Quantifying the Effect of Seizure-Onset Zone Resection on Epilepsy Surgery Outcome

Cost-effectiveness analysis of resective epilepsy surgery in drug-resistant patients: an artificial intelligence data modeling.

Development of a deep learning tool to detect drug-resistance epilepsy with EEG.

The extracellular matrix (ECM) performs several functions during development and in mature nervous tissue plasticity; ECM concentrates in lattice-like envelopes called perineuronal nets (PNNs), which surround the cell bodies and proximal dendrites, mainly of parvalbumin (PV) γ-aminobutyric acidergic interneurons. PNNs are proposed to serve synaptic plasticity regulation, synapse stabilization, and neuron protection, by forming a physical barrier from potentially damaging neurochemical stimuli. We analyzed aggrecan expression, a major component of adult PNNs, in human specimens obtained from epilepsy surgery. Postsurgical tissues were obtained from 20 patients with drug-resistant epilepsy: six cases with no histological alterations (cryptogenic epilepsy) and 14 patients showing type IIa and IIb focal cortical dysplasia (FCDII). For comparison, cortices from three autoptic controls with short postmortem delay were analyzed. Immunohistochemistry, confocal microscopy, and RNAscope technique were applied. Control autoptic cases showed high aggrecan expression in the cortex, with a clear decreasing expression gradient from occipital to frontal and temporal areas. This expression gradient was lost in cryptogenic cases, which showed severe aggrecan loss, with residual immunoreactive arrangements mainly around PV interneurons. In FCDII, altered immunolabeling was evident in the core of the dysplastic lesion, and PNNs were identified around both PV interneurons and dysmorphic neurons (DNs) presenting abnormal vGLUT1 and vGAT perisomatic basket formations. Diffuse weak staining of the white matter without PNNs was also found in FCDII. As for cryptogenic cases, FCDII perilesional cortex showed a marked aggrecan staining loss. RNAscope findings confirmed that aggrecans are produced by FCDII pathological neurons, such as DNs. These data support the notion that etiology-specific PNN remodeling is part of the epileptogenic process. FCDII tissues show altered PNN expression in DNs suggestive of a pathogenic role within the FCD lesion, and the disappearance of histochemical PNN labeling in cryptogenic and FCDII perilesional area suggests a possible role mediated by seizure activity.

Balancing seizure outcomes and cognitive deficits is always a challenge in both mesial and neocortical temporal lobe epilepsy cohorts. The present study evaluated the long-term seizure outcomes and perceived quality of life (QOL) in both of these groups, along with factors predictive of these outcomes. A retrospective analysis of patients undergoing temporal lobe epilepsy (TLE) surgery from 2015 to 2023, with at least 1 year of follow-up (N = 175), is presented. Patients were grouped as MTLE (mesial temporal sclerosis only) and NTLE (neocortical) based on neuroimaging. Surgical approaches included standard anterior temporal lobectomy with amygdalohippocampectomy (ATL + AH) and hippocampal-sparing resections. Seizure outcomes were classified using Engel's scale; QOL was assessed telephonically using a questionnaire adopted from QOLIE-10-P. Predictors for seizure freedom and perceived QOL outcomes were studied in both groups. At a mean follow-up of 55 months, 83.5% of patients achieved seizure freedom, MTLE (85%), and NTLE (81%) patients. Of the entire TLE cohort, 38% were free from drugs at the last follow-up. In MTLE, the presence of red flags significantly lowers the chances of complete seizure freedom (59% vs. 93%.) (OR 0.11, 95% CI 0.03-0.37; p < 0.001). Preserving the hippocampus in NTLE is associated with a lower the seizure freedom rate (68% vs. 86%) (OR 0.34, 95% CI 0.10-1.08). In NTLE, the odds of perceived memory decline were marginally higher in the standard ATL + AH group (OR 1.48, 95% CI 0.37-5.87) compared to hippocampus-preserving resection (p = 0.7). Approx. 75% patients reported improvement in all QOL parameters in the entire TLE cohort. No mortality or permanent neurological deficits recorded. TLE surgery provides robust seizure control and significant perceived QOL improvements for most patients in the long term. Hippocampal sparing surgery in NTLE did not seem to affect perceived memory difficulties but was more likely to be associated with suboptimal seizure outcomes.

