Objective:To investigate the value of metagenomic next-generation sequencing (mNGS) in central nervous system infection (CNSI) of critically ill patients from Neurosurgery.Methods:A prospective study was conducted. From October 2019 to April 2021, 52 patients with highly suspected CNSI in the Department of Neurosurgical Intensive Care Unit (NICU) of our hospital were chosen. The collected cerebrospinal fluid (CSF) samples were simultaneously performed mNGS and traditional culture; the clinical diagnosis of CNSI was taken as the standard, and the sensitivity, specificity, positive predictive value, negative predictive value, and time from sample collection to result feedback of these two methods were compared. Receiver operating characteristic (ROC) curve was used to analyze the diagnostic values of mNGS and traditional culture in CNSI.Results:Eventually, 25 patients with CNSI were clinically confirmed; 23 were with positive mNGS, including 16 with bacterial infection, 4 with viral infection, 1 with fungal infection, and 2 with mixed infection (1 with bacteria+virus+fungus, 1 with bacteria+virus); 8 were with positive traditional culture, all of which were bacterial infections. The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 92.0%, 85.2%, 85.2%, and 92.0%, respectively; those of traditional culture were 32.0%, 100.0%, 100.0%, and 61.4%, respectively; the time from sample collection to result feedback of mNGS and traditional culture was (31.77±5.23) h and (101.83±9.15) h, respectively, with significant difference ( P<0.05). ROC curve showed that the area under the curve (AUC) of mNGS for diagnosis of CNSI was 0.886 ( 95%CI: 0.786-0.986, P<0.001); the AUC of traditional culture for diagnosis of CNSI was 0.660 ( 95%CI: 0.508-0.812, P=0.002). Conclusion:For patients with CNSI from NICU, mNGS has good diagnostic efficacy and application value and can effectively compensate for the lack of traditional cerebrospinal fluid culture.