Haemophilus influenzae meningitis direct diagnosis by whole genome sequencing: a case report.

Abstract.Background: Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis, do not allow for one shot genotyping pathogen, as in the case of deadly Haemophilus influenzae meningitis.Case presentation: Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using Oxford Nanopore technology real-time sequencing in parallel to real-time PCR, we detected H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Blast analysis of the sequence encoding for partial DUF417 domain-containing protein, diagnosed a non-b serotype, non-typeable H. influenzae belonging to lineage H. influenzae 22.1-21.Conclusion: Oxford Nanopore metagenomic next-generation sequencing approach must be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes / serotypes