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A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting
- Source :
- Scientific Reports, Scientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
Abstract
- The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p
- Subjects :
- Male
0301 basic medicine
Hospital setting
Cns infections
lcsh:Medicine
Datasets as Topic
Central Nervous System Infections
Acute care
lcsh:Science
Child
Cerebrospinal Fluid
Multidisciplinary
High-Throughput Nucleotide Sequencing
Hospitals
medicine.anatomical_structure
Child, Preschool
Female
Meningitis
Encephalitis
DNA, Bacterial
medicine.medical_specialty
Adolescent
030106 microbiology
Central nervous system
Sensitivity and Specificity
Article
Young Adult
03 medical and health sciences
Internal medicine
medicine
Humans
Clinical microbiology
Retrospective Studies
business.industry
lcsh:R
Infant, Newborn
Laboratory techniques and procedures
Computational Biology
Infant
Sequence Analysis, DNA
medicine.disease
030104 developmental biology
Metagenomics
DNA, Viral
Etiology
Feasibility Studies
Metagenome
lcsh:Q
business
Subjects
Details
- ISSN :
- 20452322
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- Scientific Reports
- Accession number :
- edsair.doi.dedup.....decb3bf4f3d0745dcc5b773d7c9519ac