyngitis andemmtype analysis

Khosravi, Azar D.a,b; Ebrahimifard, Nasimb,*; Shamsizadeh, Ahmada,c; Shoja, Saeedb

Author Information
Journal of the Chinese Medical Association: May 2016 - Volume 79 - Issue 5 - p 276-280
doi: 10.1016/j.jcma.2016.01.002


    1. Introduction

    Group A Streptococcus (GAS) or Streptococcus pyogenes is a gram-positive cocci with humans as its specific host. It is capable of causing a large variety of infections ranging from simple benign infections like sore throats and impetigo to fatal diseases like streptococcal toxic shock syndrome and necrotizing fasciitis, acute rheumatic fever, and acute glomerulonephritis.1,2 The mortality rate of severe GAS infections remains high, both in developed and developing countries.3,4 Additionally, there are reports of outbreaks of invasive GAS infections in the community and in hospitals.5,6

    Due to an elevated global prevalence of GAS disease, epidemiological surveillance is necessary to detect changes in disease distribution in various populations. Typing of a collection of GAS isolates is important as part of the epidemiological surveillance for the disease. There are several typing methods available for screening GAS isolates. Among them, typing based on the M protein, a cell-surface protein that is the major virulence and immunological determinant of GAS, has been the most widely used method.7 The M protein which is encoded by the emm gene possesses a hypervariable region of the amino-terminal with 40–50 amino acid residues.8 A GAS typing system based on sequencing of this N-terminal hypervariable region of the M protein (emm) gene is known as emm typing and is the “gold standard” method used to characterize GAS isolates.9 This method has been used for identification of different emm types. The surface proteins are not only a suitable substrate for typing and studying the molecular epidemiology of GAS isolates, but also represents choice candidates for the development of an effective vaccine against GAS-related serious diseases due to their critical role in host–bacteria relationships.10,11 Currently, more than 170 emm types and 750 emm subtypes of GAS are known.12 The distribution of emm types reportedly varies among different countries and regions.13

    Due to the lack of comprehensive information about different types of M protein among GAS isolates in Ahvaz city, the current study was proposed to isolate GAS from the patients’ throat suffering from pharyngitis and typing their M proteins. This undertaking is the first molecular epidemiologic analysis of GAS strains associated with children's pharyngitis in south western Iran.

    2. Methods

    2.1. Sampling

    Our study reviewed a total of 1000 throat samples obtained from children with pharyngitis ranging in age from 2 years to 14 years, who were referred to Aboozar Children's Hospital in Ahvaz, southwestern Iran, from November 2012 to June 2013. The preliminary proposal of the work was reviewed and approved by the hospital's Institutional Review and Ethics Board, and the necessary permission to collect the requisite samples and initiate the work was obtained.

    Standard patient demographics and clinical data were recorded, including age, sex, and disease onset, and patient symptoms were recorded. All patients who presented with fever and sore throat were entered into the study, and those with prior antibiotic therapy or patients with other respiratory tract symptoms such as rhinorrhea or nasal congestion were excluded from the study by the available pediatrics infectious diseases specialist at the time of admission.

    2.2. Phenotypic identification of GAS

    A single throat swab was taken from each patient and immediately placed in a thioglycolate broth and transferred to the microbiology laboratory, where the broth was incubated at 37°C for 24 hours, with subsequent subculture on a sheep blood agar plate (HiMedia, Mombai, India) the next day. The identities of the colonies were confirmed based on morphological and growth characteristics, including gram staining, beta-hemolysis on blood agar medium, bacitracin susceptibility, pyrrolidonyl arylamidase test, and resistance to trimethoprim-sulfamethoxazole.14

    2.3. Antimicrobial susceptibility testing

    For confirmed GAS isolates, antimicrobial susceptibility testing was done using the standard disk-diffusion method on Müeller–Hinton agar with 5% sheep blood, incubated overnight at 37°C in air enriched with 5% CO2 according to the Clinical and Laboratory Standard Institute (CLSI) guidelines.15 The commercial antibiotic discs (MAST Co., London, UK) were as follows: penicillin G, ampicillin, ceftriaxone, vancomycin, azithromycin, chloramphenicol, clindamycin, and erythromycin. The interpretation criteria of the susceptibility testing were in accordance to the CLSI recommendations.

