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Updated: Jul 4, 2026

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens
Published on: April 17, 2026
Positive cerebrospinal fluid cultures after normal cell counts are contaminants
Megan M Boysen1, Jeffrey L Henderson, Scott E Rudkin
1Department of Emergency Medicine, University of California, Irvine Medical Center, Orange, California 92868, USA.
Abstract:
Previous literature on meningitis reports that cerebrospinal fluid (CSF) culture contaminants are threefold more common than true pathogens. Clinical follow-up of patients with CSF contaminants is costly, time-consuming, and potentially unnecessary. In this study, we hypothesized that, in immunocompetent Emergency Department (ED) patients with normal CSF cell counts and negative Gram stains, all positive bacterial cultures are contaminants and patient follow-up is unnecessary. We retrospectively reviewed 191 ED charts of patients with positive CSF cultures over 5 years. We abstracted lumbar puncture results, disposition, and follow-up activities, and determined monetary charges. There were 137 patients (72%) who met inclusion criteria with CSF white blood cells < or = 7 microL, negative Gram stain, and immunocompetence. Ninety-eight were discharged from the ED and 39 were admitted to the hospital for reasons other than meningitis. All 137 positive cultures were found to be contaminants, with coagulase-negative staphylococci found most commonly. Follow-up activities included telephone calls (49%), repeat ED visits (13%), repeat lumbar punctures (9%), unnecessary antibiotic treatment (6%), and hospitalizations (6%), generating $55,000 in charges. Follow-up may be unnecessary in ED patients with positive bacterial CSF cultures who were discharged from the ED, if their initial lumbar punctures were normal.
Insights
In Emergency Department (ED) patients with normal cerebrospinal fluid (CSF) cell counts and negative Gram stains, positive bacterial cultures are typically contaminants. This suggests that routine follow-up for these patients may be unnecessary, saving costs and resources.
Area of Science:
- Clinical Microbiology
- Infectious Diseases
- Emergency Medicine
Background:
- Cerebrospinal fluid (CSF) culture contaminants are common in meningitis diagnostics.
- Clinical follow-up for contaminants is costly and time-consuming.
- Identifying contaminants avoids unnecessary patient management.
Purpose of the Study:
- To determine if positive bacterial CSF cultures in immunocompetent ED patients with normal initial findings are contaminants.
- To assess the necessity of clinical follow-up for such patients.
Main Methods:
- Retrospective review of 191 ED patient charts with positive CSF cultures over 5 years.
- Inclusion criteria: immunocompetent, normal CSF cell count (< or = 7 microL), negative Gram stain.
- Abstracted data included lumbar puncture results, disposition, follow-up activities, and charges.
Main Results:
- 137 patients met inclusion criteria (72%).
- All 137 positive CSF cultures were contaminants, most commonly coagulase-negative staphylococci.
- Unnecessary follow-up activities (calls, repeat visits, antibiotics, hospitalizations) incurred $55,000 in charges.
Conclusions:
- Positive bacterial CSF cultures in immunocompetent ED patients with normal initial lumbar punctures are likely contaminants.
- Routine clinical follow-up for these patients is often unnecessary.
- Avoiding unnecessary follow-up can reduce healthcare costs and patient burden.
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