When the three terms were used together, only two articles previously published by us were found. Several articles had been published testing the Oxford Nanopore technologies sequencing on CSF, but no investigations were found into the direct diagnosis of CSF series. We searched PubMed up to 30 November 2021 for research articles published in English, using the following search terms “real-time metagenomics sequencing”, “meningitis”, and “direct diagnosis”. Genomic surveillance and antibiotic resistance testing are based only on bacteria isolated from cerebrospinal fluid, failing in 60% of cases. Bacterial characterisation and drug resistance profiling require additional in-vitro investigations which take over 48 h, delaying pathogen-targeted treatment. The emergency diagnosis of infectious meningitis is currently based on multiplex real-time amplification using a syndromic panel limited by the most frequent microorganisms which lead to a central nervous system prognosis. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.Ĭommunity-acquired bacterial meningitis is a life-threatening infection that can progress to mortality within 48 h. RTM identified 14 pathogen genotypes, including a majority of H. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples and after two hours in 14 additional CSFs yielding > 50% genome coverage in 19 CSFs. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H.
Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus.
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