Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach

Fluids and Barriers of the CNS

Research

Ingeborg E. van Zeggeren¹  Diederik van de Beek¹  Matthijs C. Brouwer¹  Arthur W. D. Edridge²  Lia van der Hoek²  Cormac M. Kinsella²  Martin Deijs² 

[1] Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands;Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands;Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands;Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, The Netherlands;

关键词: Bacterial meningitis;    Pathogen detection;    Cerebrospinal fluid;    Viromics;    Metagenomics;   

DOI  :  10.1186/s12987-022-00400-5

 received in 2022-09-22, accepted in 2022-12-07,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundIn patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses.MethodsWe studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis.ResultsSensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection.ConclusionWe provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.

【 授权许可】

CC BY   
© The Author(s) 2022

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