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Updated: Oct 25, 2025

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
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Comprehensive Description of Pathogens and Antibiotic Treatment Guidance in Children With Community-Acquired

Liying Sun1,2, Chi Zhang1,2, Shuhua An3

  • 1NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.

Frontiers in Cellular and Infection Microbiology
|August 9, 2021
PubMed

Insights

Molecular methods improve diagnosis of community-acquired pneumonia (CAP) in children by identifying pathogens and guiding antibiotic therapy. This approach enhances bacterial detection and optimizes treatment, potentially reducing hospital stays.

Area of Science:

  • Pediatric infectious diseases
  • Molecular diagnostics
  • Microbiology

Background:

  • Community-acquired pneumonia (CAP) is a significant cause of childhood illness.
  • Accurate etiological diagnosis is crucial for effective antibiotic management.
  • Traditional culture-based methods have limitations in pathogen detection.

Purpose of the Study:

  • To evaluate the utility of combined mass spectrometry (MS)-based and quantitative real-time PCR (combined-MS) methods for diagnosing pediatric CAP.
  • To assess the impact of molecular diagnostics on guiding antibiotic therapy.
  • To compare the diagnostic yield of molecular methods with traditional culture techniques.

Main Methods:

  • Sputum samples from 302 hospitalized children with CAP were analyzed using combined-MS methods.
  • The methods detected 19 viruses and 12 bacteria associated with CAP.
  • Etiological findings guided antibiotic selection, compared to initial empirical treatments.

Main Results:

  • Respiratory pathogens were identified in 84.4% of patients.
  • Co-infections, particularly bacterial-viral, were prevalent (51.7%).
  • Combined-MS methods increased bacterial identification by 28.5% compared to culture (61.8% vs. 33.3%).

Conclusions:

  • Quantitative molecular testing of sputum is a valuable adjunct to culture methods for pediatric CAP.
  • Early etiological diagnosis via molecular methods aids in optimizing antibiotic selection.
  • Guiding therapy with molecular results may reduce unnecessary antibiotic use and shorten hospital stays for severe CAP.
Keywords:
antibiotic therapycommunity-acquired pneumoniamass spectrometrymolecular testingrespiratory pathogens

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