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Background Nasopharyngeal colonisation with clinically relevant bacterial pathogens is a risk factor for severe infections, such as pneumonia and bacteraemia. In this study, we investigated the determinants of nasopharyngeal carriage in febrile patients in rural Burkina Faso. Methods From March 2016 to June 2017, we recruited 924 paediatric and adult patients presenting with fever, hypothermia or suspicion of severe infection to the Centre Medical avec Antenne Chirurgicale Saint Camille de Nanoro, Burkina Faso. We recorded a broad range of clinical data, collected nasopharyngeal swabs and tested them for the presence of  Streptococcus pneumoniae ,  Haemophilus influenzae ,  Moraxella catarrhalis ,  Staphylococcus aureus  and  Klebsiella pneumoniae  by quantitative polymerase chain reaction. Using logistic regression, we investigated the determinants of carriage and aimed to find correlations with clinical outcome. Results Nasopharyngeal colonisation with  S. pneumoniae ,  H. influenzae  and  M. catarrhalis  was highly prevalent and strongly dependent on age and season. Females were less likely to be colonised with  S. pneumoniae  (OR 0.71, p = 0.022, 95% CI 0.53–0.95) and  M. catarrhalis  (OR 0.73, p = 0.044, 95% CI 0.54–0.99) than males. Colonisation rates were highest in the age groups &lt; 1 year and 1–2 years of age and declined with increasing age. Colonisation also declined towards the end of the rainy season and rose again during the beginning of the dry season.  K. pneumoniae  prevalence was low and not significantly correlated with age or season. For  S. pneumoniae  and  H. influenzae , we found a positive association between nasopharyngeal carriage and clinical pneumonia [OR 1.75, p = 0.008, 95% CI 1.16–2.63 ( S. pneumoniae ) and OR 1.90, p = 0.004, 95% CI 1.23–2.92 ( H. influenzae )].  S. aureus  carriage was correlated with mortality (OR 4.01, p &lt; 0.001, 95% CI 2.06–7.83), independent of bacteraemia caused by this bacterium. Conclusions Age, sex and season are important determinants of nasopharyngeal colonisation with  S. pneumoniae ,  H. influenzae  and  M. catarrhalis  in patients with fever in Burkina Faso.  S. pneumoniae  and  H. influenzae  carriage is associated with clinical pneumonia and  S. aureus  carriage is associated with mortality in patients with fever. These findings may help to understand the dynamics of colonisation and the associated transmission of these pathogens. Furthermore, understanding the determinants of nasopharyngeal colonisation and the association with disease could potentially improve the diagnosis of febrile patients.

Nasopharyngeal colonisation dynamics of bacterial pathogens in patients with fever in rural Burkina Faso: an observational study