Comparative and clinical impact of targeted next-generation sequencing in pediatric pneumonia diagnosis and treatment

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Hui Shang1, Sini Zou1, Zhanying Ma1

  • 1Department of Pediatrics, Dongguan Maternal and Child Health Care Hospital, Dongguan, China.

Frontiers in Microbiology
|July 10, 2025
PubMed
Abstract

Insights

Targeted next-generation sequencing (tNGS) significantly improves pathogen detection in pediatric community-acquired pneumonia (CAP) compared to conventional microbial tests. This advanced method enhances diagnosis, especially for co-infections, leading to better patient outcomes.

Area of Science:

  • Microbiology
  • Pediatric Infectious Diseases
  • Genomics

Background:

  • Community-acquired pneumonia (CAP) is a major global cause of childhood illness and death.
  • Conventional microbial tests (CMTs) often fail to identify all causative agents in pediatric CAP, particularly in co-infections.
  • Targeted next-generation sequencing (tNGS) offers a more comprehensive approach to pathogen identification.

Purpose of the Study:

  • To compare the diagnostic performance of tNGS against CMTs in pediatric CAP.
  • To evaluate the effectiveness of tNGS in detecting a broader range of pathogens, including co-infections.
  • To assess the impact of tNGS on clinical management and patient outcomes.

Main Methods:

  • A retrospective analysis of 206 pediatric CAP patients was performed.
  • Bronchoalveolar lavage fluid (BALF) samples were analyzed using both tNGS and CMTs.
  • Clinical diagnoses served as the reference standard, with optimized relative abundance thresholds for tNGS to minimize false positives.

Main Results:

  • tNGS detected pathogens in 97.0% of cases, significantly outperforming CMTs (52.9%).
  • tNGS demonstrated superior detection rates for viral pathogens and bacterial co-infections.
  • tNGS results led to adjusted clinical management in 41.7% of patients, reducing hospital stays in severe cases.

Conclusions:

  • tNGS offers significantly enhanced pathogen detection in pediatric CAP compared to CMTs.
  • Optimized tNGS with standardized thresholds improves diagnostic specificity and aids in identifying co-infections.
  • Integrating tNGS into routine diagnostics can facilitate precise and timely therapeutic interventions for pediatric CAP.
Keywords:
bronchoalveolar lavage fluid (BALF)pathogen detectionpediatric pneumoniatargeted next-generation sequencing (tNGS)treatment

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