Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections
BackgroundPediatric 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 r...
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| Published in | Open forum infectious diseases Vol. 8; no. 6; p. ofab104 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
US
Oxford University Press
01.06.2021
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| Subjects | |
| Online Access | Get full text |
| ISSN | 2328-8957 2328-8957 |
| DOI | 10.1093/ofid/ofab104 |
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| Abstract | BackgroundPediatric 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.
MethodsWe 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.
ResultsWe 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.
ConclusionsMetagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.
We examined the utility of next-generation sequencing in comparison to usual care in detecting a pathogenic organism in children with central nervous system infections. |
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| AbstractList | 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.
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.
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.
Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections. 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.BACKGROUNDPediatric 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.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.METHODSWe 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.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.RESULTSWe 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.Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.CONCLUSIONSMetagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections. BackgroundPediatric 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. MethodsWe 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. ResultsWe 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. ConclusionsMetagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections. We examined the utility of next-generation sequencing in comparison to usual care in detecting a pathogenic organism in children with central nervous system infections. We examined the utility of next-generation sequencing in comparison to usual care in detecting a pathogenic organism in children with central nervous system infections. BackgroundPediatric 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. MethodsWe 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. ResultsWe 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. ConclusionsMetagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections. |
| Author | Briggs, Benjamin Coufal, Nicole G Stinnett, Rita Salyakina, Daria Janvier, Michelin Ramchandar, Nanda Clarke, Christina Xie, Heng Schwarz, Toni Warden, Anna S Enriquez, Claudia Waldeman, Bryce Schlaberg, Robert Arrieta, Antonio Sendi, Prithvi Foley, Jennifer Osborne, Stephanie Farnaes, Lauge Dimmock, David Totapally, Balagangadhar R |
| AuthorAffiliation | 5 IDbyDNA , Salt Lake City, Utah , USA 3 Rady Children’s Hospital San Diego , San Diego, California , USA 2 Department of Pediatrics, University of California , San Diego, California , USA 6 Children’s Hospital of Orange County , Orange, California , USA 1 Rady Children’s Institute for Genomic Medicine , San Diego, California , USA 7 Nicklaus Children’s Hospital , Miami, Florida , USA 4 Department of Cellular and Molecular Medicine, University of California , San Diego, California , USA |
| AuthorAffiliation_xml | – name: 1 Rady Children’s Institute for Genomic Medicine , San Diego, California , USA – name: 7 Nicklaus Children’s Hospital , Miami, Florida , USA – name: 6 Children’s Hospital of Orange County , Orange, California , USA – name: 4 Department of Cellular and Molecular Medicine, University of California , San Diego, California , USA – name: 3 Rady Children’s Hospital San Diego , San Diego, California , USA – name: 5 IDbyDNA , Salt Lake City, Utah , USA – name: 2 Department of Pediatrics, University of California , San Diego, California , USA |
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| Keywords | encephalitis next-generation sequencing metagenomics meningitis pediatric |
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| Snippet | BackgroundPediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is... Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important,... We examined the utility of next-generation sequencing in comparison to usual care in detecting a pathogenic organism in children with central nervous system... |
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| SubjectTerms | Infections Major Nervous system Pathogens Pediatrics |
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| Title | Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections |
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