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Test ID: MSCSF Bacteria, Virus, Fungus, and Parasite Metagenomic Sequencing, Spinal Fluid


Necessary Information


The following ask-at-order entry question must be answered at the time of test ordering:

Which CSF Collection Vial Number Sent (Required, Vial 1 is not acceptable)

 

Note: Answers may include "Vial 2", " Vial 3", or " Vial 4".

Test requests for specimens from  "Vial 1" will be canceled. Test requests for submitted specimens with no response or response that does not specify the collection vial number will result in testing delays while the submitting facility is contacted to provide the information.



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.


Useful 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, CSF

Specimen Type

CSF

Specimen Minimum Volume

0.5 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
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 microorganisms. 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.

Interpretation

A positive result indicates that nucleic acid of one or more potentially pathogenic microorganisms was detected. A negative result indicates absence of detectable nucleic acids from potentially pathogenic bacteria, fungi, viruses, or parasites. A negative result does not rule the presence of a pathogen due lack of a reference sequence in the database used, the presence of microbial nucleic acids in quantities lower than the limit of detection of the assay, or inhibition from high levels of competing human nucleic acid. If testing indicates inhibition, testing will be repeated. If inhibition is again detected, the result will be reported with a comment indicating that inhibition was present.

Clinical Reference

Rodino KG, Toledano M, Norgan AP, et al. Retrospective review of clinical utility of shotgun metagenomic sequencing testing of cerebrospinal fluid from a U.S. tertiary care medical center. J Clin Microbiol. 2020;58(12):e01729-20. doi:10.1128/JCM.01729-20

Day(s) Performed

Monday through Friday

Report Available

7 to 14 days

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.

LOINC Code Information

Test ID Test Order Name Order LOINC Value
MSCSF Metagenomic Sequencing, CSF 103566-6

 

Result ID Test Result Name Result LOINC Value
MSCSF Metagenomic Sequencing, CSF 103566-6

Forms

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

CPT Code Information

0480U