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HelpTest ID MSCSF Bacteria, Virus, Fungus, and Parasite Metagenomic Sequencing, Spinal Fluid
Specimen Required
Container/Tube: Sterile vial
Specimen Volume: 2 mL
Collection Instructions:
1. Masks should be worn by those collecting and processing specimens for this assay.
2. Handle all vials under sterile technique when open to the air.
3. A separate collection vial of CSF is preferred.
4. Submit specimen from collection vial 2, 3, or 4, as specimens from vial 1 are not acceptable.
5. Indicate on the label which vial is being submitted.
6. Do not centrifuge or heat inactivate.
Forms
If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.
Secondary ID
620941Useful For
Detecting and identifying pathogenic organisms including bacteria, fungi, DNA viruses, RNA viruses, and parasites in cerebrospinal fluid
This test is not recommended as a test of cure because nucleic acids may persist after successful treatment.
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| SPID2 | Specimen Identification by PCR | No, (Bill Only) | No |
Testing Algorithm
For more information see the Meningitis/Encephalitis Panel Algorithm.
Method Name
Metagenomic Next-Generation Sequencing (NGS)
Reporting Name
Metagenomic Sequencing, CSFSpecimen Type
CSFSpecimen Minimum Volume
0.5 mL
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| CSF | Frozen (preferred) | 21 days |
| Refrigerated | 7 days |
Clinical Information
The target population is patients with suspected, but undiagnosed, central nervous system infection. Infection of the central nervous system is a potentially life-threating condition that requires rapid diagnosis and clinical treatment. Infections of the central nervous system have broad pathogen etiology, including bacteria, fungi, viruses, and parasites. The breadth of causative agents challenges diagnostic test ordering and pathogen identification. Current clinical diagnostic methods, such as culture and specific-PCR assays, have limitations in the ability to detect non-viable organisms, or nucleic acids that are not targeted by specific assays, respectively. An unbiased metagenomic sequencing approach overcomes diagnostic test limitations by interrogating microbiota without bias towards any specific microorganism(s). Bioinformatic analysis of the resultant large sequencing dataset enables identification of a diversity of pathogens in this assay. The test can identify multiple pathogens in a single specimen if present.
Reference Values
Negative.
No pathogenic DNA virus detected.
No pathogenic RNA virus detected.
No pathogenic parasite detected.
No pathogenic bacterium detected.
No pathogenic fungus detected.
Cautions
This test does not detect prions. False-positive results are possible if specimens are contaminated with microbial nucleic acids from environmental contamination, patient microbiota (eg, from the skin) or microbiota of those collecting or processing the specimen.
High levels of human nucleic acids in specimens can decrease test sensitivity for microorganism detection and result in sequencing competition interpreted as inhibition.
Not all infecting central nervous system pathogens are detectable in cerebrospinal fluid (CSF) by this test.
Results are intended to be used in conjunction with clinical findings. This test is only validated for CSF collected via lumbar puncture.
Epstein Barr virus detection:
Clinical significance of Epstein Barr virus (EBV) detection in CSF is uncertain and may suggest latent infection of white blood cells, inflammatory reactivation, post-transplant lymphoproliferative disorder, or neurologic disease.
Cytomegalovirus detection:
Clinical significance of cytomegalovirus (CMV) detection in CSF is uncertain and may suggest latent infection of white blood cells, inflammatory reactivation, or neurologic disease.
Human Herpes virus 6 detection:
Clinical significance of human herpes virus 6 (HHV-6) detection in CSF is uncertain and may suggest latent infection of white blood cells, inflammatory reactivation, chromosomally integrated HHV-6, or neurologic disease.
HIV-1 detection:
HIV-1 can be detected in CSF of HIV-positive individuals; clinical significance is uncertain.
Day(s) Performed
Monday through Friday
Report Available
7 to 14 daysPerforming Laboratory
Mayo Clinic Laboratories in Rochester
Test Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
87801 Metagenomic Sequencing, CSF
87798 Specimen Identification by PCR (if appropriate)