A prospective study was conducted to compare metagenomic next-generation sequencing (mNGS) and conventional testing in investigating the pathogens of central nervous system (CNS) infections in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. A total of 53 patients with CNS disorders after allo-HSCT were enrolled in this study. A total of 35 patients were diagnosed as CNS infections, including 28 viral, 2 bacterial, 1 fungal, 3 mixed infections, and 1 infection with unknown pathogen. Among these 35 patients with CNS infections, mNGS identified 5 patients who were not identified by conventional testing. For the remaining 30 infections, mNGS made concurrent diagnoses with conventional testing in 29, while 1 was diagnosed according to the good response to the antimicrobial treatment without etiological evidence. The presence of Aspergillus detected by mNGS only in one patient was considered false positive due to lack of validation. The sensitivity of mNGS and conventional testing for diagnosing CNS infections post transplant were 97.1% and 82.9%, respectively (P = 0.106), while the specificity of mNGS and conventional testing were 94.4% and 100%, respectively (P = 1.000). These results suggest that mNGS might be a promising technology for diagnosis of CNS infections post transplant. Viruses were the most common pathogens of CNS infections in allo-HSCT recipients.
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