Circulating Cell-Free DNA for Brain Abscess Diagnosis: A Pilot Study (METABCES-PoC)

Assessment of Circulating Cell-Free DNA for the Microbiological Diagnosis of Brain Abscesses: A Pilot Proof-of-Concept Study

Brain abscess is a severe intracranial infection associated with significant morbidity and mortality. Standard management combines neurosurgical intervention, when feasible, with prolonged intravenous antibiotic therapy. Neurosurgical procedures, such as surgical drainage or stereotactic aspiration, play a key role in reducing intracranial pressure, decreasing the infectious burden, and obtaining samples for microbiological identification.

However, neurosurgical intervention is not always possible due to technical limitations or patien related contrindications. In these situations, microbiological documentation becomes particularly challenging. Conventional diagnostic methods have limited sensitivity, with blood cultures and lumbar puncture yielding positive results in only about 25% of brain abscess cases.

Recent advances in infectious disease diagnostics have introduced metagenomic approaches that may improve pathogen detection. Studies have shown that metagenomic analysis of operative samples can provide more comprehensive microbiological documentation than conventional culture-based methods. In addition, next-generation sequencing (NGS) of circulating microbial cell-free DNA in blood enables the detection of short microbial DNA fragments with a short half-life, reflecting active infection. This technology has already demonstrated promising results in clinical situations where microbiological documentation is difficult, such as febrile neutropenia. The present study aims to evaluate the performance of this approach in patients with brain abscess.

Study Overview

• Status: Not yet recruiting
• Conditions: Brain Abscess
• Intervention / Treatment: Diagnostic test: Plasma Microbial Cell-Free DNA Metagenomic Sequencing

Detailed Description

Brain abscess is a rare but severe intracranial infection, with an estimated incidence of approximately 0.8 cases per 100,000 individuals and a reported mortality rate ranging from 10% to 20%. Current management relies on a combination of neurosurgical intervention and prolonged intravenous antimicrobial therapy. When feasible, surgical drainage or stereotactic aspiration is performed to reduce intracranial pressure, decrease the infectious burden, and obtain biological samples for microbiological identification of the causative pathogen, enabling targeted antimicrobial treatment.

However, neurosurgical intervention is not always feasible. Technical factors such as small abscess size or deep anatomical location may prevent access to the lesion, and some patients may present contraindications to neurosurgical procedures. In these situations, microbiological documentation becomes particularly challenging. Conventional diagnostic methods, including blood cultures and cerebrospinal fluid analysis, have limited sensitivity in brain abscess and frequently fail to identify the causative pathogen.

Recent advances in molecular diagnostics have led to the development of metagenomic sequencing approaches for pathogen detection. Metagenomic analysis enables the unbiased identification of microbial DNA directly from clinical samples and may provide broader pathogen detection than traditional culture-based techniques. In neurosurgical infections, metagenomic sequencing performed on operative samples has shown promising results and may improve microbiological documentation compared with standard diagnostic methods.

In parallel, sequencing of circulating microbial cell-free DNA (cfDNA) in peripheral blood using next-generation sequencing represents an innovative and minimally invasive diagnostic approach. This technology detects short fragments of microbial DNA released into the bloodstream during active infection and may provide clinically relevant diagnostic information.

This study aims to evaluate the diagnostic performance of circulating microbial cfDNA metagenomic sequencing in patients with brain abscess and to compare its performance with metagenomic sequencing and conventional microbiological cultures performed on intraoperative samples when available.

This pilot study is designed to provide proof-of-concept data on the diagnostic performance of circulating microbial cfDNA sequencing in brain abscess. The results may help define the role of this diagnostic approach in improving microbiological documentation and guiding targeted antimicrobial therapy, particularly when neurosurgical sampling is not feasible.

