Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice

Abstract Background Pulmonary infection remains one of the leading infectious diseases of hospitalization. Metagenomic next-generation sequencing (mNGS) has been proven to be a promising diagnostic technology in etiological identification for pulmonary infection. But when applying mNGS to clinical practice, physicians still face many challenges. Methods We retrospectively analyzed the data of 97 patients admitted to our hospital with suspected pulmonary infection prescribed to mNGS during the past 3 years. The clinical application of mNGS in the diagnosis and management of pulmonary infection and also challenges were investigated. Results Causative or possibly causative pathogens were detected in 63.9% of patients by mNGS, performing consistently well for Mycobacterium tuberculosis, non-tuberculous mycobacteria, fungus and rare pathogens. In 43.3% of patients, 65 microbes reported as causative or possibly causative pathogens by laboratory were reclassified as colonization after fully interpretation by physicians. Antibiotics were adjusted for 34.0% of patients mainly based on positive mNGS results and not adjusted for 41.2% with pathogens identified already covered by empirical therapy or negative mNGS results. Conclusions mNGS is a promising tool in etiological diagnosis of pulmonary infection. However, physicians should go beyond the reported pathogens by laboratory and investigate fully in clinical practice. The effect on clincal treatment deserves further investigation from aspect of cost effectiveness and also application scenarios should be illustrated.