Focal cortical dysplasia type 1 (FCD1) is a rare and heterogeneous cause of drug-resistant epilepsy (DRE) in children. Its clinical characteristics remain poorly understood, and surgical outcomes may be less favorable than in FCD2. We conducted a population-based study to characterize the clinical presentation and long-term seizure and cognitive outcomes of pediatric patients undergoing epilepsy surgery for isolated FCD1. We retrospectively reviewed all children ≤18 years who underwent resective epilepsy surgery at Helsinki University Hospital between 1994 and 2022. Thirty-eight patients with histopathologically confirmed isolated FCD1 and no clinical or EEG features suggesting FCD2 were included. Clinical features, presurgical evaluations, surgical variables, postoperative outcomes, and cognitive trajectories were systematically extracted. Cognitive outcomes were assessed using a trajectory-based approach at 2 years after surgery (or 2 years post-reoperation). The median age at epilepsy onset was 1.5 years, and 63% presented with recently accelerated cognitive decline. Two years after surgery, 34% achieved Engel class 1. At a median long-term follow-up of 8.4 years, Engel class 1 remained stable at 32%. Residual MRI-visible lesion following surgery strongly predicted seizure recurrence. Frontal resections were most common (42%). Surgery diminished the recently accelerated cognitive decline in 46% of affected patients, with either stabilization or improvement in their cognitive trajectory at 2 year follow-up. Two patients required life-saving palliative procedures due to super-refractory epilepsy. In this nationwide cohort, isolated FCD1 frequently presented with early-onset DRE and preoperative accelerated cognitive decline. Although complete seizure freedom was achieved in a minority, over half of the patients experienced worthwhile improvement in seizure outcomes, along with stabilization or enhancement of cognitive trajectory. As FCD1 can cause life-threatening epilepsy and contribute to cognitive regression, epilepsy surgery should be actively considered for children with FCD1-related drug-resistant epilepsy. Focal cortical dysplasia type 1 is a rare brain abnormality that can cause severe epilepsy in children that does not respond to medication. In this nationwide study of 38 children who underwent brain surgery for this condition, about one-third became seizure-free, and over half experienced meaningful improvement. Nearly two-thirds of patients showed worsening thinking and learning abilities before surgery, and surgery helped slow or stop this decline in almost half of them. These findings suggest that brain surgery should be considered for children with this difficult-to-treat condition.

Static 2-[18F] fluoro-2-deoxy-D-glucose positron emission tomography has mixed specificity and sensitivity in targeting epileptic zones in the noninvasive stage of epilepsy surgery evaluations. We compared the signal quality of static PET (sPET) compared to a method of interictal dynamic PET (iD-PET). We calculated the signal quality of sPET and iDPET obtained from a cohort of adult patients with focal epilepsy. We developed a Bayesian Regional Estimated Signal Quality (BRESQ) technique to objectively compare signal quality by region of interest (ROI) within subjects. Adjusting for ROI size and neighboring regions, iDPET was superior to sPET with probability >95% in 8/36 regions; >90% in 21/36 regions; >80% in 29/36 regions. The top five regions with the largest adjusted signal quality differences (greatest magnitude of iDPET superiority) were the Temporal Mesial (Left and Right), Occipital Lateral (Left and Right), and the Left Frontal Inferior Base. We found that iDPET yielded a superior signal quality in most ROI. BRESQ offers a scalable and generalizable method to quantify signal quality between brain mapping modalities.

Diagnostic accuracy of artificial intelligence models for seizure outcome prediction after epilepsy surgery: A systematic review and meta-analysis.

Surgical management of super-refractory status epilepticus (SRSE): a structured narrative review with considerations on refractory status epilepticus (RSE).

Internal and external validation of comprehensive high-frequency activity biomarkers for epilepsy surgery.

