Prevalence of key bacterial pathogens among children with pharyngotonsillitis in The Gambia – a case-control study

OBJECTIVES: Causes of pharyngotonsillitis in Africa, beyond Streptococcus pyogenes, are poorly understood. We aimed to describe the prevalence of S. pyogenes, Fusobacterium necrophorum, and Streptococcus dysgalacatiae subspecies equisimilis (SDSE) in children in The Gambia and evaluate the usefulness of clinical decision rules, originally developed for S. pyogenes or beta-haemolytic streptococci, for their prediction. METHODS: We conducted a case-control study on causes of pharyngotonsillitis in children (0-15 years). Samples from age-matched cases and asymptomatic controls were included from two previous studies in The Gambia, conducted June 2021 to September 2022. Pharyngeal swabs were analysed with multiplex-PCR, targeting S. pyogenes, F. necrophorum, and SDSE. Cases and controls were compared, and performance of clinical decision rules evaluated. RESULTS: Only S. pyogenes was more frequently detected among cases (N=376) than controls (n=105) (32% vs. 11%, p<0.0001). No difference was seen for F. necrophorum (9% vs. 10%, p=0.95) or SDSE (11% vs. 14% p=0.19). Clinical decision rules poorly predicted any of the pathogens. CONCLUSIONS: S. pyogenes was the only pathogen more prevalent among cases. F. necrophorum was more common in pharyngeal samples from children in The Gambia than previously described in high-income countries, yet neither F. necrophorum or SDSE differed between cases and controls.