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Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report
Madjid Morsli1,2, Quentin Kerharo1, Jeremy Delerce1
1IHU Méditerranée Infection, 13005 Marseille, France.
Abstract:
Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. 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 an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes.
Insights
Rapid sequencing accurately identified the pathogen causing meningitis, enabling quick serotype diagnosis. This advance offers a faster point-of-care diagnostic tool for infectious meningitis.
Area of Science:
- Medical Microbiology
- Genomics
- Infectious Diseases
Background:
- Current real-time PCR methods for meningitis diagnosis lack pathogen genotyping capabilities.
- Haemophilus influenzae meningitis is a serious, potentially deadly infection.
- Rapid and accurate diagnosis is crucial for effective patient management.
Purpose of the Study:
- To evaluate Oxford Nanopore Technologies (ONT) real-time sequencing for direct pathogen genome detection and genotyping from cerebrospinal fluid (CSF).
- To compare ONT sequencing with standard real-time PCR for diagnosing infectious meningitis.
- To assess the utility of ONT metagenomic sequencing for point-of-care diagnosis.
Main Methods:
- Real-time PCR was used for initial diagnosis of H. influenzae meningitis.
- Oxford Nanopore Technologies real-time sequencing was performed in parallel on the CSF sample.
- Bioinformatic analysis, including BLAST, was used to identify the pathogen and its serotype.
Main Results:
- ONT sequencing detected the H. influenzae genome directly from CSF within six hours.
- BLAST analysis identified a non-b serotype, non-typeable H. influenzae (lineage 22.1-21).
- The method allowed for one-shot genotyping alongside pathogen identification.
Conclusions:
- Oxford Nanopore metagenomic next-generation sequencing is a viable tool for point-of-care diagnosis of infectious meningitis.
- This approach enables direct identification and genotyping/serotyping of pathogenic genomes.
- ONT sequencing offers a significant advancement over current methods for rapid meningitis diagnosis.
