Next generation sequencing to detect pathogens causing paediatric community-acquired pneumonia - A systematic review...

Paediatric community-acquired pneumonia (CAP) is a major public health challenge in children, requiring accurate and timely diagnosis of causative pathogens for effective antibiotic treatment. We aimed to explore the utility of next-generation sequencing (NGS) in precise diagnosis of pediatric CAP and its effect on treatment outcome of these children.

A systematic review and meta-analysis was conducted to compare NGS-guided antibiotic therapy with conventional methods in pediatric CAP. The study followed PRISMA guidelines and searched for electronic databases including PubMed/MEDLINE, Embase, Scopus, and Web of Sciences from 2012 to 2023. Studies on pediatric CAP (<18 years) using NGS alongside conventional diagnostics, were included.

Database search identified 721 studies and 6 were finally included for review, published between 2019 and 2023. Meta-analysis revealed an overall odds ratio of 2.39 (95 % CI 1.22, 3.56) for NGS vs conventional methods. Detection rates using NGS ranged from 86% to 100 %, surpassing conventional methods (26%-78.51 %). Five out of selected 6 studies (83.33 %) have documented that change in treatment based on NGS finding resulted in clinical improvement of patients. There was no significant heterogeneity and potential bias among the studies. Nearly 80 % of the studies were of good quality.

The NGS (particularly metagenomic sequencing) is a promising tool for diagnosing paediatric CAP with high accuracy. It can improve antibiotic usage practices and patient outcomes, potentially reducing antibiotic resistance. Based on meta-analysis, training of healthcare professionals in NGS methodologies and result interpretation is highly recommended.