Background: Streptococcus pyogenes (Group A streptococcus) is an important Gram-positive human pathogen affected the upper respiratory tract, such as the tonsils and pharynx, and is also induces post-infection diseases such as rheumatic fever and glomerulonephritis. This study aim to isolate Streptococcus pyogenes from children with pharyngitis and to evaluate the molecular identification of S. pyogenes compared with conventional methods. Methods: A cross sectional study was conducted on total of 200 throat swab samples which were collected from children with pharyngitis referred to Wad medani Pediatric Teaching Hospital and Wad medani ENT hospital from January to November 2021. Demographic and clinical data were collected by questionnaire. Throat swabs were tested with the standard microbiological techniques to isolated Group A streptococcus (GAS). Antimicrobial susceptibility testing was performed to all GAS isolates using the Kirby Bauer disk diffusion method according to clinical laboratory standard institute (CLSI) guidelines. Additionally, PCR was used to identify Spy 1258 gene of isolated bacteria. Results: From all throat swab samples screened, 51 isolates (25.5%) were identified as GAS. Antibiotic susceptibility testing revealed that all the GAS isolates were sensitive to Penicillin and Azithromycin. Sensitivity to Erythromycin, Gentamicin, Clarithromycin, Amoxicillin and Cephalexin were 88.2%, 86.3%, 45.1%, 41.2%, 13.7%, respectively. Based on PCR identification of Spy 1258 gene the percentage of isolated bacteria was 21%. Conclusion: The rate of isolated Streptococcus pyogenes was 25.

Background: Streptococcus pyogenes (group A streptococcus, GAS) is an important human bacterial pathogen. This organism possesses many virulence factors, Streptococcal pyrogenic exotoxinone of these. Aim: Detection of Streptococcal pyrogenic exotoxin SpeA and SpeB in isolated Streptococcus pyogenes. Methods: Tow hundred throat swab samples were collected from children with pharyngitis referred to Pediatric Teaching hospital and ENT hospital Wad medani, Sudan, from January to November 2021. The questionnaire was filled out to collect clinical and demographic data. Throat swabs were collected and processed with the standard microbiological procedure to isolate Streptococcus pyogenes. Antimicrobial susceptibility testing was done on all GAS isolates using the Kirby Bauer disk diffusion method according to clinical laboratory standard institute (CLSI) guidelines. Detection of Spy 1258 gene and Streptococcal pyrogenic exotoxins SpeA and SpeB were done by using Multiplex PCR. Results: Amongst the Tow hundred collected samples fifty-one isolates (25.5%) were identified as S. pyogenes. Antibiotic susceptibility testing showed that all the GAS isolates were sensitive to Azithromycin and Penicillin. Sensitivity to Erythromycin, Gentamicin, Clarithromycin, Amoxicillin and Cephalexin were 88.2%, 86.3%, 45.1%, 41.2%, 13.7%, respectively. SpeA was detected in 17 (33.3%) and SpeB in 48 (94.1%). Conclusion: Streptococcal pyrogenic exotoxin genes SpeA and SpeB were detected in 17 (33.3%) and 48 (94.1%