Landscape of the upper and lower airway microbiota in children with community-acquired pneumonia

Community-acquired pneumonia (CAP) is one of the most common causes of death in children. Obtaining lower airway samples from children with CAP has so far remained challenging. This multicenter study enrolled 198 children with CAP indicated for fiberoptic bronchoscopy. Nasopharyngeal aspirates and bronchoalveolar lavage fluid (BALF) were collected for targeted next-generation sequencing (tNGS) and 16S ribosomal RNA (rRNA) sequencing to compare the pathogens and microbiota. Firstly, diversities of the microbiota between the upper and lower airways were compared. Then, diversities of the lower airway microbiota were analyzed among different pathogen groups and outcome groups. The high consistency was observed between the first pathogen detected in the upper and lower airways of children with CAP by tNGS. Diversity indices were higher in the upper airways than in the lower airways in children with CAP. The upper airway richness indices were higher in the group with consistent top pathogens between the upper and lower airways. Mycoplasma infection was related to the reduced diversity of the lower airway microbiota compared to Bacteria and Virus groups. The oxygen group showed higher abundance of Pseudomonas, with Moraxella being the most representative microbiota in this group.