Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia

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 <i>Mycoplasma pneumoniae</i> and respiratory viruses and may have greater application advantages in combination with CMTs, such as <i>M. pneumoniae</i> 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.