To characterize variation in diagnostic testing, autoimmune workup, treatment, and follow-up across hospitals in the Neuroinfections Emerging in the Americas Study (NEAS) cohort in Colombia.

Encephalitis of unknown etiology requires timely identification of treatable infectious and autoimmune causes. A mixed public-private system delivers care across Colombian cities of varying sizes, most within arbovirus-endemic zones (dengue, Zika, chikungunya). Uneven diagnostic infrastructure and absence of harmonized institutional protocols may allow hospital context to shape evaluation, treatment, and follow-up.

Patients diagnosed with encephalitis of unknown etiology were enrolled in an observational cohort at 12 Colombian high-complexity hospitals, 2016–2025 (N=127). Hospitals were classified by ownership (public [N=76]; private [N=51]) and metropolitan size (large ≥1M [N=82]; intermediate <1M [N=45]).

Cerebrospinal fluid (CSF) analysis was performed in 118 (93%), with herpes simplex virus (HSV) PCR ordered in 63 (53%) of those. Among all 127 patients, acyclovir was administered empirically to 55 (43%), steroids to 31 (24%), intravenous immunoglobulin and plasmapheresis each to 4 (3%). Private hospitals had higher magnetic resonance imaging (MRI) rates than public hospitals (73% vs 51%, p=0.026). Intermediate-city hospitals had higher CSF analysis rates (100% vs 89%, p=0.026), head computed tomography (CT) (84% vs 63%, p=0.014), and electroencephalogram (EEG) (61% vs 24%, p<0.001); large-metro hospitals had shorter time to MRI (median 1 vs 4 days, p=0.006). MRI, EEG, and CT rates varied across hospitals (p≤0.020). Clinical follow-up rate was higher in large-metro than intermediate-city hospitals (72% vs 16%, p<0.001).

Diagnostic practice, autoimmune workup, and clinical follow-up varied by hospital ownership and metropolitan size. Molecular microbiology testing and immunotherapy use were low across settings, and follow-up was documented in fewer than 1 in 6 patients at intermediate-city hospitals. These patterns are consistent with context-dependent decision-making shaped by structural and geographic factors; standardized diagnostic and follow-up protocols could support more consistent care throughout.