Resilience of the nasopharyngeal microbiota following childhood lower respiratory tract infection

Introduction: Lower respiratory tract infections (LRTI) are highly prevalent in children, and are often followed by recurrent respiratory problems. Dysbiosis of the nasopharyngeal microbiota appears important to LRTI pathogenesis, but it is unknown how the microbiota recover after the infection is cleared, and if this relates to infection recurrence. Methods: We therefore characterised the nasopharyngeal microbiota of 154 children with a LRTI at hospital admission and 2 months after discharge, and of 307 matched healthy controls. Results: First, we observed that 2 months after hospital discharge, the microbiota composition had largely normalised (i.e. comparable to healthy controls), and this ‘ecological recovery’ was mostly independent of antibiotic therapy. However, we observed that in 64% of cases a recurrent infection had occurred during follow-up: for this group, a significant difference remained in the microbiota composition compared to healthy matched controls, with especially increased abundance of typically oral taxa like Prevotella oris. Moreover, when analysing the microbiota composition at time of admission stratifying for consecutive recurrence of infection, we also observed a significant difference, which was mostly explained by a more pronounced increase in abundance of Haemophilus influenzae, P. oris and other oral taxa in cases with consecutive recurrence. Stratifying for age and infection phenotype showed that especially older children with wheezing-type LRTI had both increased risk of recurrence and decreased microbiota recovery. Conclusion: Our results imply that both host and microbiota during and following LRTI are involved in risk of recurrence of infections.