26138 Bacteria PCR & Sequence (BRBPS)

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).

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

Specimen Type: Fresh tissue or biopsy

1. Collect fresh tissue specimen.

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

3. Freeze specimen.

Specimen Type:  Fluid

1.  Collect fresh fluid specimen.

2. Freeze specimen. 

Specimen type:  Section of FFPE tissue block

Perform microtomy and prepare five separate 10-micron sections.  Each section (scroll) must be placed in a separate sterile container for submission.

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).

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.

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).

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."