Drug-resistant epilepsy is defined as failure of 2 appropriately chosen and tolerated antiseizure medications (ASMs), after which referral for surgical evaluation is recommended. However, many children undergo additional ASM trials before referral. We aimed to identify preoperative factors associated with a higher number of ASM trials before referral in a nationwide, population-based pediatric epilepsy surgery cohort. We conducted a retrospective study of all children (younger than19 years) undergoing resective epilepsy surgery at the national pediatric epilepsy surgery center in Finland between 2002 and 2022. Patients were identified from a prospective surgical registry. Preoperative clinical characteristics, including etiology, seizure frequency, and resection location, were analyzed. Patients were categorized according to ≤3 vs >3 ASM trials before referral. Univariable and multivariable logistic regression analyses were performed to identify independent predictors of referral after >3 ASM trials. Seizure outcomes 2 years after the final surgery were classified using the Engel classification. Among 239 children, the median number of ASM trials before referral was 4.0 (IQR, 3.0); 68% were referred after >3 ASMs. Younger age at epilepsy onset, daily seizures, and extratemporal, multilobar, or hemispheric resections were independently associated with referral after >3 ASM trials. Compared with patients referred after ≤3 ASMs, those referred after >3 ASMs had longer onset-to-referral intervals and were less likely to achieve Engel class 1 (odds ratio 2.0, 95% CI 1.0-3.9, P = .047) and more likely to require reoperation (20.9% vs 5.3%, P = .002). The number of prereferral ASM trials decreased over time. In this population-based cohort, most children underwent more ASM trials than recommended before referral for epilepsy surgery. Greater ASM exposure was associated with more severe epilepsy phenotypes. These findings reinforce the importance of timely recognition of drug-resistant epilepsy and consideration of surgical evaluation alongside escalation of ASM trials.

There are several clinical and research applications for determining the amount of brain tissue resected after epilepsy surgery; however, manual segmentation of postoperative magnetic resonance imaging (MRI) is imprecise and time-consuming. In this study, we developed and benchmarked ResectVol DL, a freely available deep learning-based tool that performs this task automatically. To create ResectVol DL, we trained a UNet-like deep learning model using postoperative T1-weighted MRI from epilepsy surgery patients and evaluated it against manual delineations (ground truth). ResectVol DL was also compared with three automated methods (ResectVol 1.1.2, DeepResection, and Auto3DSeg) using Dice similarity coefficient (DSC), Pearson correlation coefficient, and relative volume difference from manual segmentation. To assess false-positive detections and generalizability beyond epilepsy, we additionally processed images from healthy controls (no resection) and brain tumor cases. The final epilepsy cohort comprised 120 patients (57 women, mean age at surgery = 31.5 ± 15.9 [SD] years), split into training (n = 72) and test (n = 48) sets. An additional 42 images (22 healthy controls and 20 brain tumor cases) were included to test for false positives and generalizability. Segmentation performance differed across methods (Friedman test, p < .001). ResectVol Dl achieved the highest median DSC (.925), significantly outperforming ResectVol 1.1.2, DeepResection, and Auto3DSeg after Bonferroni correction. Volume-based metrics were similar for Auto3DSeg and ResectVol DL (r = .988, relative difference = 8.4% vs. r = .985, 8.1%; no significant difference), yet Auto3DSeg produced three false-positive cavities in no-surgery controls (3/22, 95% confidence interval [CI] = 3%-35%), whereas none was observed for ResectVol DL and DeepResection (0/22, 95% CI = 0%-15%). ResectVol DL provides accurate, fully automated segmentation of postoperative resection cavities, offering a robust and reproducible methodological tool for large-scale postoperative imaging studies in epilepsy surgery. ResectVol DL also provides volumetric information derived from region labeling, which may serve as potential input for predictive models associated with surgery outcome; however, this application has not yet been validated.