    2.4. Polymerase chain reaction amplification for the detection of the emm gene

    For DNA extraction from the isolates, a commercial extraction and purification kit (Roche, Berlin, Germany) was used according to the manufacturer's instructions. The extracted DNA purity was measured with a photobiometer (Eppendorf, Hamburg, Germany) in 260/280 nm UV long waves. In order to amplify the emm gene, the set of primers of emm1 (5′-TATTCGCTTAGAAAATTAA-3′) and emm2 (5′-GCAAGTTCTTCAGCTTGTTT-3′) were used,16 which amplifies a 914 bp fragment of the target gene. Polymerase chain reaction (PCR) amplification was performed in a final volume of 25 μL containing 1 × PCR buffer, 1.5mM MgCl2, 200μM deoxynucleotide, 0.4mM of each primer, 1.5 U Taq polymerase, and 1 μL of template DNA. All the reagents were purchased from Qiagen, Hilden, Germany. Amplification was performed on a thermocycler nexus gradient (Eppendorf) and the cycling program consisted of initial denaturation at 94°C for 5 minutes, followed by 30 cycles of denaturation at 94°C for 30 seconds, annealing at 46°C for 45 seconds, extension at 72°C for 59 seconds, and a final extension at 72°C for 7 minutes. A control positive for S. pyogenes ATCC 8668 and a control negative for S. pyogenes ATCC 8668 were included in each PCR run. The products were run on 1.5% agarose gel (w/vol.) containing 0.5 μg/mL ethidium bromide (Qiagen). Results were recorded using the gel documentation system (Protein Simple, San Jose, CA, USA). A 100-bp DNA ladder was used as a size marker (Roche). The PCR products were sent for sequence analysis (Bioneer Co., Daejeon, South Korea). The emm sequences were blasted against the emm database at the BLAST program, National Center for Biotechnology ( to determine the emm sequence type.

    The data were analyzed using SPSS version 14.0 (SPSS Inc., Chicago, IL, USA). In the univariate analysis, continuous and categorical data were analyzed using Student t test and the Mantel–Haenszel test, respectively.

    3. Results

    From 1000 throat samples obtained from children with sore throat of different severities (mild to severe), 25 samples were positive (2.5%) in which the isolates were identified as GAS on the basis of phenotypic identification criteria. The GAS isolates belonged to 14 (56%) male and 11 (44%) female patients. The results from susceptibility testing are presented in Table 1, showing fully and 84% sensitivity to penicillin and erythromycin, respectively. Chloramphenicol accounted for the least effective antibiotic (48%).

    Table 1:
    Antimicrobial susceptibility testing results for group A streptococcus isolates.

    The presence of the emm gene was analyzed using PCR, which generated a 914-bp band for all GAS isolates (Fig. 1). Blast analysis of sequence similarities for the 25 GAS isolates represented three different emm sequence types. The frequency of emm types among the GAS isolates were as follows: emm type 1, four isolates (16%); emm3, 20 isolates (80%); and emm75, one isolate (4%).

    Fig. 1:
    Polymerase chain reaction amplification of emm gene in streptococcus pyogenes. Lane 1, DNA size marker; Lane 2, positive control Streptococcus pyogenes ATCC 8668; Lane 3, negative control; Lanes 4–12, emm gene with length 914 bp.

    All of our GAS strains were isolated from patients with purulent pharyngitis and it seems that the emm3 type is mainly associated with severe pharyngitis in the region of study. The association between antimicrobial profile and emm type was also investigated in this study, where no significant correlation was observed (results not shown). In Table 2, the distribution of emm types are presented according to patients’ age and sex. The emm75 and emm3 types sequences were confirmed by GenBank with accession numbers LM999955 and LM999956, respectively.

