title: Evaluation of microbial bacterial and fungal diversity in cerebrospinal fluid shunt infection.
abstract: BACKGROUND
  Cerebrospinal fluid shunt infection can be recalcitrant. Recurrence is common despite appropriate therapy for the pathogens identified by culture. Improved diagnostic and therapeutic approaches are required, and culture-independent molecular approaches to cerebrospinal fluid shunt infections have not been described.
  
  
  OBJECTIVE
  To identify the bacteria and fungi present in cerebrospinal fluid from children with cerebrospinal fluid shunt infection using a high-throughput sequencing approach, and to compare those results to those from negative controls and conventional culture.
  
  
  METHODS
  This descriptive study included eight children ≤18 years old undergoing treatment for culture-identified cerebrospinal fluid shunt infection. After routine aerobic culture of each cerebrospinal fluid sample, deoxyribonucleic acid (DNA) extraction was followed by amplification of the bacterial 16S rRNA gene and the fungal ITS DNA region tag-encoded FLX-Titanium amplicon pyrosequencing and microbial phylogenetic analysis.
  
  
  RESULTS
  The microbiota analyses for the initial cerebrospinal fluid samples from all eight infections identified a variety of bacteria and fungi, many of which did not grow in conventional culture. Detection by conventional culture did not predict the relative abundance of an organism by pyrosequencing, but in all cases, at least one bacterial taxon was detected by both conventional culture and pyrosequencing. Individual bacterial species fluctuated in relative abundance but remained above the limits of detection during infection treatment.
  
  
  CONCLUSIONS
  Numerous bacterial and fungal organisms were detected in these cerebrospinal fluid shunt infections, even during and after treatment, indicating diverse and recalcitrant shunt microbiota. In evaluating cerebrospinal fluid shunt infection, fungal and anaerobic bacterial cultures should be considered in addition to aerobic bacterial cultures, and culture-independent approaches offer a promising alternative diagnostic approach. More effective treatment of cerebrospinal fluid shunt infections is needed to reduce unacceptably high rates of reinfection, and this work suggests that one effective strategy may be reduction of the diverse microbiota present in infection.
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America ; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.
authors.forename: Tamara D
authors.initials: TD
authors.lastname: Simon
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Pope
authors.affiliation: Department of Neurological Surgery, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America.
authors.forename: Samuel R
authors.initials: SR
authors.lastname: Browd
authors.affiliation: Department of Neurological Surgery, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America.
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Ojemann
authors.affiliation: Division of Pediatric Neurosurgery, Primary Children's Medical Center, Department of Neurosurgery, University of Utah, Salt Lake City, Utah, United States of America.
authors.forename: Jay
authors.initials: J
authors.lastname: Riva-Cambrin
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America ; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.
authors.forename: Nicole
authors.initials: N
authors.lastname: Mayer-Hamblett
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America ; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.
authors.forename: Margaret
authors.initials: M
authors.lastname: Rosenfeld
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America ; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.
authors.forename: Danielle M
authors.initials: DM
authors.lastname: Zerr
authors.affiliation: Department of Pediatrics, University of Washington/Seattle Children's Hospital, Seattle, Washington, United States of America ; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, Washington, United States of America ; Department of Microbiology, University of Washington, Seattle, Washington, United States of America ; Center for Infection and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, United States of America.
authors.forename: Lucas
authors.initials: L
authors.lastname: Hoffman
mesh_terms: D001419:Bacteria / Q000235:genetics*; D002557:Cerebrospinal Fluid Shunts / Q000009:adverse effects*; D003141:Communicable Diseases / Q000175:diagnosis / Q000209:etiology* / Q000382:microbiology*; D005658:Fungi / Q000235:genetics*; D014644:Genetic Variation; D006801:Humans; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S