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26138 Broad Range Bacterial PCR and Sequencing, Varies(BRBPS)

Broad Range Bacterial PCR and Sequencing, Varies(BRBPS)
Test Code: BRBPSSO
Synonyms/Keywords
​16S rRNA gene sequencing
Bacterial sequencing
Broad range
Broad-range
16S
Broad
Mycobacteria
Mycobacterial
Ribosomal RNA
rRNA
Sequencing
Next Generation Sequencing
NGS
Test Components

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).

Useful 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 (CSF); and both fresh and formalin-fixed paraffin-embedded (FFPE) tissues

This test is not recommended as a test of cure because nucleic acids may persist for long periods of time after successful treatment.

Highlights:

This test is used for detection and identification of bacteria (including mycobacteria) in normally sterile specimens.

This test is optimal for situations in which bacteria (including mycobacteria) are visualized in the specimen but other laboratory methods have failed to yield a diagnosis.

Specimen Requirements
​​Samples must be sent to Microbiology to "hold for review and approval" before forwarding onto Mayo Clinic Laboratories, to assure that unnessary testing is not performed.​​​​​​
​ ​ ​ ​ ​
Specimen Type
 Preferred Container/Tube Acceptable Container/Tube Specimen Volume Specimen Minimum Volume
(allows for 1 repeat)		 Pediatric Minimum Volume
(no repeat)
​Submit only 1 of the following specimens:  ​ ​ ​ ​ ​
Tissue, fresh (bone, lymph node, joint, heart valve, brain, viscera, organ, lung)   ​Sterile container ​ ​5 mm (3) ​5 mm (3) ​5 mm (3)
​Tissue Block Formalin-fixed, paraffin-embedded tissue block ​ Five separate 10-micron sections Two separate 10-micron sections ​
​Normally sterile body fluids such as cerebrospinal, vitreous humor, pleural, abdominal, peritoneal, ascites, pericardial, pelvicScrew-capped sterile container​​1 mL​0.5 mL​
​Synovial fluid​Sterile container or Red Top Tube (RTT)​EDTA Lavender Top Tube (LTT), EDTA Pink Top Tube, EDTA Royal Blue Top Tube​1 mL​0.5 mL​
Collection Processing Instructions

Specimen source is required.

   Submit specimens collected using sterile technique. Fresh tissue is preferred over formalin-fixed, paraffin-embedded tissue.

Specimen Type: Fresh tissue or biopsy

   Normally sterile tissue such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung

1. Collect fresh tissue specimen.

2. Submit tissue only, do not add fluid to tissue.

3. Freeze specimen.

Specimen Type:  Fluid

   Normally sterile body fluids such as cerebrospinal, vitreous humor, pleural, abdominal, peritoneal, ascites, pericardial, pelvic

1.  Collect fresh fluid specimen.

2. Freeze specimen. 

Specimen type:  Section of FFPE tissue block

   Normally sterile or deep tissues such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung

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
Specimen Type Temperature Time
​Tissue ​Frozen (preferred) or Refrigerated ​< 14 days
​Tissue Block ​Ambient (preferred) or Refrigerated ​N/A
​Fluid ​Frozen (preferred) or Refrigerated ​< 14 days
​Synovial Fluid ​Frozen (preferred) or Refrigerated ​< 14 days
Rejection Criteria
 Tissue in formalin, formaldehyde, acetone, or any other fluid  
​Blood, bone marrow, decalcified bone, slides, skin biopsy,colon biopsy
 Specimens submitted on swabs​
Interference

This test does not detect nonbacterial organisms (eg, viruses, fungi, helminths, protozoa), but does detect mycobacteria.

False-positive results are theoretically possible if patient specimens are contaminated with bacterial nucleic acids either from the environment or from patient microbiota (eg, skin microbiota contamination).

This test is validated for normally sterile sources.

In extenuating circumstances, sequencing, especially next-generation sequencing, may be associated with an extended turnaround time, approaching or possibly exceeding the published maximum laboratory time (28 days).