Timely and accurate classification of postepilepsy surgery outcomes using Engel and International League Against Epilepsy (ILAE) scales is essential for clinical follow-up, yet electronic health record documentation often lacks the structured detail needed for reliable scoring. This study aimed to validate large language model (LLM) agents for autonomous extraction of standardized postsurgical outcomes from unstructured follow-up notes. We performed a retrospective validation study of deidentified postoperative epilepsy follow-up notes from patients who underwent epilepsy-related surgery or neuromodulation between 2000 and 2025 (n = 170). Each note was processed once with two fixed GPT-4-turbo prompt configurations: a concise definition-based prompt and a context-aware prompt incorporating temporal, causal, and adherence logic. Human-adjudicated consensus served as the reference standard. Prespecified metrics included exact score agreement, clinically adjacent agreement, ordinal distance, Wilson 95% confidence intervals (CIs), and paired tests comparing prompt configurations. Valid follow-up intervals were available for 170 cases; the median time from surgery to analyzed note was 32.7 months (interquartile range = 9.6-97.9). Human reviewers achieved 91.2% raw agreement for Engel major class (Cohen kappa = .86, 95% bootstrap CI = .79-.92) and 83.5% raw agreement for ILAE category (quadratic weighted kappa = .93, 95% CI = .89-.96). The definition-based prompt achieved 56.5% exact Engel subclass agreement (95% CI = 49.0-63.7) and 60.6% exact ILAE agreement (95% CI = 53.1-67.6). The context-aware prompt improved exact agreement to 94.7% for Engel (95% CI = 90.2-97.2) and 93.5% for ILAE (95% CI = 88.8-96.3), with lower ordinal distance for both scales (paired sign tests p < .001). The meaningful finding is not that a general LLM can recite outcome definitions, but that a context-aware LLM agent can apply seizure-outcome logic to heterogeneous real-world notes with high agreement against adjudicated human consensus. Definition-only prompting remained unreliable in nuanced categories, supporting the need for explicit clinical reasoning structure, auditability, and privacy-preserving deployment.

Stereoelectroencephalography (SEEG) plays a central role in the presurgical evaluation of patients with drug-resistant epilepsy, particularly when noninvasive investigations are inconclusive. Beyond localization of the epileptogenic zone (EZ), its role in guiding therapeutic decision-making remains incompletely defined. To evaluate the safety, clinical outcomes, and therapeutic impact of SEEG, including SEEG-guided radiofrequency thermocoagulation (RF-TC), and to develop a structured clinical decision-making framework based on SEEG findings. We performed a retrospective analysis of 71 consecutive patients with drug-resistant epilepsy who underwent SEEG monitoring between 2016 and 2025. Clinical, neuroimaging, and electrophysiological data were analyzed, along with procedural variables, complications, and outcomes following RF-TC and resective surgery. SEEG findings were used to stratify patients into distinct therapeutic pathways. A total of 958 electrodes were implanted (mean 14 ± 4.5 per patient). SEEG confirmed the preimplantation hypothesis in 85% of cases. Based on SEEG findings, 52% of patients were candidates for resective surgery, while 48% were managed conservatively or with neuromodulation strategies. RF-TC was performed in 37 patients (52%), resulting in seizure improvement in 73% at 12months, although complete seizure freedom was limi. Response to RF-TC influenced subsequent treatment decisions, favoring conservative management in responders and resective surgery in non-responders. Favorable outcomes (Engel I-II) after resective surgery were achieved in 71% of patients at 12months. Complications were predominantly minor, with a 1% rate of permanent neurological deficit. SEEG is a safe and effective tool not only for localizing the EZ but also for structuring therapeutic decision-making in drug-resistant epilepsy. SEEG findings enable patient stratification into individualized treatment pathways and support a dynamic, staged approach in which RF-TC may serve as both a therapeutic and decision-modulating tool. This framework highlights the evolving role of SEEG as a central platform in modern epilepsy surgery.

Invasive presurgical evaluation plays a key role in pediatric epilepsy surgery, particularly in magnetic resonance imaging (MRI)-negative cases, by guiding resective, disconnective, or ablative procedures. This International League Against Epilepsy (ILAE) Pediatric Epilepsy Surgery Taskforce study provides an updated global overview of current invasive evaluation practices. Group-level data were collected from 61 epilepsy surgery programs (49 pediatric-only) in 29 countries across six continents. Included were children and adolescents who underwent presurgical evaluation and epilepsy surgery in 2023. The study was designed to enable comparison with the similar ILAE survey conducted in 2004. A total of 2427 patients were included. Invasive evaluations were performed in 21.1% of cases, most frequently in North America (33.7%, higher than Europe: 18.0%, p = .003). Among invasive cases, 32.3% had no detectable MRI abnormalities. The main indication for invasive evaluation was seizure onset localization (88.1%), followed by motor or sensory mapping (17.2%) and language mapping (14.2%). Stereoelectroencephalography (SEEG) was the predominant technique (19.8% overall, 93.6% of invasive cases), more common in North America (30.0%, p = .021) and less common in South America (7.4%, p < .001). Subdural electrodes were used in only 3.2% of invasive cases, and combined depth and subdural approaches in 3.2%. SEEG-guided radiofrequency thermocoagulation (RF-TC) was performed in 40.9% of SEEG cases, most commonly in Asia (63.8%). In 16.2% of invasive evaluations, patients did not proceed to resection, disconnection, or ablation, with the highest rate in Europe (28.5%). This global survey provides the first broad overview of invasive evaluation practices in pediatric epilepsy surgery across participating centers worldwide. It highlights the widespread adoption of SEEG, declining use of subdural electrodes, and increasing application of SEEG-guided RF-TC. The high proportion of MRI-negative cases and the considerable proportion of patients not proceeding to resection, disconnection, or ablation underscore the complexity of contemporary surgical candidates and the need for further refinement of selection strategies.

