Use of quantitative 16S rRNA PCR to determine bacterial load does not augment conventional cerebrospinal fluid (CSF) cultures among children undergoing treatment for CSF shunt infection

Diagn Microbiol Infect Dis. 2014 Feb;78(2):188-95. doi: 10.1016/j.diagmicrobio.2013.06.027. Epub 2013 Aug 13.


The aim of this study was to develop a quantitative 16S rRNA assay for determination of bacterial nucleic acid load in cerebrospinal fluid (CSF) shunt infection and to compare quantitative 16S rRNA polymerase chain reaction (PCR) findings to those of conventional bacterial culture in patients treated for CSF shunt infection. We developed a quantitative 16S rRNA PCR assay that detected bacterial load across a range of 2.5 × 10(9) down to 2.5 × 10(4) 16S copies/mL CSF under experimental conditions for numerous Gram-positive and Gram-negative organisms. However, when applied to archived CSF samples from 25 shunt infection episodes, correlations between positive bacterial culture and 16S rRNA levels were seen in only half of infections, and 16S rRNA levels dropped precipitously after an initial peak on the first day of sample collection. Bacterial load measured using 16S rRNA PCR does not provide sufficient information beyond bacterial culture to inform CSF shunt infection treatment.

Keywords: Bacterial load; Cerebrospinal; Children; Infection; Shunt.

MeSH terms

  • Adolescent
  • Anti-Bacterial Agents / therapeutic use
  • Bacteria / classification
  • Bacteria / genetics*
  • Bacterial Infections / diagnosis*
  • Bacterial Infections / drug therapy
  • Bacterial Infections / microbiology*
  • Bacterial Load*
  • Cerebrospinal Fluid / microbiology*
  • Cerebrospinal Fluid Shunts / adverse effects*
  • Child
  • Humans
  • RNA, Ribosomal, 16S*
  • Real-Time Polymerase Chain Reaction


  • Anti-Bacterial Agents
  • RNA, Ribosomal, 16S