• Study Type: Interventional
• Enrollment (Estimated): 15
• Phase: Not Applicable

Contacts and Locations

• Study Contact: Name: Saber touati, PhD; Phone Number: 04 76 76 58 05; Email: stouati1@chu-grenoble.fr
• Study Contact Backup: Name: Marion LE MARECHAL, MD,PhD; Phone Number: 04 76 76 52 91; Email: MLemarechal@chu-grenoble.fr

Study Locations

• France
  • Grenoble, France
    • CHU de Grenoble Alpes, Laboratoire de bactériologie
    • Contact: Yvan Caspar, PharmD; PhD; Phone Number: 04 76 76 63 12; Email: YCaspar@chu-grenoble.fr
  • Grenoble, France
    • CHU de Grenoble Alpes, Service de réanimation neurochirurgicale
    • Contact: Clotilde Schilte, MD; Phone Number: 04 76 76 66 88; Email: CSchilte@chu-grenoble.fr

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: Adult; Older Adult
• Accepts Healthy Volunteers: No

Description

Inclusion Criteria:

• Participant ≥ 18 years of age.
• Participant presenting with a brain abscess requiring neurosurgical
• Signed Informed Consent
• Covered by health insurance

Exclusion Criteria:

• Participant in exclusion period for another study
• Participant referred to in articles L1121-5 to L1121-8 of the CSP (corresponding to all protected persons : pregnant woman, parturient, breastfeeding mother, person deprived of liberty by judicial or administrative decision, persons undergoing psychiatric care under articles L.3212-1 and L.3213-1 who do not fall under article L.1121-8, persons admitted to a healthcare or social institution for purposes other than research, minors, person under legal protection or unable to express consent).
• Staff members with a hierarchical relationship to the principal investigator

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Diagnostic
• Allocation: N/A
• Interventional Model: Single Group Assignment
• Masking: None (Open Label)

Number of Arms

1

Arms and Interventions

Participant Group / Arm

Intervention / Treatment

Experimental: Metagenomic Diagnostic Evaluation

Diagnostic test: Plasma Microbial Cell-Free DNA Metagenomic Sequencing; A 20 mL peripheral blood sample will be collected prior to neurosurgical intervention for metagenomic next-generation sequencing (mNGS) analysis of circulating microbial cell-free DNA. Results will be compared with metagenomic analysis and conventional culture of intraoperative brain abscess specimens, which serve as the reference standard for microbiological identification.

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Blood and Brain Abscess Metagenomic Concordance	Comparison of bacterial species identified by metagenomic next-generation sequencing of cell-free DNA (cfDNA) from blood samples versus metagenomic analysis of per-operative brain abscess samples.	Day 0

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Metagenomic Next-Generation Sequencing vs. Culture Concordance	Evaluation of bacterial species identification using metagenomic next-generation sequencing compared to gold-standard culture techniques on per-operative brain abscess samples.	Day 0
Plasma Cell-Free DNA vs. Abscess Culture Correlation	Comparison of bacterial species identified by metagenomic analysis of circulating cell-free DNA (cfDNA) from blood samples versus species identified by conventional culture of per-operative brain abscess samples.	Day 0
Potential Clinical Impact on Antimicrobial Treatment	Assessment of potential therapeutic modifications or antibiotic optimization induced by metagenomic next-generation sequencing results compared to standard culture-based diagnosis.	At 1 Month

Collaborators and Investigators

• Sponsor: University Hospital, Grenoble

Study record dates

Study Major Dates

• Study Start (Estimated): April 1, 2026
• Primary Completion (Estimated): March 31, 2028
• Study Completion (Estimated): March 31, 2028

Study Registration Dates

• First Submitted: March 12, 2026
• First Submitted That Met QC Criteria: March 12, 2026
• First Posted (Actual): March 18, 2026

Study Record Updates

• Last Update Posted (Actual): March 18, 2026
• Last Update Submitted That Met QC Criteria: March 12, 2026
• Last Verified: March 1, 2026

More Information

Terms related to this study

• Keywords: Metagenomics; Brain Abscess; Cell-Free DNA
• Additional Relevant MeSH Terms: Brain Diseases; Central Nervous System Diseases; Nervous System Diseases; Infections; Suppuration; Central Nervous System Infections; Abscess; Brain Abscess
• Other Study ID Numbers: 38RC24.0243

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No