Performing Laboratory Information
Performing Location Day(s) Test Performed Report Available​Methodology/Instrumentation
​Mayo Clinic Laboratories ​Monday through Friday ​14 to 28 days​16S Ribosomal RNA Gene Polymerase Chain Reaction (PCR) followed by Sequencing
Reference Lab
Mayo Clinic Laboratories
Test Information
Cultures from patients with suspected bacterial infection involving normally sterile sites may fail to provide bacterial (including mycobacterial) growth for identification due to the presence of fastidious or slow-growing bacteria or as a result of antecedent antimicrobial chemotherapy. Polymerase chain reaction amplification of a portion of the 16S ribosomal RNA (rRNA) gene followed by sequencing of the amplified product can be used to detect bacterial (including mycobacterial) nucleic acids in such situations, enabling a diagnosis. Sterile sources accepted for testing may have more than one bacterial species present or the presence of copy variants of the 16S rRNA gene within a single bacterial species, confounding Sanger sequencing analysis. Next-generation sequencing can be useful in such cases. Ideal specimens are those in which bacteria (includes mycobacteria) are visualized by microscopy. Heart valves from patients with endocarditis with positive Gram stains are, for example, especially suitable.
Reference Range Information
Performing Location Reference Range
​Mayo Clinic Laboratories ​No Bacterial DNA Detected
Interpretation
​

A positive broad-range polymerase chain reaction (PCR)/sequencing result indicates that bacterial nucleic acid of the specified organism was detected, which may be due to bacterial infection or environmental or contaminating nucleic acids in the specimen.

A negative broad-range PCR/sequencing result indicates the absence of detectable bacterial (including mycobacterial) nucleic acids in the specimen but does not rule-out false-negative results that may occur due to sampling error, sequence variability underlying the primers, the presence of bacterial nucleic acids in quantities less than the limit of detection of the assay, or inhibition of PCR. If PCR testing appears to be negative but there is evidence of PCR inhibition, testing will be repeated. If inhibition is again detected, the result will be reported as "PCR inhibition present."

Outreach CPTs
CPT Modifier
(if needed)		 Quantity Description Comments
​87801 ​ ​1 ​Broad Range Bacterial PCR and Sequencing ​
87798​ ​ ​1 ​Bacterial Identification by Sequencing ​If needed
​87798 ​ ​1 Specimen ​Identification by PCR ​If needed
​87798​​1​Ident by Next Generation Sequencing​if needed
​87483​​1​Meningitis Encephalitis Panel, PCR​If needed
Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.
Synonyms/Keywords
​16S rRNA gene sequencing
Bacterial sequencing
Broad range
Broad-range
16S
Broad
Mycobacteria
Mycobacterial
Ribosomal RNA
rRNA
Sequencing
Next Generation Sequencing
NGS
Test Components

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).

Ordering Applications
Ordering Application Description
​COM​Broad Range Bacterial PCR and Sequencing (BRBPS)
If the ordering application you are looking for is not listed, contact your local laboratory for assistance.
Specimen Requirements
​​Samples must be sent to Microbiology to "hold for review and approval" before forwarding onto Mayo Clinic Laboratories, to assure that unnessary testing is not performed.​​​​​​
​ ​ ​ ​ ​
Specimen Type
 Preferred Container/Tube Acceptable Container/Tube Specimen Volume Specimen Minimum Volume
(allows for 1 repeat)		 Pediatric Minimum Volume
(no repeat)
​Submit only 1 of the following specimens:  ​ ​ ​ ​ ​
Tissue, fresh (bone, lymph node, joint, heart valve, brain, viscera, organ, lung)   ​Sterile container ​ ​5 mm (3) ​5 mm (3) ​5 mm (3)
​Tissue Block Formalin-fixed, paraffin-embedded tissue block ​ Five separate 10-micron sections Two separate 10-micron sections ​
​Normally sterile body fluids such as cerebrospinal, vitreous humor, pleural, abdominal, peritoneal, ascites, pericardial, pelvicScrew-capped sterile container​​1 mL​0.5 mL​
​Synovial fluid​Sterile container or Red Top Tube (RTT)​EDTA Lavender Top Tube (LTT), EDTA Pink Top Tube, EDTA Royal Blue Top Tube​1 mL​0.5 mL​
Collection Processing

Specimen source is required.

