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Test ID: BRBPS Broad Range Bacterial PCR and Sequencing, Varies

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; 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 in Special Instructions:

-Infective Endocarditis: Diagnostic Testing for Identification of Microbiological Etiology

-Meningitis/Encephalitis Panel Algorithm

Method Name

16S Ribosomal RNA Gene Polymerase Chain Reaction (PCR) followed by Sequencing

Reporting Name

Broad Range Bacteria PCR+Sequencing

Specimen Type

Varies

Specimen Required


Necessary 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

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 <14 days (preferred)/Refrigerated <14 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

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

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

Container/Tube: Screw-capped, sterile container

Specimen Volume: 1 mL

Collection Instructions:

1. Collect fresh fluid specimen.

2. Freeze specimen.

Specimen Stability Information: Frozen <14 days(preferred)/Refrigerated <14 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 <14 days (preferred)/ Refrigerated <14 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

Clinical 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 Values

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."

Clinical Reference

1. Oyvind K, Simmon K, Karaca D, Langeland N, Wiker HG: Dual priming oligonucleotides for broad-range amplification of the bacterial 16S rRNA gene directly from human clinical specimens. J Clin Microbiol. 2012;50(4):1289-1294. doi: 10.1128/JCM.06269-11

2. Gomez E, Cazanave C, Cunningham SA, et al: Prosthetic joint infection diagnosis using broad-range PCR of biofilms dislodged from knee and hip arthroplasty surfaces using sonication. J Clin Microbiol. 2012;50:3501-3508

3. Virk A, Pritt B, Patel R, et al: Mycobacterium lepromatosis Lepromatous leprosy in US citizen who traveled to disease-endemic areas. Emerg Infect Dis. 2017 Nov; 23(11):1864-1866. doi: 10.3201/eid2311.171104

4. Liesman RM, Pritt BS, Maleszewski JJ, Patel R: Laboratory diagnosis of infective endocarditis. J Clin Microbiol. 2017 Sep;55(9):2599-2608. doi: 10.1128/JCM.00635-17

5. Ramakrishna JM, Libertin CR, Yang JN, Diaz MA, Nengue AL, Patel R: 16S rRNA Gene PCR/sequencing of cerebrospinal fluid in the diagnosis of post-operative meningitis. Access Microbiology. 2020 Feb 3;2. doi: 10.1099/acmi.0.000100

Day(s) Performed

Monday through Friday

Report Available

14 to 28 days

Test 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 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

Forms

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