Metagenomic next-generation sequencing of bronchoalveolar lavage fluid from children with severe pneumonia in pediatric intensive care unit

Background: Severe pneumonia from lower respiratory tract infections is a major cause of morbidity and mortality in children, and noninfectious syndromes can mimic infection, complicating diagnosis and targeted therapy. This study applied metagenomic next-generation sequencing (mNGS) to bronchoalveolar lavage fluid (BALF) from children with severe pneumonia in a PICU to characterize the microbiome and identify potential pathogens. Methods: From February 2018 to February 2020, 126 BALF samples from PICU patients meeting WHO criteria for severe pneumonia were tested by mNGS at the DNA and/or RNA level. Identified microorganisms were correlated with serum inflammatory markers, lymphocyte subsets, and clinical symptoms. Results: mNGS detected potentially pathogenic bacteria in BALF and showed that higher bacterial diversity indices correlated positively with serum inflammatory indicators and lymphocyte subtypes. Potential viral coinfections (e.g., Epstein–Barr virus, Cytomegalovirus, Human betaherpesvirus 6B) were identified, with viral abundance positively associated with immunodeficiency and pneumonia severity, suggesting possible viral reactivation. Potential fungal coinfections (e.g., Pneumocystis jirovecii, Aspergillus fumigatus) were found; increased potentially pathogenic eukaryotic diversity in BALF was positively associated with death and sepsis.