Background: Accurate etiological diagnosis of community-acquired pneumonia (CAP) is essential for guiding targeted therapy. However, conventional bronchoalveolar lavage (cBAL) is susceptible to contamination by commensal or background microorganisms, potentially compromising diagnostic accuracy. This study aimed to evaluate the clinical value of hand-drawn navigation-guided transbronchial precision bronchoalveolar lavage (TB-PBAL) combined with metagenomic next-generation sequencing (mNGS) in enhancing the etiological diagnosis of CAP.

Methods: A total of 50 CAP patients were enrolled in the study. Each patient underwent TB-PBAL under hand-drawn navigation guidance and cBAL. The lavage fluids obtained by these two techniques were designated as the experimental group (TB-PBAL) and the control group (cBAL), respectively. All samples were analyzed using mNGS, and detection rates of pathogens, pathogenic bacteria, and background bacteria were compared. Differences in pathogen detection rate, relative abundance of pathogenic bacteria, background bacterial detection rate, mixed infection rate, pathogenic bacteria signal-to-noise ratio (S/N ratio), and clinician preference for test reports were statistically analyzed.

Results: The overall pathogen detection rates showed no significant difference between the two groups (95.70% vs. 93.20%, p > 0.05). Notably, TB-PBAL demonstrated a significantly higher relative abundance of pathogenic bacteria compared with cBAL (67.42% ± 11.28% vs. 31.25% ± 9.46%, p < 0.001), with predominant pathogens including Haemophilus influenzae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis. TB-PBAL yielded significantly lower background microbial interference, as evidenced by reduced background bacterial detection rates (38% vs. 64%, p = 0.009) and sequence counts (25.30 ± 10.60 vs. 82.70 ± 15.40, p < 0.001). Consequently, the signal-to-noise ratio for pathogenic bacteria was markedly higher in the TB-PBAL group (6.50 ± 2.12 vs. 3.23 ± 1.45, p < 0.001). In blinded clinical assessments, physicians demonstrated significantly greater preference for TB-PBAL-derived mNGS reports (50% vs. 30%, p = 0.041).

Conclusion: Hand-drawn navigation-guided TB-PBAL combined with mNGS significantly improves etiological diagnosis of CAP by enriching the relative abundance of true pathogens, minimizing background microbial interference, enhancing the signal-to-noise ratio, and increasing clinician confidence in sequencing results.