A Novel Balamuthia Lineage Causing Fatal Granulomatous Amoebic Encephalitis in an Immunocompetent Infant.

Objectives: To characterize a genetically distinct Balamuthia lineage causing fatal granulomatous amoebic encephalitis (GAE) in a 10-month-old infant and highlight diagnostic challenges compounded by SARS-COV-2 infection comorbidity.

Methods: Case report of a 10-month-old male with GAE. Metagenomic next-generation sequencing (mNGS) and PCR sequencing of 18S/12S rRNA genes from brain biopsy tissue were performed. Phylogenetic analysis was conducted to identify the genetic characteristics of the pathogen.

Results: The patient presented with recurrent fever, seizures, and rapidly progressive neurological deterioration. He had documented SARS-CoV-2 infection two weeks prior to symptom onset. The mNGS of biopsy tissue identified Balamuthia infection. Genetic analysis revealed 18S rRNA similarity of 95.33% and mitochondrial 12S rRNA similarity of 85.49% versus known species. Phylogenetic trees confirmed a distinct clade, suggesting a potential novel species. Despite aggressive treatment, the patient died after 13 days of hospitalization.

Conclusions: This case highlights the challenges in diagnosing and managing GAE, particularly in pediatric patients with atypical presentations. The discovery of a genetically distinct Balamuthia strain indicates the importance of global surveillance for emerging pathogens. Clinicians should consider Balamuthia as a potential cause of encephalitis in children with unexplained neurological symptoms, even in non-endemic regions.