PCR-based detection reveals threefold underdiagnoses of Group A Streptococcus and Pathogenic Non-Group A Streptococci Predominance in Iraqi Tonsillitis Patients

<ns3:p>Background Beta-hemolytic streptococci (BHS) constitute a significant etiology of tonsillitis and rheumatic heart disease (RHD), affecting approximately 55 million individuals and causing 360,000 deaths annually worldwide. In the Middle East and North Africa region, RHD prevalence reaches 389 per 100,000 population, though diagnostic inadequacies may obscure the true disease burden. This investigation compared polymerase chain reaction (PCR)-based detection with conventional culture-based methods for BHS identification in Iraqi tonsillitis patients and assessed associated clinical, immunological, and systemic dissemination parameters. Methods A prospective cross-sectional study included 250 tonsillitis patients at Ramadi General Hospital, Iraq (April 2020–January 2025) and 25 healthy controls. Diagnostics comprised throat culture with Lancefield serogrouping, bacitracin testing, and PCR targeting the spy1258 gene. Blood specimens underwent PCR for systemic bacterial detection. Statistical analyses included chi-square testing, logistic regression, and diagnostic accuracy calculations. Results PCR detected Group A Streptococcus (GAS) in 52 of 83 (62.7%) culture-positive specimens, whereas Lancefield serogrouping identified only 19 (22.9%), representing a statistically significant threefold detection disparity (p &lt; 0.001). PCR demonstrated 100% sensitivity and 100% specificity. Groups C and F streptococci comprised the majority of isolates. Elevated anti-streptolysin O (ASO) titers (≥200 IU/mL) were observed in 42.2% of non-GAS infections. Among severe cases, 45.7% demonstrated positive blood PCR for GAS DNA, indicating systemic dissemination. The highest disease burden occurred in the 6–15 years age cohort (54.2% of all isolates). DNA extraction optimization achieved an estimated efficiency of 90.4% compared to negligible efficiency with standard methodologies. Conclusion PCR-based diagnostics detected threefold more GAS cases than serological methods, revealing significant underdiagnosis. Non-Group A streptococci showed pathogenic potential and may cause post-infectious complications, warranting revised diagnostic paradigms.</ns3:p>