Our study showed that some differences in the microbiological diagnosis via endotracheal aspirate (ETA) mNGS and bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) appear to exist. Clinicians also expressed a lack of confidence in the diagnostic results of ETA.

Although BALF mNGS did not result in better long-term prognosis compared with ETA mNGS, we still do not recommend ETA mNGS as the first-choice method for diagnosing airway pathogenic specimens from severe pneumonia patients, given the greater improvement in pneumonia, shorter mechanical ventilation time, and shorter ICU stay in the BALF group.

An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections.

However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%.

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