   Submit specimens collected using sterile technique. Fresh tissue is preferred over formalin-fixed, paraffin-embedded tissue.

Specimen Type: Fresh tissue or biopsy

   Normally sterile tissue such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung

1. Collect fresh tissue specimen.

2. Submit tissue only, do not add fluid to tissue.

3. Freeze specimen.

Specimen Type:  Fluid

   Normally sterile body fluids such as cerebrospinal, vitreous humor, pleural, abdominal, peritoneal, ascites, pericardial, pelvic

1.  Collect fresh fluid specimen.

2. Freeze specimen. 

Specimen type:  Section of FFPE tissue block

   Normally sterile or deep tissues such as bone, lymph node, joint, heart valve, brain, viscera, organ, lung

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
Specimen Type Temperature Time
​Tissue ​Frozen (preferred) or Refrigerated ​< 14 days
​Tissue Block ​Ambient (preferred) or Refrigerated ​N/A
​Fluid ​Frozen (preferred) or Refrigerated ​< 14 days
​Synovial Fluid ​Frozen (preferred) or Refrigerated ​< 14 days
Rejection Criteria
 Tissue in formalin, formaldehyde, acetone, or any other fluid  
​Blood, bone marrow, decalcified bone, slides, skin biopsy,colon biopsy
 Specimens submitted on swabs​
Interference

This test does not detect nonbacterial organisms (eg, viruses, fungi, helminths, protozoa), but does detect mycobacteria.

False-positive results are theoretically possible if patient specimens are contaminated with bacterial nucleic acids either from the environment or from patient microbiota (eg, skin microbiota contamination).

This test is validated for normally sterile sources.

In extenuating circumstances, sequencing, especially next-generation sequencing, may be associated with an extended turnaround time, approaching or possibly exceeding the published maximum laboratory time (28 days).

Useful 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 (CSF); and both fresh and formalin-fixed paraffin-embedded (FFPE) tissues

This test is not recommended as a test of cure because nucleic acids may persist for long periods of time after successful treatment.

Highlights:

This test is used for detection and identification of bacteria (including mycobacteria) in normally sterile specimens.

This test is optimal for situations in which bacteria (including mycobacteria) are visualized in the specimen but other laboratory methods have failed to yield a diagnosis.

Test Components

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).

Reference Range Information
Performing Location Reference Range
​Mayo Clinic Laboratories ​No Bacterial DNA Detected
Interpretation
​

A positive broad-range polymerase chain reaction (PCR)/sequencing result indicates that bacterial nucleic acid of the specified organism was detected, which may be due to bacterial infection or environmental or contaminating nucleic acids in the specimen.

A negative broad-range PCR/sequencing result indicates the absence of detectable bacterial (including mycobacterial) nucleic acids in the specimen but does not rule-out false-negative results that may occur due to sampling error, sequence variability underlying the primers, the presence of bacterial nucleic acids in quantities less than the limit of detection of the assay, or inhibition of PCR. If PCR testing appears to be negative but there is evidence of PCR inhibition, testing will be repeated. If inhibition is again detected, the result will be reported as "PCR inhibition present."

For more information visit:
Performing Laboratory Information
Performing Location Day(s) Test Performed Report Available​Methodology/Instrumentation
​Mayo Clinic Laboratories ​Monday through Friday ​14 to 28 days​16S Ribosomal RNA Gene Polymerase Chain Reaction (PCR) followed by Sequencing
Reference Lab
Mayo Clinic Laboratories
For billing questions, see Contacts
Outreach CPTs
CPT Modifier
(if needed)		 Quantity Description Comments
​87801 ​ ​1 ​Broad Range Bacterial PCR and Sequencing ​
87798​ ​ ​1 ​Bacterial Identification by Sequencing ​If needed
​87798 ​ ​1 Specimen ​Identification by PCR ​If needed
​87798​​1​Ident by Next Generation Sequencing​if needed
​87483​​1​Meningitis Encephalitis Panel, PCR​If needed
Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.
For most current information refer to the Marshfield Laboratory online reference manual.