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Characterization of cerebrospinal fluid (CSF) microbiota from patients with CSF shunt infection and reinfection using high throughput sequencing of 16S ribosomal RNAgenes
- Source :
- PLoS ONE, Vol 16, Iss 1, p e0244643 (2021), PLoS ONE
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- Background Nearly 20% of patients with cerebrospinal fluid (CSF) shunt infection develop reinfection. It is unclear whether reinfections are caused by an organism previously present or are independent infection events. Objective We used bacterial culture and high throughput sequencing (HTS) of 16S ribosomal RNA (rRNA) genes to identify bacteria present in serial CSF samples obtained from children who failed CSF shunt infection treatment. We hypothesized that organisms that persist in CSF despite treatment would be detected upon reinfection. Design/methods Serial CSF samples were obtained from 6 patients, 5 with 2 infections and 1 with 3 infections; the study was limited to those for which CSF samples were available from the end of infection and beginning of reinfection. Amplicons of the 16S rRNA gene V4 region were sequenced. Taxonomic assignments of V4 sequences were compared with bacterial species identified in culture. Results Seven infection dyads averaging 13.5 samples per infection were analyzed. A median of 8 taxa [interquartile range (IQR) 5–10] were observed in the first samples from reinfection using HTS. Conventional culture correlated with high abundance of an organism by HTS in all but 1 infection. In 6 of 7 infection dyads, organisms identified by culture at reinfection were detected by HTS of culture-negative samples at the end of the previous infection. The median Chao-Jaccard abundance-based similarity index for matched infection pairs at end of infection and beginning of reinfection was 0.57 (IQR 0.07–0.87) compared to that for unmatched pairs of 0.40 (IQR 0.10–0.60) [p = 0.46]. Conclusion(s) HTS results were generally consistent with culture-based methods in CSF shunt infection and reinfection, and may detect organisms missed by culture at the end of infection treatment but detected by culture at reinfection. However, the CSF microbiota did not correlate more closely within patients at the end of infection and beginning of reinfection than between any two unrelated infections. We cannot reject the hypothesis that sequential infections were independent.
- Subjects :
- 0301 basic medicine
Bacterial Diseases
Microbiological culture
Physiology
Staphylococcus
Pathology and Laboratory Medicine
Nervous System
law.invention
Cerebrospinal fluid
Medical Conditions
Interquartile range
Staphylococcus epidermidis
law
RNA, Ribosomal, 16S
Contaminants
Medicine and Health Sciences
Child
Materials
Polymerase chain reaction
Cerebrospinal Fluid
Multidisciplinary
biology
High-Throughput Nucleotide Sequencing
Genomics
Microbial Cultures
Cerebrospinal Fluid Shunts
Body Fluids
Bacterial Pathogens
Infectious Diseases
Medical Microbiology
Physical Sciences
Medicine
Biological Cultures
Anatomy
Pathogens
Hydrocephalus
Research Article
Staphylococcus aureus
Adolescent
Science
030106 microbiology
Materials Science
Microbial Genomics
Bacterial Cultures
Research and Analysis Methods
Microbiology
03 medical and health sciences
Genetics
Humans
Microbiome
Molecular Biology Techniques
Sequencing Techniques
Staphylococcus Epidermidis
Molecular Biology
Microbial Pathogens
Staphylococcal Infection
Bacteria
High Throughput Sequencing
Organisms
Biology and Life Sciences
Ribosomal RNA
biology.organism_classification
16S ribosomal RNA
030104 developmental biology
Reinfection
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 16
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....1dab97b18c9c53241db091f55d7fc7ed