Early and appropriate antibiotic therapy is the key to reduce the mortality of patients with severe infection, and the correct identification of pathogenic microorganisms is the prerequisite for appropriate antibiotic therapy. However, for the detection of pathogenic microorganisms, most of the traditional microbiology methods have a certain target or direction. When clinicians suspect the coexistence of multiple pathogenic microorganisms, multiple microbiological tests may be required simultaneously. In recent years, next-generation sequencing (NGS) technology has been applied in the diagnosis and treatment of some special pathogenic microbial infections. However, as a new laboratory diagnostic technique, the available evidence is insufficient to support the routine clinical application of NGS.