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. 2021 Mar 6;8(6):ofab104.
doi: 10.1093/ofid/ofab104. eCollection 2021 Jun.

Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections

Nanda Ramchandar  1   2 , Nicole G Coufal  1   2   3 , Anna S Warden  4 , Benjamin Briggs  5 , Toni Schwarz  5 , Rita Stinnett  5 , Heng Xie  5 , Robert Schlaberg  5 , Jennifer Foley  3 , Christina Clarke  1 , Bryce Waldeman  1 , Claudia Enriquez  6 , Stephanie Osborne  6 , Antonio Arrieta  6 , Daria Salyakina  7 , Michelin Janvier  7 , Prithvi Sendi  7 , Balagangadhar R Totapally  7 , David Dimmock  1 , Lauge Farnaes  1   5
Affiliations

Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections

Nanda Ramchandar et al. Open Forum Infect Dis. .

Abstract

Background: Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management and in characterizing prognosis. Usual care testing by culture and polymerase chain reaction is often unable to identify a pathogen. We examined the systematic application of metagenomic next-generation sequencing (mNGS) for detecting organisms and transcriptomic analysis of cerebrospinal fluid (CSF) in children with central nervous system (CNS) infections.

Methods: We conducted a prospective multisite study that aimed to enroll all children with a CSF pleocytosis and suspected CNS infection admitted to 1 of 3 tertiary pediatric hospitals during the study timeframe. After usual care testing had been performed, the remaining CSF was sent for mNGS and transcriptomic analysis.

Results: We screened 221 and enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 25 (35.7%) subjects by any diagnostic modality. Metagenomic next-generation sequencing of the CSF samples identified a pathogen in 20 (28.6%) subjects, which were also all identified by usual care testing. The median time to result was 38 hours.

Conclusions: Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.

Keywords: encephalitis; meningitis; metagenomics; next-generation sequencing; pediatric.

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Figures

Figure 1.
Figure 1.
(A) A heat map comparing Pediatric Infectious Disease Precision Medicine Using Sequencing Evaluation of CSF (PIPSEC) subjects with bacterial and viral diagnoses identified 409 differentially expressed genes with false discovery rate >0.05 and fold change ≥1.5. (B) Volcano plot identifying differentially expressed genes between bacterial and viral meningitis. (C) Scatter plot depicting mean, standard error of the mean, and individual values. **P-adjusted value (p-adj) < .01, ***p-adj < .0001 compared with all other groups with a fold change of 10.0 for interleukin (IL)1B and 18.0 for CXCL8 in bacterial meningitis, and 14.0 for CCL8 in viral meningitis compared with all other samples. (D) Receiver operator characteristic (ROC) for IL1B and CCL8. AUC, area under curve.
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