Abstract
Ventricular reservoir infections and cerebrospinal fluid (CSF) shunt infections are diagnosed when bacteria are recovered from microbiological cultures of CSF samples from these devices. We applied high throughput sequencing (HTS) to understand the course of changes in ventricular reservoir and shunt infection microbiota.
Evaluate the utility of monitoring microbiota in CSF (1) from ventricular reservoirs to detect development of an infection and (2) during treatment of CSF shunt infections to assess treatment response.
Study populations included (1) neonates with temporizing ventricular reservoirs who developed reservoir infection and (2) children undergoing treatment for conventional culture-confirmed CSF shunt infection. The V4 region of the 16S ribosomal RNA gene was amplified and sequenced. Comparison of taxonomic results of HTS with standard microbiological culture results (when available) was described for each CSF sample. A robust HTS signal was defined by a microbial load of ≥1e5 microbial genome equivalents/mL.
In none of the five ventricular reservoir infection cases was there a robust HTS signal for the responsible bacteria immediately prior to infection. In six of the seven CSF shunt infection cases, there was a robust HTS signal for the genus of the responsible bacteria in the sample at the time of positive CSF culture. The proportion of sequences from the genus associated with the responsible bacteria decreased during infection treatment.
These pilot data suggest limited utility in using HTS for surveillance for ventricular reservoir infections, as they emerge abruptly. In CSF shunt infection, HTS demonstrates a return to heterogeneous microbiota when bacterial cultures become negative.