    Table 2:
    emm type distribution according to patients’ age and sex.

    4. Discussion

    Streptococcal infections are a major problem in medical and health care centers. Typing of GAS is an important part of the epidemiological and pathogenetic studies of streptococcal diseases. Most of the understanding regarding GAS epidemiology is based on the M typing system including emm typing.17

    In our study, low strain diversity was noticed by emm typing, where emm3 was the most prevalent type with a frequency of 80%. This lower emm distribution is similar to a recent study from Northern Iran, in which four sequence types of emm5, emm12, emm79, and emm86 were reported with emm5 as the most prevalent.18 None of the types are similar to ours, which could be explained by the difference in climate and geographical conditions which may affect the GAS strain diversity; their study was conducted in a distinctly opposite geographical area, with a considerably different climate. In a similar study from China, 13 different emm types were identified among 185 GAS isolates from pharyngitis cases with emm1 and emm12 as the more prevalent types.12 However, in the study of Bahnan et al,19 from Lebanon, 33 different emm types were discovered in 103 GAS strains examined and the most prevalent types were reported as emm1 and emm22. Also, the reported prevalent types from Taiwan were emm1, emm4, and emm12, discovered in noninvasive streptococcal disease.20 Steer et al7 in a detailed study reported the similarities in emm type distribution between the developing and developed countries. For instance, the most common pharyngeal types reported in Asia, were emm44, emm12, and emm75, respectively. This variation in distribution of emm type profiles from different parts of the world shows that specific geographic conditions affect the emm diversity.

    In our study emm75 showed the lowest frequency and was different from the study of Sagar et al,21 in which they reported emm75 as the major type in isolates from patients’ throats.

    According to the susceptibility testing results, all our tested isolates were sensitive to penicillin and ampicillin which agrees with the findings of Jafarpour et al,18 Behnan et al,19 Le Hello et al,9 and Wu et al.22 Most researchers know erythromycin to be the best alternative drug for cases of penicillin allergy in infections caused by GAS in the oral cavity. Although the resistance to erythromycin is low in most countries, in recent years some local resistance to the drug has been reported due to overuse. In our study, a 4% resistance to erythromycin was noticed which is lower than the 15.6% in the study of Rijal et al,23 and 10% resistance in the study of Bahnan et al.19 Moreover, an incremental increase in GAS strains with resistance to erythromycin has been reported in Taiwan, Europe, and the USA.22

    Based on these results, it can be concluded that GAS still has good sensitivity to penicillin, and there is no obvious penicillin-resistant GAS at the present time in the studied region. Therefore, penicillin can be applied in the treatment of bacterial pharyngitis with or without susceptibility testing.

    4.1. Limitations

    This study had several limitations. Firstly, the number of cases included in our study was too small. Although we tested 1000 children with sore throats of different severities, and we tried to exclude those with antibiotic consumption or other respiratory complications, since this hospital is a referral children hospital for the whole province, the exact control of this exclusion criterion was difficult and perhaps this explains the low number of GAS recovered from this study population. Due to the same reason, we could not find any significant relationship between emm types and severity of the disease and antibiotic resistance.

    In conclusion, although the number of positive samples in our work was low, this study is the first report on emm typing from the southern part of Iran. Based on our findings, emm type 3 was the most prevent type in the region, and we still have no problem in the treatment of GAS pharyngitis cases with penicillin and erythromycin. From this study we may conclude that emm typing provides new insights on the genetic diversity of the M proteins and is of value for molecular studies of GAS. This is more valid when extended studies with higher numbers of isolates are conducted in the future.


    This work is part of the Master of Science thesis of Nasim Ebrahimifard which has been approved by the Infectious and Tropical Diseases Research Center and was financially supported by Research Affairs (Grant No. 92119), Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.


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    antibiotic resistance; emm typing; Streptococcus pyogenes

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