Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status.

PURPOSE

Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions.

PATIENTS AND METHODS

A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status.

RESULTS

In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, =9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was (42/180, 23.3%) in bacterum level, in fungus level (44/180, 24.4%), and (39/180, 27.5%) in virus level. However, for mNGS results, in 34.9% of positive patients, and in 7.7% of positive cases were confirmed as pathogens causing pneumonia. detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. was more likely to infect immunocompromised patients (=0.002). (14.8% vs 0.0%, =0.008) and (26.1% vs 5.3%, =0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including , and majority of viruses.

CONCLUSION

mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.