Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing (mNGS) in Hospital-Acquired Pneumonia: A Stratified Retrospective Study of Responders and Non-Responders.

Introduction: Hospital-acquired pneumonia (HAP) remains a major challenge in clinical practice, particularly due to polymicrobial infections and antimicrobial resistance. Traditional diagnostic methods, such as culture and PCR, are limited by low sensitivity, slow turnaround time, and inability to detect fastidious or novel pathogens. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to pathogen detection and may improve diagnostic accuracy and clinical decision-making. Methods: We conducted a retrospective study of 300 adult HAP patients admitted to Beijing Rehabilitation Hospital, China. Bronchoalveolar lavage fluid samples were analyzed using the Illumina sequencing platform for mNGS. Detection rates, pathogen spectrum, resistance gene identification, and treatment modifications were compared with conventional culture methods. Results: mNGS achieved a pathogen detection rate of 92%, significantly higher than the 72% achieved by culture. It identified a broader spectrum of bacteria, fungi, and viruses, including Pseudomonas, Klebsiella, and Aspergillus, which were often missed by culture. Polymicrobial infections were detected in 28% of cases, and antibiotic resistance genes were identified in 30% of samples. The median turnaround time for mNGS results was 48 hours after BAL sampling. Based on mNGS findings, treatment regimens were adjusted in 26% of patients. Conclusion: mNGS demonstrated superior diagnostic performance compared with culture by increasing pathogen detection rates, identifying resistance genes, and guiding treatment adjustments in HAP patients. Despite its promise for precision medicine, further studies are needed to assess cost-effectiveness and generalizability, given the retrospective and single-center design of this study.