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Abstract Background Lower respiratory tract infections, notorious for high mortality, are inadequately addressed by traditional diagnostics, highlighting the need for more effective methods. The advent of next-generation sequencing (NGS) offers a promising solution. This study evaluates the performance of three NGS methodologies—metagenomic NGS (mNGS), amplification-based targeted NGS (tNGS), and capture-based tNGS—in identifying pathogens in bronchoalveolar lavage fluid. Methods We compared these methods against conventional microbiological tests and comprehensive clinical diagnosis in 205 patients, focusing on sensitivity, specificity, and pathogen detection capabilities. Results Capture-based tNGS demonstrated the highest sensitivity (99.43%) and positivity (90.73%), significantly outperforming the others in samples negative by conventional tests. While mNGS showed broader pathogen coverage, it underperformed in detecting RNA viruses. Amplification-based tNGS, constrained by primer and panel design, missed certain bacteria and DNA viruses. Both tNGS methods effectively identified SARS-CoV-2 genotypes, with capture-based tNGS providing more detailed distinctions. The study also detected several antimicrobial resistance genes and virulence factors, indicating a broader spectrum of pathogen identification by capture-based tNGS. Conclusion These findings suggest that the choice of NGS method should be tailored to specific clinical needs and objectives, with capture-based tNGS showing superior diagnostic utility.
Li et al. (Wed,) studied this question.