Streptococcus pneumoniae – Real-time PCR
Background
This page provides molecular testing information for Streptococcus pneumoniae at Public Health Ontario (PHO).
Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.
Specimen Requirements
| Test Requested | Required Requisition(s) | Specimen Type | Minimum Volume | Collection Kit |
Streptococcus pneumoniae PCR |
CSF |
300 μl |
||
Streptococcus pneumoniae PCR |
Respiratory Tissue sample |
1-2 grams |
||
Streptococcus pneumoniae PCR |
Sterlie site specimens (e.g., pleural fluid) PHO’s approval) |
300 μl |
Submission and Collection Notes
Label the specimen container with the patient’s full name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. Failure to provide this information may result in rejection or testing delay.
Storage and Transport
Place specimen in biohazard bag and seal. Specimens should be stored at 2-8°C following collection and shipped to PHO on ice packs.
If transport of specimen to testing laboratory will be delayed more than 72 hours, specimens should be frozen and shipped on dry ice.
Test Frequency and Turnaround Time (TAT)
The Streptococcus pneumoniae – Real-time PCR test is performed as needed Monday to Friday.
Turnaround time is up to 3 business days from receipt at PHO
STAT and Critical Specimens Testing
Testing on weekends and/or holidays may be performed under special circumstances. Contact PHO Laboratory’s Customer Service Centre at 416-235-6556/1-877-604-4567 or After-Hours Emergency Duty Officer at 416-605-3113 for consultation.
Specific Streptococcus pneumoniae nucleic acids are tested for from direct clinical specimens using a Real-Time PCR multiplex assay.
The sensitivity of the Real-time PCR test is higher than conventional culture.
Testing for presence of inhibitory substances within the PCR reaction are not done.
Targets:
ply gene: Pneumolysin, encoded by the pneumolysin ply gene is one of the virulence factors expressed by all serotypes of S. pneumoniae.
lytA gene: Autolysin, encoded by the lytA gene, is required for S. pneumoniae pathogenesis and is a well-characterized virulence marker.
kdgk gene: 2-keto-3-deoxygluconate kinase-encoding (kdgk) gene is used to clarify discrepancies between the ply and lytA genes.
Interpretation
| Result | Interpretation | Comments |
|---|---|---|
| All targets Not Detected | Streptococcus pneumoniae NOT detected by PCR | Negative results do not exclude the presence of this bacteria. |
| All targets Detected | Streptococcus pneumoniae Detected by PCR | |
| One or more targets Indeterminate | Streptococcus pneumoniae Indeterminate by PCR | An indeterminate result may represent a low level of genetic material in this specimen. |
| Pneumolysin gene target Detected, other targets Not Detected | Streptococcus pneumoniae Inconclusive by PCR | Pneumolysin gene can be detected in several species within viridans group streptoccoci, including Streptococcus penumoniae. |
| Invalid | Streptococcus pneumoniae Invalid by PCR | Test results are uninterpretable due to failed amplification of the extraction control. Unable to report PCR result |
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