Profile of bacterial meningitis pathogens circulating in a cohort of school children in Côte d’Ivoire using 16S rRNA gene sequencing

BACKGROUND: Bacterial meningitis represents a critical public health concern in sub-Saharan African school settings, where conditions favor its transmission. This study uses 16S rRNA gene sequencing to investigate the presence, relative abundance, and genetic relatedness of the three main bacterial meningitis pathogens in oropharyngeal samples from schoolchildren aged 8-12 years in Côte d'Ivoire. METHODS: 76 children from two Ivorian primary schools (37 Korhogo, 39 Abidjan) were followed up for six months. Nucleic acids from oropharyngeal swabs (444 samples) were analyzed by 16S rRNA sequencing, and phylogenetic relationships were inferred using the Maximum Likelihood method. RESULTS: H. influenzae showed the highest carriage prevalence (81.94%, 59/72), Abidjan (81.6%, 31/38) and Korhogo (82.4%, 28/34). Neisseria meningitidis and Streptococcus pneumoniae were rare (1.39%, 1/72 and 2.78%, 2/72, respectively) and detected only in Korhogo (2.9% and 5.9%). Genus-level relative abundances were 15.4% (Haemophilus), 12.9% (Streptococcus) and 5.4% (Neisseria). Species-level relative abundances of Hi, Nm, and Sp were 0.16%, 0.03%, and 0.003%, respectively. Mixed-effects logistic regression showed that Nm (OR = 0.056, 95% CI: 0.014-0.231, p < 0.001) and Sp (OR = 0.055, 95% CI: 0.007-0.407, p = 0.004) were less likely to colonize than Hi. No significant difference was observed between cities (OR = 0.96, 95% CI: 0.58-1.60, p = 0.887). High inter-individual variability (SD = 0.91) was observed, with one-third of bacterial species shared between sites. CONCLUSION: These findings highlight the utility of 16S rRNA sequencing for culture-independent detection of carriage of key meningitis pathogens, pending further species-level confirmation.