Evaluating the Diagnostic Utility of 16S Oxford Nanopore Technology Sequencing in Patients With Central Nervous System Infections and Its Usefulness in Antimicrobial Stewardship

<h4>Background</h4>Central nervous system (CNS) infections pose a significant public health challenge in resource-limited settings. Traditional culture-based and targeted molecular diagnostic methods have limitations in sensitivity and speed. This study retrospectively analyzed the data and cerebrospinal fluid (CSF) samples from our previous study to assess the diagnostic efficacy of untargeted 16S Oxford Nanopore Technology (ONT) sequencing compared to conventional CSF culture methods, with the goal of improving diagnostic accuracy, reducing time to treatment, and enhancing patient outcomes.<h4>Methods</h4>A total of 329 patients from 4 hospitals were enrolled in the study. CSF samples were collected and processed for both CSF culture and 16S ONT sequencing. DNA were extracted from CSF and amplified for 16S rRNA sequencing using the MinION platform. Descriptive analyses were conducted to assess pathogen detection rates and the potential impact of sequencing on antimicrobial stewardship.<h4>Results</h4>Of the 329 samples, 40 (12%) were positive for bacterial or fungal pathogens. 16S ONT detected pathogens in 28 samples (9%), while CSF culture identified pathogens in 23 samples (7%). 16S ONT sequencing identified 17 pathogens not detected by CSF culture, including Streptococcus suis and Acinetobacter baumannii. Based on 16S ONT findings, 61% of patients were found to have received inappropriate empirical antibiotic therapy and could have benefited from improved antimicrobial management, including de-escalation in 11, escalation in 5, and adjustments in 2 cases.<h4>Conclusions</h4>16S ONT sequencing showed higher sensitivity and diagnostic yield than CSF culture, providing clinical insights for managing CNS infections through targeted antibiotic use and enhanced antimicrobial stewardship in resource-limited settings.