Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit

Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients’ clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children’s Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.