Sign in →

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

Important Note

Order as "MISC"

Additional Codes

Mayo Test Code:  MSCSF


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.

7. Shunt fluid and ventricular fluid specimens are not acceptable.


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 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
CSF Frozen (preferred) 21 days
  Refrigerated  7 days

Reject Due To

Gross hemolysis Reject
Shunt fluid Reject
Ventricular fluid Reject
Heat-inactivated specimen Reject

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.

 

One organism per class of pathogen was used to establish the limits of detection, providing an estimation of the assay's capability to detect each class of pathogen. Actual detection capability may vary by specific organism based on genome size and other factors.

 

Epstein Barr virus detection:

Clinical significance of Epstein Barr virus 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 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 days

Specimen Retention Time

14 days

Performing 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.

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

1. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Microbiology Test Request (T244)

-Neurology Specialty Testing Client Test Request (T732)

2. Bacteria, Virus, Fungus, and Parasite Metagenomic Sequencing Patient Information

CPT Code Information

0480U