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Decoding pulmonary infections through targeted next-generation sequencing: comprehensive pathogen profiling in 999

Haiqiang Hu¹, Lu Liu², Shuli Yu¹

¹The First People's Hospital of Linping District, Department of Clinical diagnostics laboratory, Hangzhou, Zhejiang, China.

Frontiers in Cellular and Infection Microbiology

|June 1, 2026

Summary

Targeted next-generation sequencing (tNGS) rapidly identifies diverse respiratory pathogens in pulmonary infections, outperforming conventional methods. This advanced technique reveals complex microbial landscapes and aids in precise patient management.

Keywords:

mixed infection pathogen detection pulmonary infection respiratory microbiology targeted next-generation sequencing

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Area of Science:

Microbiology
Infectious Diseases
Genomics

Background:

Pulmonary infections pose a global health threat.
Conventional diagnostics often fail to identify pathogens.
Targeted next-generation sequencing (tNGS) offers multiplexed pathogen detection.

Purpose of the Study:

To validate the diagnostic and epidemiologic value of tNGS in a large clinical cohort.
To evaluate the pathogen spectrum and diagnostic yield of tNGS for respiratory infections.
To characterize age- and season-specific differences in pathogen prevalence.

Main Methods:

Analysis of pulmonary samples (sputum, BALF, throat swabs) from 999 patients.
Utilized a tNGS assay targeting 153 common pathogens.
Evaluated diagnostic yield, pathogen spectrum, and demographic variations.

Main Results:

tNGS identified pathogens in 84.5% of cases, revealing a diverse microbial landscape.
Viral pathogens were more common in children; bacterial pathogens (e.g., M. tuberculosis, M. pneumoniae) predominated in adults.
Mixed infections were frequent (70.5% of positive cases), highlighting complex pathogen interactions.

Conclusions:

tNGS provides comprehensive and rapid detection of respiratory pathogens, including those missed by standard methods.
Application of tNGS to pulmonary samples offers valuable insights for diagnosing and managing respiratory infections.
The study underscores the utility of tNGS in uncovering complex infection patterns and supporting precision medicine.