Evaluating clinical decision rules and rapid diagnostic tests for the diagnosis of Streptococcus pyogenes pharyngitis in Gambian children: A diagnostic accuracy study

Objectives: Accurate diagnosis of Streptococcus pyogenes (S. pyogenes) pharyngitis is imperative in high rheumatic heart disease-burden countries. We aimed to assess the diagnostic accuracy of two rapid diagnostic tests and five clinical decision rules (CDRs) in The Gambia. Methods: Children under 16 years presenting with signs and symptoms of pharyngitis were recruited at Sukuta Health Centre, The Gambia. A rapid antigen detection test (SD Bioline; LFT) and a rapid gene-amplification test (ID NOW™ STREP A2) were assessed for diagnostic accuracy alongside five CDRs against culture and qPCR for S. pyogenes. Logistic regression was used to determine risk factors for S. pyogenes pharyngitis. Results: Among 376 participants, S. pyogenes positivity was 9·8% (37/376) by culture, 32·4% (122/376) by PCR, 31·6% (119/376) by LFT, and 33·3% (122/366) by ID NOW. The ID NOW had sensitivities and specificities of 94·6% and 73·6% against culture, and 93·5% and 87·6% against PCR. The LFT had sensitivities and specificities of 83·8% and 74·0% against culture and 55·7% and 80·0% against PCR. The Smeesters CDR performed best with an area under the curve (AUC) of 0·694 against culture. S. pyogenes pharyngitis risk increased with age. Recent chest infection/cough (aOR 1·89, 1·08–3·28) and concurrent skin infection (aOR 2·11, 1·21–3·69) were associated with increased S. pyogenes pharyngitis. Conclusions: The LFT and the CDRs had poor performance in detecting S. pyogenes pharyngitis compared to PCR and culture. Molecular methods detected a higher proportion of S. pyogenes than culture. Affordable and sensitive diagnostics are urgently needed to improve S. pyogenes management in resource-limited settings.