Circulating Cell-Free DNA for Brain Abscess Diagnosis: A Pilot Study

Overview

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.

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.