Spatiotemporal dynamics of the oropharyngeal microbiome in a cohort of Ivorian school children

The respiratory tract harbours microorganisms of the normal host microbiota which are also capable of causing invasive disease. Among these, Neisseria meningitidis a commensal bacterium of the oropharynx can cause meningitis, a disease with epidemic potential. The oral microbiome plays a crucial role in maintaining respiratory health. An imbalance in its composition is associated with increased risk of invasive disease. The main objective of this study was to evaluate changes in the spatio-temporal dynamics of the oropharyngeal microbiota considering meningococcal carriage in a cohort of 8-12-year-old school children within (Korhogo) and outside (Abidjan) of the meningitis belt of Côte d'Ivoire. A significant geographic difference in the oropharyngeal microbiome was identified between the two study sites in terms of bacterial abundance and diversity (p < 0.001), with greater diversity in children in Abidjan than in Korhogo. Meningococcal carriage was low in the cohort with eight Neisseria carriers identified in Korhogo (3.64%) including one Neisseria meningitidis (0.45%). No Neisseria were detected in Abidjan indicating geographical differences in carriage (p = 0.006). Negative correlations were also found between Neisseria abundance and humidity. Meningococcal carriage was very low during the study; however, Neisseria carriage differed between the two study areas, with a higher frequency in children in Korhogo. Analysis of the oropharyngeal microbiome showed significant differences between children followed in Abidjan and Korhogo with higher microbial diversity in Abidjan, which is generally associated with better health status. Significant correlations between Neisseria or other pathogens carriage and climatic variables (Temperature, Relative humidity, and Wind speed) were also demonstrated, indicating an important role of climate in the carriage of these bacteria; an important element to note in the current context of climate change.