Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence.

Summary

In a prospective study of 78 pneumonia patients, tNGS accurately identified causative pathogens (accuracy 0.852), while concurrently detecting AMR and virulence genes. Presence of virulence genes was associated with higher rates of severe pneumonia and ARDS, suggesting tNGS can inform both diagnosis and severity assessment.

Key Findings

• Prospective analysis of 78 samples (67 BALF, 11 sputum) using tNGS, mNGS, and conventional tests.
• tNGS pathogen detection accuracy was 0.852 (95% CI 0.786–0.918), comparable to mNGS and superior to conventional tests.
• Detection of 81 AMR genes and direct identification of 75.8% (25/33) of priority drug-resistant pathogens.
• Identification of 144 virulence genes; virulence-positive patients had higher rates of severe pneumonia (95.0% vs 42.9%, P=0.009) and ARDS (55.0% vs 0%, P=0.022).

Clinical Implications

tNGS can streamline early etiologic diagnosis, guide targeted antimicrobials via AMR profiling, and flag high-risk patients (e.g., virulence-positive) for closer monitoring for ARDS. Implementation could complement or replace slower conventional testing in select settings.

Limitations

• Single-center study with a modest sample size (n=78).
• Clinical outcome impact, turnaround time, and cost-effectiveness were not directly assessed.

Future Directions

Multicenter validation, integration into antimicrobial stewardship and ICU triage, and prospective assessment of turnaround time, clinical impact, and cost.