Generic Portal

TY - JOUR

T1 - Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach

AU - Kinsella, Cormac M

AU - Edridge, Arthur W D

AU - van Zeggeren, Ingeborg E

AU - Deijs, Martin

AU - van de Beek, Diederik

AU - Brouwer, Matthijs C

AU - van der Hoek, Lia

N1 - Funding Information: Computational work was carried out on the Dutch national e-infrastructure with the support of SURF Cooperative. Funding Information: This work was supported by a European Union Horizon 2020 research and innovation program Grant [Marie Skłodowska-Curie agreement No. 721367 (HONOURs) to Lia van der Hoek], the Netherlands Organization for Health Research and Development (ZonMw; NWO-Vidi Grant [Grant number 917.17.308 to Matthijs C. Brouwer], NWO-Vici-Grant [Grant number 918.19.627 to Diederik van de Beek]) and the European Research Council (ERC Consolidator grant [Grant 101001237 to Matthijs C. Brouwer]). Publisher Copyright: © 2022, The Author(s).

PY - 2022/12/22

Y1 - 2022/12/22

N2 - BACKGROUND: In 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.METHODS: We 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.RESULTS: Sensitivity 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.CONCLUSION: We 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.

AB - BACKGROUND: In 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.METHODS: We 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.RESULTS: Sensitivity 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.CONCLUSION: We 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.

KW - Bacterial meningitis

KW - Cerebrospinal fluid

KW - Metagenomics

KW - Pathogen detection

KW - Viromics

UR - http://www.scopus.com/inward/record.url?scp=85144538371&partnerID=8YFLogxK

U2 - 10.1186/s12987-022-00400-5

DO - 10.1186/s12987-022-00400-5

M3 - Article

C2 - 36550487

VL - 19

SP - 102

JO - Fluids and barriers of the CNS

JF - Fluids and barriers of the CNS

SN - 2045-8118

IS - 1

M1 - 102

ER -