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Next-generation sequencing (NGS) has emerged as a powerful tool for sensitive and unbiased screening of tissue or body fluid specimens. This study aimed to investigate the underlying aetiology of patients with suspected infectious CNS diseases. Between April 2013 and October 2021, we collected brain tissue samples from 33 patients diagnosed with encephalitis or encephalitis-like CNS diseases, obtained via biopsy or autopsy, and underwent metagenomic NGS (mNGS) in conjunction with pathological evaluations. Moreover, we employed PCR-based assays and pathogen-specific immunostaining to corroborate the presence of pathogens within the tissue samples. Among the 33 patients, mNGS elucidated pathogen-specific genomic sequences in 7 cases (21.2%), including halobacteria (archaea), Balamuthia mandrillaris, Epstein\u2013Barr virus, Toxoplasma gondii and herpes simplex virus. Additionally, brain tissue mNGS ruled out known pathogens, identifying 14 cases (42.4%) of non-infectious CNS diseases, which included neoplastic, autoimmune\/inflammatory and amyloid angiopathy conditions. The adjustment of therapeutic strategies based on these findings led to improvements in clinical symptoms, imaging outcomes and patient prognosis. Brain biopsy serves as both a direct pathological research target and a valuable source of samples for unbiased high-throughput sequencing. Our study illustrates the reliability of mNGS on brain tissue, which significantly improves the diagnostic rate for suspected encephalitis or encephalitis-like diseases of unknown aetiology. These findings underscore the importance of mNGS in guiding more precise and effective therapeutic interventions for patients in clinical practice.<\/jats:p>","DOI":"10.1093\/braincomms\/fcaf165","type":"journal-article","created":{"date-parts":[[2025,4,26]],"date-time":"2025-04-26T08:18:24Z","timestamp":1745655504000},"source":"Crossref","is-referenced-by-count":6,"title":["Brain biopsy and metagenomic sequencing enhance aetiological diagnosis of encephalitis"],"prefix":"10.1093","volume":"7","author":[{"given":"Yusuke","family":"Sakiyama","sequence":"first","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-Hui","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akiko","family":"Yoshimura","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mika","family":"Takeuchi","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshimitsu","family":"Maki","sequence":"additional","affiliation":[{"name":"Department of Neurology, Kagoshima City Hospital , Kagoshima, 890-8760 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takuma","family":"Mori","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Takei","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Ando","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Hiramatsu","sequence":"additional","affiliation":[{"name":"Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences , Kagoshima, 890-8520 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