Metagenomic Next-Generation Sequencing for Brain Abscess: Improved Pathogen Detection, Targeted Antimicrobial...

Brain abscesses demand prompt, accurate pathogen identification; however, identification using conventional culture is limited, especially for anaerobic and polymicrobial infections. We compared the diagnostic and clinical utility of metagenomic next-generation sequencing (mNGS) with that of conventional culture in patients with brain abscess.

We retrospectively included 115 patients with confirmed brain abscess pathogens. Seventy-two patients underwent both mNGS and conventional culture, and 43 underwent culture alone. We evaluated diagnostic performance, pathogen profiles, adjustments to antimicrobial regimens, and clinical outcomes.

mNGS detected pathogens in 86.1% of patients versus 44.4% for culture (Cohen's kappa test p=0.004; McNemar's test p=0.0001). It identified mixed infections in 53.2% of cases, whereas culture predominantly revealed single pathogens. mNGS produced substantially higher detection rates than culture for anaerobic bacteria (50.0% vs 16.7%) and oral-derived bacteria (77.6% vs 61.1%). Antimicrobial regimens were adjusted in 54.2% of patients based on mNGS results; 61.5% of these adjustments involved de-escalation, and vancomycin was discontinued in 77.8% of patients. mNGS use was associated with a lower surgical intervention rate (47.2% vs 65.1%, P = 0.002). There were no differences in length of hospital stay, fever duration, Glasgow Outcome Scale score, or hospitalization costs. In eight patients without reported dental history, mNGS revealed occult odontogenic foci, enabling source control and potentially reducing recurrence risk.

mNGS outperformed conventional culture for detecting mixed infections, anaerobes, and pathogens of d origin. It may inform targeted antimicrobial therapy and assist in identifying the infection source. In this single‑center retrospective study, which is subject to potential selection bias, mNGS use was associated with a lower rate of surgical intervention; however, this finding should be interpreted as an association rather than causation, and prospective studies are needed to confirm this observation. These findings support the integration of mNGS into diagnostic algorithms for brain abscess.