Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailored antibiotic treatment. We investigated if the 16S amplicon sequencing performed by MinION, a nanopore sequencer, was capable of rapid pathogen identification in bacterial meningitis. Six retrospective cases of confirmed bacterial meningitis and two prospective cases were included. The initial cerebrospinal fluid (CSF) samples of these patients were used for the experiments. DNA was extracted from the CSF, and PCR was performed on the 16S ribosomal DNA (16S rDNA). Sequencing libraries were prepared using the PCR products, and MinION sequencing was performed for up to 3 h. The reads were aligned to the bacterial database, and the results were compared to the conventional culture studies. Pathogenic bacteria were successfully detected from the CSF by 16S sequencing in all retrospective cases. 16S amplicon sequencing was more sensitive than conventional diagnostic tests and worked properly even in antibiotics-treated samples. MinION sequencing significantly reduced the turnaround time, and even 10 min of sequencing was sufficient for pathogen detection in certain cases. Protocol adjustment could further increase the sensitivity and reduce the turnaround time for MinION sequencing. Finally, the prospective application of MinION 16S sequencing was successful. Nanopore 16S amplicon sequencing is capable of rapid bacterial identification from the CSF of the bacterial meningitis patients. It may have many advantages over conventional diagnostic tests and should therefore be applied in a larger number of patients in the future.

尽早使用抗生素对细菌性脑膜炎的治疗至关重要。快速的病原体鉴定有助于对细菌性脑膜炎做出明确的诊断，并能够进行量身定制的抗生素治疗。我们调查了由纳米孔测序仪MinION进行的16S扩增子测序是否能够快速鉴定细菌性脑膜炎中的病原体。包括确诊的细菌性脑膜炎的6例回顾性病例和2例前瞻性病例。这些患者的初始脑脊液（CSF）样品用于实验。从脑脊液中提取DNA，然后对16S核糖体DNA（16S rDNA）进行PCR。使用PCR产物制备测序文库，MinION测序进行长达3小时。读数与细菌数据库比对，并将结果与​​常规培养研究进行比较。在所有回顾性病例中，均通过16S测序成功地从CSF中检测出致病菌。16S扩增子测序比常规诊断测试更为灵敏，即使在抗生素处理过的样品中也能正常工作。MinION测序显着减少了周转时间，在某些情况下，甚至10分钟的测序也足以检测病原体。协议调整可以进一步提高灵敏度，并减少MinION测序的周转时间。最终，MinION 16S测序的前瞻性应用成功。纳米孔16S扩增子测序能够从细菌性脑膜炎患者的脑脊液中快速鉴定细菌。