Early Targeted Next-Generation Sequencing Accelerates Clinical Recovery in Children with Community-Acquired Pneumonia: A Retrospective Study

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Abstract
Background & Objective: The clinical impact of testing timing for targeted next-generation sequencing (tNGS) in pediatric community-acquired pneumonia (CAP) is poorly understood. We hypothesized that early tNGS implementation accelerates clinical recovery and evaluated its comprehensive value. Methodology: In a retrospective study at Fujian Children's Hospital (2021-2023), 199 hospitalized children with CAP (BALF tested) were analyzed. Patients were grouped by tNGS vs. conventional testing (CT), with the tNGS group stratified into early (≤48h) and late (>48h) testing. We compared diagnostic yield, clinical outcomes, therapeutic adjustments, and costs. Results: tNGS demonstrated significantly higher sensitivity than CT for both bacteria (86.0% vs. 19.0%, P<0.001) and viruses (88.1% vs. 26.2%, P<0.001), and excelled at identifying mixed infections (55.8%). Critically, the early-testing group showed significantly shorter times to cough improvement (median 6.0 vs. 9.0 days, P=0.002) and rale resolution (median 7.0 vs. 8.0 days, P=0.027) compared to the late-testing group. This was associated with more timely therapeutic adjustments (P<0.05). A non-significant trend toward lower costs and shorter hospital stays was also observed. Conclusion: Early tNGS implementation in pediatric CAP not only enhances diagnostic yield but, more importantly, accelerates clinical recovery by facilitating timely, targeted therapeutic interventions. These findings provide strong evidence for integrating early tNGS into clinical workflows, marking a shift from simple pathogen identification to an outcome-driven diagnostic strategy.

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