Comparative Metagenomic Analysis of the Nasopharyngeal Microbiome in Healthy and Community-Acquired Pneumonia Pediatric Patients

Objective This study investigated the nasopharyngeal microbiome in Egyptian children with community-acquired pneumonia (CAP), comparing it with that of healthy children and their mothers, to better understand its role in disease progression and potential diagnostic value. Material and Methods Nasopharyngeal swabs from 31 participants were analyzed using shotgun metagenomic sequencing and bioinformatics to profile microbial communities and their functional potential. Results Children with CAP showed higher levels of pathogens such as Moraxella catarrhalis and Streptococcus pneumoniae, alongside a marked reduction in beneficial Dolosigranulum pigrum. Healthy children displayed a balanced community dominated by Dolosigranulum pigrum and Corynebacterium species, while mothers’ microbiomes were enriched with Cutibacterium acnes. Functional profiling revealed CAP-associated enrichment of specific metabolic pathways, indicating possible therapeutic targets. Conclusion Alterations in the nasopharyngeal microbiota appear to be closely linked to pediatric CAP, highlighting its potential role in early diagnosis and informing future treatment approaches