Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen...

Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%, P < 0.001), bacterial (69.29% vs 12.60%, P < 0.001), and fungal (11.81% vs 3.15%, P = 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%, P = 0.99) and Mycoplasma pneumoniae (48.03% vs 45.67%, P = 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for M. pneumoniae had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of M. pneumoniae and respiratory viruses. Different detection methods should be rationalized for different pathogens.

This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of Mycoplasma pneumoniae and respiratory viruses and may have greater application advantages in combination with CMTs, such as M. pneumoniae IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.