Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

Abstract

Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.

Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections

“…Furthermore, the viral pathogen spectrum detected in CNS infections is typically complex and diverse, with potentially low viral loads. Conventional methods such as polymerase chain reaction (PCR) and antibody detection (enzyme immunoassays) often exhibit poor utility in such cases ( 7 ).…”

Clinical metagenomics—challenges and future prospects

“…mNGS can capture millions to billions of nucleic acids sequences at once and detect multiple organisms including novel pathogens that may be present in a clinical specimen ( John et al, 2021 ). The time required for sample preparation, sequencing, and preliminary bioinformatic analysis depends on the nature of sequencing platform being used ( Morsli et al, 2021a , b , 2022a , b ). For example, newly available long-read sequencing platforms, such as Oxford Nanopore sequencing, provide real time pathogen detection within minutes and additional information regarding genotyping and bacterial profiling in less than 6 h ( Morsli et al, 2021a , b , 2022a , b ).…”

“…The time required for sample preparation, sequencing, and preliminary bioinformatic analysis depends on the nature of sequencing platform being used ( Morsli et al, 2021a , b , 2022a , b ). For example, newly available long-read sequencing platforms, such as Oxford Nanopore sequencing, provide real time pathogen detection within minutes and additional information regarding genotyping and bacterial profiling in less than 6 h ( Morsli et al, 2021a , b , 2022a , b ). Also, Oxford Nanopore Technologies is currently the most prevalent and cost-effective mNGS platform in low- and middle-income countries ( Yek et al, 2022 ).…”

Microbial signatures of neonatal bacterial meningitis from multiple body sites

“…Compared with amplicon sequencing, WMS has more potential in clinical practice since amplicon sequencing suffers from off-target amplification ( Bedarf et al., 2021 ), biased abundance estimation, limited taxonomic resolution, insensitivity to degraded DNA, and unable to simultaneously capture all microorganisms (e.g., bacteria, fungi, archaea, and virus) in one sequencing ( Knight et al., 2018 ). However, WMS is not a perfect solution since it also suffers from high cost and low microbial biomass samples, while the limited availability and volume from invasive procedures such as lumbar puncture makes it difficult to extract high quality DNA from CSF ( Graff et al., 2021 ; Morsli et al., 2022 ). To overcome the difficulties in metagenomic sequencing of low microbial biomass such as CSF and blood samples, we innovatively employed 2bRAD-M in this study, which has been proven to be effective in dealing with 1pg total DNA, 50 bp highly degraded DNA, and 99% host contaminated DAN samples ( Sun et al., 2022a ).…”