Pathogenic variants in COL4A1/2 compromise vascular basement membrane integrity, causing intrauterine hemorrhage and infarction leading to extensive structural brain lesions. Vascular disruptions during critical windows of neuronal migration can result in malformations of cortical development (MCD), which may drive epileptogenicity. While surgery is established for drug-resistant focal epilepsy, COL4A1/2 patients with widespread or bilateral MRI abnormalities are frequently deemed ineligible. In selected patients, this necessitates a refined surgical rationale, shifting from strictly curative goals to "non-curative" strategies focused on seizure mitigation and functional preservation. This retrospective multicenter study analyzed six previously unpublished patients (3 COL4A1, 3 COL4A2) from three German epilepsy centers. We evaluated presurgical diagnostics (MRI, PET), surgical techniques, histopathology, and outcomes. Results were contextualized with a review of 11 previously published cases. All patients experienced daily seizures and developmental delay prior surgery. MRI revealed bilateral abnormalities in 4/6 patients (e.g., ventriculomegaly, white matter lesions). Surgical procedures included hemispherotomy (n = 4) and posterior quadrant disconnection/resection (n = 2). Mean follow-up was 5 years 11 months (range 2 years 10 months-8 years 9 months). Seizure freedom (ILAE 1) was achieved in 2/6 patients (33%), both of whom had unilateral lesions. While patients with bilateral lesions remained at ILAE 4, 83% showed postoperative developmental improvement. Histopathology confirmed cortical malformations in three patients (FCD IIId, mMCD II, GW-matter blurring), supporting the hypothesis that secondary cortical malformations, rather than macroscopic lesions, drive epileptogenicity. No surgical or neurovascular complications were observed. Epilepsy surgery is a feasible and safe treatment option for COL4A1/2-associated epilepsy. While curative in patients with unilateral lesions, bilateral cases can benefit from a "non-curative" approach focused on seizure mitigation and neurodevelopmental protection. Multimodal imaging, specifically FDG-PET, can be helpful in identifying highly epileptogenic cortical areas within widespread structural damage and serve as a basis for surgical planning.

Epileptogenic zone (EZ) localization is crucial for surgical treatment of patients with medication-resistant epilepsy. Although simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) can detect interictal discharges for EZ localization, clinical adoption is limited by the need for specialized equipment and expertise. Prior EEG-fMRI work has shown that interictal discharges produce fMRI activation in the EZ and deactivation in the default mode network. Here we use dynamic functional connectivity (dFC) to detect these opposing activations and localize potential interictal activity using fMRI without simultaneous EEG in a cohort composed primarily of temporal lobe epilepsy (TLE). We quantified dFC with the edge timeseries approach and present examples of negative dynamic functional connectivity peaks following interictal discharges in two patients with TLE who received simultaneous EEG-fMRI. We defined the rate of these peaks as the "dFC peak index," hypothesizing it to be elevated in epileptic tissue. We assessed this hypothesis in 62 medication-resistant patients with focal epilepsy who underwent fMRI without simultaneous EEG (49 unilateral temporal, 11 bilateral temporal, 1 frontal, and 1 parietal). We Z-scored dFC peak index in each patient to healthy controls (n = 109) to identify regions with abnormally high values and tested whether these aligned with patients' EZs or correlated with clinical parameters. The dFC peak index was elevated in epileptic medial temporal structures in patients with TLE (pFWE <.05). Resection of regions with higher values correlated with better seizure outcomes after surgery (area under the curve [AUC] = .80, p = .0002), even in patients without hippocampal lesions on MRI (AUC = .79, p = .04). This study presents the dFC peak index, which aims to detect interictal epileptic activity using fMRI without simultaneous EEG. Our results indicate that this measure is elevated in epileptic tissue in TLE, suggesting that it could provide unique information to guide epilepsy surgery.

