Test Catalog

Test Id : MSCSF

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Bacteria, Virus, Fungus, and Parasite Metagenomic Sequencing, Spinal Fluid

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Overview

Test Catalog

Useful For
Suggests clinical disorders or settings where the test may be helpful

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.

Highlights

This test detects and identifies bacteria, DNA and RNA viruses, fungi, and parasites in cerebrospinal fluid using next generation sequencing.

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial tests.

Test Id Reporting Name Available Separately Always Performed
SPID2 Specimen Identification by PCR No, (Bill Only) No

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For more information see the Meningitis/Encephalitis Panel Algorithm.

Method Name
A short description of the method used to perform the test

Metagenomic Next-Generation Sequencing (NGS)

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

No

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Metagenomic Sequencing, CSF

Aliases
Lists additional common names for a test, as an aid in searching

Sequencing

NGS

Metagenomic

Bacterial sequencing

Next Gen Sequencing Test

Next Generation Sequencing

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For more information see the Meningitis/Encephalitis Panel Algorithm.

Specimen Type
Describes the specimen type validated for testing

CSF

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
MSCSF Which CSF Collection Vial Number Sent (Required, Vial #1 is not acceptable)

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

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.

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

0.5 mL

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Gross hemolysis Reject
Shunt fluid Reject
Heat-inactivated specimen Reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
CSF Frozen (preferred) 21 days
Refrigerated 7 days

Useful For
Suggests clinical disorders or settings where the test may be helpful

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.

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

For more information see the Meningitis/Encephalitis Panel Algorithm.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Negative.

No pathogenic DNA virus detected.

No pathogenic RNA virus detected.

No pathogenic parasite detected.

No pathogenic bacterium detected.

No pathogenic fungus detected.

Interpretation
Provides information to assist in interpretation of the test results

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.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

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.

Supportive Data

Fifty-six cerebrospinal fluid (CSF) specimens positive for a microorganism using a specific polymerase chain reaction (PCR), culture, serology, and/or multiplex PCR were tested. In addition, 30 CSF samples negative by multiplex PCR testing were evaluated. Overall sensitivity of the assay was 86%, and specificity 100% compared to predicate testing.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

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

Method Description
Describes how the test is performed and provides a method-specific reference

Cerebrospinal fluid is collected in a sterile container and the test portion aliquoted and bead beat. Specimens are separated into equal volume RNA and DNA pools following total nucleic acid isolation and spiked with internal controls. The RNA pool is treated before undergoing reverse transcription to convert total RNA into complementary DNA. RNA and DNA are then prepared for sequencing through size-selection, adapter addition, and addition of unique dual indices. Sequencing is performed on an Illumina NextSeq 1000. Run controls consist of two negative extraction controls, a difficult to lyse DNA positive extraction control, an RNA positive extraction control, and internal DNA and RNA phage inhibition controls for each sample.(Unpublished Mayo method)

 

Bioinformatic analysis uses a cloud-based solution for data analysis. This software provides pathogen identification from complex specimen types. The pipeline includes sequencing QC, human sequence deletion, and organism sequence alignment. The website includes a graphical user interface, cloud-based data upload and analyses, and alignment of generated sequencing data to National Center for Biotechnology Information’s pathogen reference database.

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday through Friday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

7 to 14 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

14 days

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their account representative. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

87801 Metagenomic Sequencing, CSF

87798 Specimen Identification by PCR (if appropriate)

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
MSCSF Metagenomic Sequencing, CSF 103566-6
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
MSCSF Metagenomic Sequencing, CSF 103566-6

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | PHP Pdf | CMS Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports