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HelpTest Code BRBPS Broad Range Bacterial PCR and Sequencing, Varies
Secondary ID
65058Useful For
Detecting and identifying bacteria (including mycobacteria) from normally sterile sources, including synovial fluid; body fluids such as pleural, peritoneal, and pericardial fluids, cerebrospinal fluid; and both fresh and formalin-fixed paraffin-embedded tissues
This test is not recommended as a test of cure because nucleic acids may persist for long periods of time after successful treatment.
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| ISBA | Bacterial Ident by Sequencing | No, (Bill Only) | No |
| ISNGS | Ident by Next Generation Sequencing | No, (Bill Only) | No |
| SPID2 | Specimen Identification by PCR | No, (Bill Only) | No |
| CSFME | Meningitis Encephalitis Panel, PCR | Yes | No |
Testing Algorithm
If polymerase chain reaction (PCR) testing is negative, no sequencing is performed, and the test is resulted as negative.
If PCR testing is positive, sequencing is performed. Strong positive results are first submitted to Sanger sequencing, which can yield results in as few as 4 days. Weak positive results, or Sanger sequencing results that are mixed, are submitted to next-generation sequencing (ie, targeted metagenomics testing).
The following algorithms are available:
-Infective Endocarditis: Diagnostic Testing for Identification of Microbiological Etiology
Method Name
Polymerase Chain Reaction (PCR) followed by Sequencing
Reporting Name
Broad Range Bacteria PCR+SequencingSpecimen Type
VariesNecessary Information
Specimen source is required.
Specimen Required
Fresh tissue is preferred over formalin-fixed, paraffin-embedded tissue.
Submit only 1 of the following specimens:
Preferred Specimen Type:
Specimen Type: Fresh tissue or biopsy
Sources: Normally sterile tissue such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung, prostate
Container/Tube: Sterile container
Specimen Volume: Entire collection or 5 mm(3)-approximately the size of a pencil eraser
Collection Instructions:
1. Collect fresh tissue specimen.
2. Submit tissue only, do not add fluid to tissue.
3. Freeze specimen.
Specimen Stability Information: Frozen <21 days (preferred)/Refrigerated <21 days
Alternate Specimen Type:
Preferred: Paraffin-embedded tissue block:
Supplies: Tissue Block Container (T553)
Specimen Type: Formalin-fixed, paraffin-embedded (FFPE) tissue block
Sources: Normally sterile or deep tissues such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung, prostate
Container/Tube: Tissue block
Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block to be cut and returned.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Acceptable: Paraffin-embedded tissue block:
Specimen Type: Section (scrolls) of FFPE tissue block
Sources: Normally sterile or deep tissues such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung, prostate
Container/Tube: Sterile container for each individual cut section (scroll)
Collection Instructions: Perform microtomy and prepare five separate 10-micron sections. Each section (scroll) must be placed in a separate sterile container for submission.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Specimen Type: Fluid
Sources: Normally sterile body fluids such as cerebrospinal, vitreous humor, pleural, abdominal, peritoneal, ascites, pericardial, pelvic, prostatic
Container/Tube: Screw-capped, sterile container
Specimen Volume: 1 mL
Collection Instructions:
1. Collect fresh fluid specimen.
2. Freeze specimen.
Specimen Stability Information: Frozen <21 days(preferred)/Refrigerated <21 days
Specimen Type: Synovial fluid
Container/Tube:
Preferred: Red top or sterile container
Acceptable: Lavender top (EDTA), pink top (EDTA), royal blue top (EDTA), or sterile vial containing EDTA-derived aliquot
Specimen Volume: 1 mL
Collection Instructions: Send specimen in original tube (preferred).
Specimen Stability Information: Frozen <21 days (preferred)/ Refrigerated <21 days
Specimen Minimum Volume
Fluid: 0.5 mL
Fresh tissue or biopsy: 5 mm(3)
Paraffin-embedded tissue block: two 10-micron sections
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Varies | ||
Reject Due To
| Specimen received in anaerobe vial Tissue received in any fluid (saline, broth, formalin, formaldehyde, acetone, etc) Wrapping (gauze, drapes, etc) Blood Culture bottles (Bactec FX and/or BacT/ALERT bottles) Bone marrow Decalcified bone Slides Skin biopsy Colon biopsy |
Reject |
Reference Values
No bacterial DNA detected
Method Description
This test utilizes specimen processing, DNA extraction, and polymerase chain reaction (PCR) of a highly variable fragment of the 16S ribosomal RNA (rRNA) gene. The variability of the targeted V1-V3 region allows for taxonomically specific reporting. If positive by PCR based on signal strength, the amplified DNA is sequenced to obtain identification of the source organism. If PCR is negative, no sequencing is performed. PCR inhibition is detected with a second PCR reaction and amplification is performed on a LightCycler. Only high-quality consensus sequence of 400 base pairs or more (usable data for both forward and reverse direction) is used for Sanger sequencing identification. If sequence data is not interpretable using Sanger sequencing, next-generation sequencing (NGS) is performed. Quality filtering is performed for NGS and only results with 100X coverage are used in analysis. Positive and negative controls are used throughout all processes to ensure assay performance. Sequence quality (specimen score) and data analysis for organism identification is accomplished with Pathogenomix RipSeq software.(Unpublished Mayo method)
Day(s) Performed
Monday through Friday
Report Available
14 to 28 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-Broad Range Bacterial PCR and Sequencing
87798-Bacterial Ident by Sequencing (if appropriate)
87798-Specimen Identification by PCR (if appropriate)
87798-Ident by Next Generation Sequencing (if appropriate)
87483-Meningitis Encephalitis Panel, PCR (if appropriate)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| BRBPS | Broad Range Bacteria PCR+Sequencing | 76575-0 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| BRBPS | Broad Range Bacteria PCR+Sequencing | 76575-0 |
Special Instructions
Forms
If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.