A search for bacteria identified from cerebrospinal fluid shunt infections in previous surgical events

Abstract

Shunt infections are a common complication when treating hydrocephalus by cerebrospinal fluid (CSF) shunt placement. The source of infecting pathogens is not well understood. One hypothesis, which we explored here, is that microorganisms persist chronically in the host long before a symptomatic infection occurs and may be detectable in surgical events preceding infection. A cohort of 13 patients was selected, for which CSF samples were available from an infection episode and from a previous surgery event, which was either an initial shunt placement or a revision. Microbiota were analyzed both directly from CSF and from isolates cultured from CSF on aerobic and anaerobic media. The detection and identification of bacteria was done with high throughput DNA sequencing methods and mass spectrometry. The presence of bacteria was confirmed in 4 infection samples, of which 2 were after initial placement and 2 after revision surgery. Taxonomic identification was consistent with clinical microbiology laboratory results. Bacteria were not detected in any of the CSF samples collected at the time of the previous surgical events. While our findings do not provide direct evidence for long-term persistence of pathogens, they suggest the need for consideration of additional source material, such as biofilm and environmental swabs, and/or the use of more sensitive and specific analytical methods.

Fig 1. Methods approach.

CSF in 2 forms and clinical data were collected from study subjects. CSF and CSF-derived cultures were used for taxonomic identification using multiple experimental approaches.

Fig 2. Taxonomic distribution of 16S RNA amplicons shown as raw counts (A) and proportions (B).

Patient labels are as in Table 1, with the number after the dot indicating previous surgery (1) or infection (2). Negative controls consist of extraction (EXC) and no-template (NTC) controls. Positive controls are the mock community (M.n), where n is the 10ⁿ dilution factor, and pure cultures of Cutibacterium acnes (CA) and Staphylococcus aureus (SA). Taxonomic categories that appeared in at least one sample at a proportion of 0.1 or more are given by name. The inset shows qPCR measurements of 16S RNA in genome equivalents (GE) per ml. Data for all 13 patients is shown in S1 Fig.

Fig 3. Taxonomic distribution of WGA-SS non-human reads shown as raw counts (A) and proportions (B).

Labels for patients and control samples are as in Fig 2. Data for all 13 patients is shown in S2 Fig.