Diagnostic Value of 16S ONT Sequencing for CNS Infections and Antimicrobial Stewardship

Overview

This study evaluated the diagnostic performance of untargeted 16S Oxford Nanopore Technology (ONT) sequencing compared to conventional cerebrospinal fluid (CSF) culture in 329 patients with suspected central nervous system (CNS) infections. The 16S ONT method demonstrated higher sensitivity and detected more pathogens, enabling improved antimicrobial stewardship by identifying inappropriate empirical antibiotic use.

Background

Central nervous system infections such as meningitis and encephalitis are serious conditions requiring rapid diagnosis and treatment to reduce morbidity and mortality. Traditional CSF culture, while the gold standard, is slow and less sensitive, especially after antibiotic pretreatment. Molecular methods like PCR improve detection but are limited by targeted panels and local pathogen variability. Next-generation sequencing, particularly 16S rRNA gene sequencing using ONT, offers rapid, broad-range pathogen detection that may enhance diagnosis and guide antimicrobial therapy, especially in resource-limited settings like Vietnam where many CNS infections remain undiagnosed.

Data Highlights

Key Findings

• 16S ONT sequencing detected pathogens in 28 of 329 CSF samples (9%), outperforming CSF culture which detected pathogens in 23 samples (7%).
• Seventeen pathogens identified by 16S ONT sequencing were missed by CSF culture, including clinically important bacteria such as Streptococcus suis and Acinetobacter baumannii.
• Overall, 12% of samples were positive for bacterial or fungal pathogens by either method.
• Based on 16S ONT results, 61% of patients had received inappropriate empirical antibiotic therapy, indicating a significant opportunity for antimicrobial stewardship.
• Antibiotic therapy adjustments suggested by sequencing data included de-escalation in 11 cases, escalation in 5 cases, and other modifications in 2 cases.
• 16S ONT sequencing offers faster turnaround and broader pathogen detection, supporting improved clinical decision-making in CNS infections.

Clinical Implications

The higher sensitivity and broader pathogen detection of 16S ONT sequencing can facilitate earlier and more accurate diagnosis of CNS infections, particularly in settings where traditional culture methods are limited. This enables targeted antimicrobial therapy, reducing inappropriate antibiotic use and promoting stewardship. Implementing 16S ONT sequencing may improve patient outcomes by guiding timely treatment adjustments and reducing diagnostic delays.

Conclusion

Untargeted 16S ONT sequencing demonstrates superior diagnostic yield compared to conventional CSF culture for CNS infections and provides actionable data to optimize antimicrobial therapy. Its adoption in resource-limited settings could enhance diagnostic accuracy and stewardship efforts, ultimately improving patient care.

References

1. Dubot-Pérès et al 2023 -- WHO Case Definition for CNS Infections
2. Previous Study 2023 -- Targeted FilmArray Meningitis/Encephalitis Panel in Vietnam
3. Studies 2020-2023 -- 16S ONT Sequencing for Pathogen Detection