A nationwide study of pathogens in hospitalized patients with lower respiratory tract infections by metagenomic next-generation sequencing.

Lower respiratory tract infections remain a major cause of morbidity and mortality, yet timely etiologic diagnosis is difficult because of the breadth of possible pathogens and the limitations of conventional microbiological tests. We retrospectively analyzed 30,819 clinical specimens from 27,507 hospitalized patients with lower respiratory tract infections across 31 provincial-level regions in mainland China from April 2019 to May 2025 to characterize the pathogen spectrum detected by metagenomic sequencing. In total, 323 pathogens were identified, 33.74% of which were fastidious or unculturable microorganisms. The overall positivity rate was 80.12%, and 65.48% of positive specimens showed co-detections. The top 20, 50, 100, 150, and 200 pathogens accounted for 70.17%, 87.56%, 95.59%, 98.18%, and 99.26% of all reported pathogens, respectively. Pathogen distributions differed by age, season, geography, clinical department, and comorbidity, and several epidemiological shifts were observed across the pre-pandemic, pandemic, and post-restriction periods, including persistent declines in Streptococcus pneumoniae and Chlamydia psittaci. These findings demonstrate the breadth of organisms detected by metagenomic sequencing in routine practice and support its value for broad etiologic assessment of lower respiratory tract infections.IMPORTANCELower respiratory tract infections are frequently managed before the etiologic agent is established because many bacteria, viruses, fungi, and other organisms can produce similar clinical syndromes, and conventional tests do not capture this diversity well. By analyzing more than 30,000 real-world specimens from hospitalized patients across mainland China, this study shows which organisms are most often detected by metagenomic sequencing, how frequently mixed detections occur, and how pathogen patterns vary by age, geography, season, clinical setting, and the 2019 coronavirus disease period. These findings clarify where broad-range sequencing can add value for microbiology, surveillance, and future targeted panel design.