June 3, 2026

Rapid Fusobacterium Brain Abscess Diagnosis with mNGS: TVGH Case Study

Brain abscesses remain among the most diagnostically challenging central nervous system infections. Culture-negative rates reach as high as 63%, and polymicrobial infections occur in 4-33% of cases, meaning the causative organism is frequently never identified or only partially characterized. Anaerobic bacteria such as Fusobacterium nucleatum — a strict anaerobe and common oral commensal — are particularly difficult to recover by conventional culture due to their oxygen sensitivity and slow growth. In this December 2024 mNGS Symposium presentation, Dr. Po-Hsiang Liao and Dr. Yen-Chia Chen from Taipei Veterans General Hospital (TVGH) presented two brain abscess cases where metagenomic next-generation sequencing (mNGS) identified F. nucleatum within 24 hours, dramatically outpacing culture-based diagnosis.

Watch the full presentation: Rapid Fusobacterium Brain Abscess Diagnosis with mNGS

Key Takeaways

mNGS identified Fusobacterium nucleatum in brain abscess aspirate within 24 hours in both cases, while culture required 12 days in one case and returned negative in the other.
Brain abscess culture-negative rates reach up to 63%, making unbiased metagenomic approaches particularly valuable for CNS infections.
F. nucleatum is a strict anaerobe and common oral commensal that is inherently difficult to culture, yet is a recognized cause of brain abscesses via hematogenous spread.
Host depletion using the Devin filter improved sequencing sensitivity by removing the overwhelming proportion of human DNA from brain abscess aspirate.
The PaRTI-Seq bioinformatic pipeline provided rapid taxonomic classification, enabling same-day pathogen identification from metagenomic sequencing data.

The Diagnostic Challenge of Brain Abscesses

Brain abscesses present a dual clinical problem: they are life-threatening emergencies requiring prompt targeted antimicrobial therapy, yet the causative organism remains unidentified in a large proportion of cases. Culture-negative rates of up to 63% reflect several compounding factors — prior antibiotic exposure, fastidious or anaerobic organisms that fail to grow under standard culture conditions, and polymicrobial infections where not all species are recovered.

Anaerobes are disproportionately affected by this diagnostic gap. Organisms such as F. nucleatum are strict anaerobes that require specialized culture conditions and extended incubation times. Even when culture eventually succeeds, the delay — often exceeding a week — means that initial antimicrobial therapy is empiric rather than targeted. This delay has direct consequences for patient outcomes, particularly when the empiric regimen does not adequately cover the actual pathogen.

mNGS offers a fundamentally different approach: rather than requiring organisms to grow, it sequences all DNA present in the sample and identifies pathogens bioinformatically. This is especially advantageous for non-viable organisms, anaerobes, and samples collected after antibiotic administration. As validation data from sterile body fluids has demonstrated, mNGS achieves high sensitivity and specificity even in specimen types where culture frequently fails.

Two Cases of Fusobacterium nucleatum Brain Abscess

Case 1 — 55-Year-Old Female with Multiple Brain Abscesses

A 55-year-old female presented with multiple brain abscesses. Brain abscess aspirate was collected and sent for both conventional culture and mNGS testing. mNGS identified F. nucleatum within 24 hours of sample receipt, enabling the clinical team to initiate targeted antimicrobial therapy promptly. Conventional anaerobic culture eventually grew the same organism, but required 12 days — an 11-day diagnostic delay compared to the metagenomic result.

This case illustrates the core advantage of mNGS for anaerobic CNS infections: the pathogen was identifiable from the same clinical specimen in a fraction of the time. The 12-day culture delay is consistent with the known difficulty of recovering strict anaerobes, which require prolonged incubation under oxygen-free conditions.

Case 2 — 58-Year-Old Male Initially Misdiagnosed as Stroke

A 58-year-old male initially presented with neurological symptoms attributed to stroke. Subsequent imaging and clinical evaluation revealed brain abscess as the true diagnosis. mNGS testing of the abscess aspirate identified the causative pathogen within 24 hours, correcting the clinical trajectory and enabling appropriate targeted therapy.

This case highlights a second diagnostic dimension where mNGS adds value: not only speed of pathogen identification but also diagnostic confidence in cases where the clinical presentation is ambiguous. The initial misdiagnosis as stroke — a common clinical scenario with brain abscess — meant that appropriate antimicrobial therapy was delayed until the infectious etiology was recognized.

How mNGS and Host Depletion Close the Diagnostic Gap

Brain abscess aspirate presents a particular technical challenge for metagenomic sequencing because the sample is overwhelmingly composed of human DNA — from host immune cells, necrotic tissue, and inflammatory debris. Without intervention, the vast majority of sequencing reads map to the human genome, leaving insufficient depth for microbial detection.

Host depletion using the Devin filter addresses this by selectively removing human DNA before library preparation, enriching the remaining microbial fraction and improving the signal-to-noise ratio. This enrichment is critical for detecting organisms present at low abundance in high-human-background specimens. Validation studies across multiple laboratories have confirmed that host depletion filtration significantly improves pathogen detection sensitivity.

Following host depletion and sequencing, the PaRTI-Seq pipeline provides rapid bioinformatic classification of the metagenomic reads. The combination of effective sample preparation and streamlined analysis enabled the 24-hour turnaround time reported in both TVGH cases — a timeline that is clinically actionable for brain abscess management, where early targeted therapy is associated with improved outcomes.

These cases from TVGH add to a growing body of evidence — including ICU pathogen detection data and broader perspectives on clinical metagenomics adoption — demonstrating that mNGS with host depletion is transitioning from a research tool to a practical clinical diagnostic for CNS infections where culture routinely fails.

About the Speakers

Dr. Po-Hsiang Liao is an Attending Physician in the Emergency Department at Taipei Veterans General Hospital (TVGH). Dr. Yen-Chia Chen is a Department Chief and corresponding author at Taipei Veterans General Hospital, where their work focuses on applying metagenomic diagnostics to challenging CNS infections.