Exploring the Spectrum of Microbiota in Central Nervous System Infections Through Metagenomic Next-Generation Sequencing

Jun-Mei Wang,1,2,* Yu-Ying Pan,1,2,* Jian-Chen Hong,3,* Zai-Jie Jiang,1 Shi-Ying Zhang,1 Rui-Jie Fan,1 Bi-Hui Yang,1 Zhi-Qiang Wang,1 Ji-Ting Zhu,1,2 Xiang-Ping Yao1,2 1Department of Neurology, Fujian Institute of Neurology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People’s Republic of China; 2Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, People’s Republic of China; 3Department of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People’s Republic of China*These authors contributed equally to this workCorrespondence: Xiang-Ping Yao, Department of Neurology, Fujian Institute of Neurology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, People’s Republic of China, Email yaoxiangping@fjmu.edu.cnPurpose: This study leveraged CSF metagenomic next-generation sequencing (mNGS) to bridge this knowledge gap and elucidate the microbiota spectrum of CNS infections.Patients and Methods: We retrospectively analyzed CSF mNGS reports and clinical data from 264 patients with suspected CNS infections, who were enrolled from September 2019 to November 2023.Results: According to diagnostic criteria, 145 patients were diagnosed with CNS infections, including bacterial (27 cases, 18.6%), Mycobacterium tuberculosis (30, 20.7%), fungal (23, 15.9%), and viral (65, 44.8%) infections. The mNGS positive detection rate was 46.2% (67/145), with significant differences among groups (p < 0.001). A total of 22 pathogens were identified, most commonly Cryptococcus neoformans (16, 23.9%), Mycobacterium tuberculosis (10, 14.9%), and Epstein-Barr virus (9, 13.4%). The most frequent background microorganisms detected by mNGS were Cutibacterium acnes (58.6%), Moraxella osloensis (29.0%), and Malassezia restricta (26.2%).Conclusion: High-throughput sequencing using mNGS revealed the microbial compositions in CSF samples from patients with CNS infections. This approach may enhance our understanding of pathogens and assist clinicians in making effective therapeutic decisions.Keywords: central nervous system infection, microbiota, metagenomic next-generation sequencing, cerebrospinal fluid