Balamuthia mandrillaris—EBV co-infective encephalitis diagnosed by MetaCAP: comparative mNGS validation and epidemiological landscape from 41 Chinese cases

OBJECTIVE: This study aimed to present the first documented case of fatal granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris and Epstein-Barr virus (EBV) co-infection, to evaluate the diagnostic performance of MetaCAP targeted sequencing against mNGS, and to provide a national epidemiological profile of this disease in China. METHODS: A 55-year-old male presenting with fever and altered consciousness was comprehensively evaluated. Parallel testing of blood, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid (BALF) was conducted using both MetaCAP and mNGS technologies. The diagnostic sensitivity of both platforms was directly compared. Additionally, a retrospective analysis of 41 confirmed cases in China was performed to delineate the epidemiological and clinical characteristics. RESULTS: MetaCAP sequencing confirmed the presence of B. mandrillaris and EBV in CSF and blood, with the amoeba also detected in BALF. It demonstrated superior sensitivity, identifying B. mandrillaris at significantly higher levels in blood (1064 vs 7 RPM) and in BALF (7 RPM vs undetected by mNGS). The epidemiological analysis revealed a unique adult-predominant pattern and geographic clustering among Chinese cases. CONCLUSION: This study reports a novel viral-amoebic co-infective GAE and validates MetaCAP as a highly sensitive diagnostic tool, outperforming mNGS for detecting fastidious pathogens. The integrated national cohort data provide critical insights into the disease's profile in China, suggesting that MetaCAP can significantly improve diagnostic yield and guide earlier intervention.