Brain abscesses constitute a significant neurosurgical emergency, characterized by localized intracranial purulent collections. Despite notable advancements in diagnostic techniques and antimicrobial treatments, these abscesses remain associated with considerable risks of mortality and long-term neurological complications (1, 2). Effective management of brain abscesses generally necessitates a comprehensive approach, integrating surgical procedures for pathogen identification and abscess drainage with extended antibiotic therapy (3, 4).

The etiology of brain abscesses is frequently associated with contiguous spread from otogenic or odontogenic sources, hematogenous spread from distant locations, or penetrating cranial injuries (5–8). Anaerobic bacteria, especially those originating from the oral cavity, are commonly implicated and present significant diagnostic challenges. Prevotella loescheii and Porphyromonas gingivalis, which are fastidious, obligate anaerobic Gram-negative bacilli, are prevalent components of the oral microbiota and are well-known contributors to periodontal disease (9, 10). Their isolation and identification through conventional culture methods are notoriously difficult, often leading to delayed diagnosis and inappropriate empirical treatment.

Metagenomic next-generation sequencing (mNGS) has emerged as a robust and unbiased diagnostic modality for the direct identification of pathogens from clinical specimens, demonstrating particular utility in the diagnosis of rare, polymicrobial, or culture-negative central nervous system infections (11, 12). Concurrently, the surgical management of complex, multi-loculated abscesses is undergoing significant advancements. Traditional methods such as excision or simple aspiration remain standard treatments; however, endoscopic lavage and drainage present a minimally invasive yet comprehensive alternative, facilitating the evacuation of pus, disruption of loculations, and debridement of the cavity under direct visualization (13, 14).

In this report, we discuss a challenging case involving a young male patient with refractory, multiple brain abscesses attributed to P. loescheii and P. gingivalis. This case underscores the critical diagnostic role of mNGS in identifying fastidious pathogens and illustrates the therapeutic efficacy of a combined approach utilizing targeted antibiotic therapy alongside advanced endoscopic surgical techniques.

This case provides several significant insights into the diagnosis and management of complex intracranial infections, particularly those caused by fastidious anaerobic bacteria, highlighting the crucial role of modern technologies in guiding treatment toward a successful outcome.

Although P. loescheii and P. gingivalis are common oral commensals, they are rare etiological agents of severe intracranial infections. These bacteria typically enter the bloodstream through disruptions in the oral mucosa, which can occur due to periodontal disease, dental procedures, or even minor trauma from chewing (15–17). In our case, the initial empirical therapy with ceftriaxone, which has variable anaerobic coverage, and even the escalated regimen of vancomycin and meropenem, failed to halt disease progression. This underscores the difficulty of managing such infections without identifying a definitive pathogen and the potential for initial treatment failure despite broad-spectrum coverage.

The turnaround time for traditional culture methods can range from several days to weeks, with often low yield, particularly in cases where the patient has previously received antibiotics, as was observed in this instance. mNGS has transformed the management of our patient by enabling rapid, comprehensive, and culture-independent identification of the causative pathogens within a few days (18–20). This technology facilitates the unbiased detection of virtually all nucleic acids present in a sample, rendering it exceptionally valuable for diagnosing atypical, polymicrobial, or culture-negative infections (21–23). The precise identification of P. loescheii and P. gingivalis confirmed the anaerobic and likely odontogenic nature of the infection. This not only validated the continued use of carbapenem therapy but also negated the necessity for additional antifungal or antiviral treatments, thereby allowing for a more targeted and potentially safer therapeutic approach.

The standard care for brain abscesses typically involves surgical drainage or excision in conjunction with antibiotic therapy (24–26). However, the optimal surgical strategy for managing multiple or deep-seated abscesses remains a subject of ongoing debate. The patient’s initial open excision and decompressive craniectomy were insufficient, possibly because the procedure failed to address all loculations and deeply seated pockets of infection adequately, or because it caused significant inflammatory disruption, potentially exacerbating the condition.

Neuro-endoscopy presents a minimally invasive yet highly effective alternative, as underscored by an expanding body of literature. Endoscopic aspiration and lavage facilitate direct visualization, allowing for more comprehensive evacuation of pus from multiple sites, meticulous disintegration of septations, and efficient irrigation of the cavity (27, 28). This technique is associated with reduced cerebral trauma compared to open craniotomy, more thorough debridement than blind aspiration, and potentially lower recurrence rates (29). In our patient, the strategic transition to endoscopic lavage and drainage marked a definitive turning point following the failure of other interventions, resulting in rapid clinical and radiological improvement. This outcome is consistent with reported cases where endoscopic lavage successfully managed severe intracranial infections that were unresponsive to external drainage alone (30).

The initially empirical antibiotic regimen of meropenem and vancomycin was ultimately deemed appropriate. Although metronidazole is frequently regarded as the gold standard for anaerobic infections, carbapenems such as meropenem offer excellent anaerobic coverage and effectively penetrate the central nervous system, rendering them a suitable therapeutic option. The continuation of this regimen, once informed by mNGS, was thus justified. Importantly, the identification of an oral source emphasizes the critical need for comprehensive dental evaluation and subsequent definitive dental care in such patients to prevent recurrence, a step that is occasionally overlooked during the acute management phase.

This case report presents a severe and life-threatening instance of multiple brain abscesses caused by Prevotella loescheii and Porphyromonas gingivalis of oropharyngeal origin. It underscores several key considerations for clinicians: (1) Maintain a high index of suspicion: odontogenic pathogens should be included in the differential diagnosis of cryptogenic brain abscesses, particularly in young adults without other risk factors. A thorough oral examination is an essential, non-invasive component of the diagnostic workup. (2) Adopt advanced diagnostic techniques: mNGS is a transformative tool capable of rapidly identifying the etiology of culture-negative, refractory CNS infections. This enables precise and timely antimicrobial therapy, effectively overcoming the limitations associated with conventional microbiological methods. (3) Customize the surgical strategy: in cases of complex, multi-loculated abscesses that are unresponsive to initial drainage, endoscopic lavage and drainage offer a highly effective and minimally invasive surgical option. This approach can provide superior decompression and debridement compared to traditional methods, potentially leading to faster recovery and improved outcomes. Overall, a multidisciplinary approach that integrates neurosurgery, infectious diseases, and dental medicine, guided by rapid molecular diagnostics and advanced surgical techniques, is essential for the successful management of such challenging cases.