Metagenomics-driven rapid diagnosis of an imported fatal case of rare amoebic meningoencephalitis.

We identified Naegleria fowleri as the aetiologic agent from cerebrospinal fluid (CSF) of a patient with a travel history to Karachi. We demonstrate the benefit of metagenomics-based rapid diagnosis of primary amoebic meningoencephalitis (PAM) when routine clinical tests fail to provide a definitive diagnosis. We reconstructed the N. fowleri genome.