We hypothesized that [18F]FDG PET/MRI would improve presurgical lesion detection compared with MRI alone in pediatric patients with focal epilepsy. We analyzed surgical outcomes and the presurgical evaluation pipeline. Methods: We included pediatric patients undergoing [18F]FDG PET/MRI between January 2017 and October 2021. Eligible patients were 18 y or younger, had a diagnosis of focal epilepsy under surgical evaluation, and had a negative or inconclusive MRI result. Data analysis phases included evaluation of prior MRI data (phase 0), masked review of PET/MRI-acquired MR sequences (phase 1), joint (nuclear medicine/neuroradiology) PET/MRI assessment (phase 2), and verification of PET/MRI findings against the hypothesized epileptogenic zone (EZ) (through electroencephalography in all cases; through stereoelectroencephalography outcomes and histology when relevant) (phase 3). Results: Seventy-nine patients were included in the study (49 male; mean age, 9.5 y). Patients' mean duration of epilepsy was 4.4 y, and 65 (83%) had drug-resistant seizures. Initial MRI results were inconclusive in 26 (33%) patients and negative in 53 (67%) patients. Blinded 3-T MRI identified suspect lesions in 36 (46%) patients, identifying additional lesions in 10 patients. Joint PET/MRI reading revealed that 46 (58%) patients had concordant PET-positive/MRI-positive results, 24 (30%) had PET-positive/MRI-negative results, and 8(10%) had PET-negative/MRI-negative results. Concordant PET-positive/MRI-positive findings demonstrated high accuracy in identifying epileptogenic lesions, particularly focal cortical dysplasia. PET/MRI showed metabolic alterations in 70 (89%) patients: 67 of 70 (96%) with hypometabolism and 6 of 70 (9%) with mixed areas of hypometabolism and hypermetabolism. The results were concordant with the electroclinical hypothesis in 45 (98%) of 46 patients with PET-positive/MRI-positive results and in 15 (63%) of 24 patients with PET-positive/MRI-negative results. Twenty-four patients underwent resection or disconnection, and 5 underwent thermocoagulation. Of these, 22 (76%) achieved Engel Class IA outcomes (average follow-up, 2.1 y). Conclusion: [18F]FDG PET/MRI offered significant diagnostic and prognostic value, especially in MRI-negative or inconclusive cases, enhancing presurgical evaluation precision and guiding clinical decision-making in pediatric epilepsy surgery.

Despite substantial interest in how neural systems recover over time after acute neurological events, there is a dearth of longitudinal assessment from minutes to months surrounding these events. We compared rare intraoperative recordings in three patients, obtained immediately before and after anterior temporal lobe resection during a semantic prediction task, with longitudinal source-localized electroencephalography (EEG) obtained 2-6 weeks before, and 2 and 6-14 months after surgery. Relative to controls (n= 20), task performance showed sustained impairment in the two left-hemisphere patients and delayed impact in the right-hemisphere patient. Consistent with theories on ipsilateral and contralateral hemisphere compensation, all patients exhibited bilateral EEG alterations in speech responses and effective connectivity that did not fully recover to pre-operative levels. Direct dataset comparisons of intrinsic neurophysiological biomarkers associated with timescales of processing (τINT) and excitatory-inhibitory balance (aperiodic slope, χSPEC) showed a striking months-long reduction in rapid neural timescales of processing and gradually increasing aperiodic slope (putatively reflecting increased cortical inhibition or reduced excitation) specifically in the ipsilateral hemisphere of all three patients. Amidst these neurophysiological alterations, semantic task performance did not return to pre-operative levels. These rare longitudinal data advance a mechanistic framework to non-invasively evaluate neurophysiological impact over multiple timeframes in other patient cohorts.Significance statementWe report rare longitudinal recordings obtained minutes to months before and after epilepsy surgery. Using state-of-the-art measures of neurophysiological biomarkers and network dynamics, we observed immediate disruption followed by consistent, longer-lasting alterations in neural excitability and temporal functionality.

IntroductionApproximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.Methods and analysisThis is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3–50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-naïve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.Ethics and disseminationThe study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 – parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.Trial registration numberClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.