Evaluating the Molecular Identification of Streptococcus pyogenes Isolated from Children with Pharyngitis in Gezira State, Sudan

Background: Streptococcus pyogenes (Group A streptococcus) is an important Gram-positive human pathogen that affects the upper respiratory tract, such as the tonsils and pharynx, and also induces post-infection diseases such as rheumatic fever and glomerulonephritis. The infection rate is more than 600 million infections annually resulting in more than 500,000 deaths a year.

Aim: This study aims 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 a 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 isolate Group A streptococcus (GAS). Antimicrobial susceptibility testing was performed on all GAS isolates using the Kirby Bauer disk diffusion method according to Clinical Laboratory Standard Institute (CLSI) guidelines. Additionally, PCR was used to identify the Spy 1258 gene of isolated bacteria. Statistical analysis was done by SPSS statistical software.

Results: From all throat swab samples screened, 51 isolates (25.5%) were identified as GAS. The study showed the Spy 1258 gene specific for S. pyogenes only when tested for other species including Staphylococcus aureus, Coagulase negative staphylococci, other streptococci, E. coli and human DNA. 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 25.5% by conventional methods and 21% by PCR. The bacteria were sensitive to Penicillin and Azithromycin. The Spy 1258 gene was specific for the detection of Streptococcus pyogenes.