Molecular detection and serotyping by PCR
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Molecular detection and serotype determination of Streptococcus pneumoniae by PCR.
- Bacteraemia
- Pneumococcal meningitis
Swab, sputum, nasopharyngeal aspirate, urine, and CSF
Specimens may be subject to rejection if they are not the appropriate sample type, have insufficient volume, or are not accompanied by relevant patient information.
At least 1 mL of fluid, or swab samples re-suspended in appropriate transport medium required for testing. Samples are preferably supplied in screw-capped tubes made of freeze-thaw and shatter-resistant plastic. Dry swabs are not acceptable for testing; any swabs sent must be supplied in appropriate storage medium as well as storage at proper shipping temperatures prior to sending.
No further processing at the sending lab is required once specimens are collected according to the above instructions. All specimens should be stored at refrigeration temperature (2 – 8°C) or frozen after collection. Ensure that specimens are held at the appropriate temperature when shipped to the NML (e.g. frozen specimens shipped with dry ice, refrigerated specimens with cold packs).
Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.
Disease due to Streptococcus pneumoniae.
Completed Requisition for Streptococcus pneumoniae Molecular Detection and Serotyping by PCR. The information found on the requisition may also be sent in an excel file to nml.strepsti-lnm.strepits@phac-aspc.gc.ca, as well as a paper copy with the shipment.
If a test performed by the submitting lab produced a positive result, indicate this in the documentation. Duplicate samples should not be submitted without prior consent as they may not be processed.
DNA from all Streptococcus pneumoniae samples received at the NML for molecular detection and serotype testing are initially extracted using a commercially-available kit. Screening results are determined by the presence of the targets lytA (Carvalho et al. 2007), piaA (Trzcinski et al. 2013), and SP2020 (Tavares et al. 2019). Serotyping is performed using a CDC designed protocol (Pimenta et al. in 2013), which targets 37 serotypes, including the 13 serotypes of the PCV13 vaccine. A nontypeable result indicates none of the 37 serotypes targeted in the assay were present.
14 calendar days. Urgent specimens will be granted priority status, and completed as soon as possible.
- Carvalho, M.dG.S., Tondella, M.L., McCaustland, K., Weidlich, L., McGee, L., Mayer, L.W., Steigerwalt, A., Whaley, M., Facklam, R.R., Fields, B., Carlone, G., Ades, E.W., Dagan, R., Sampson, J.S. Evaluation and Improvement of Real-Time PCR Assays Targeting lytA, ply, and psaA Gene for Detection of Pneumococcal DNA. Journal of Clinical Microbiology. 2007; 45(8): 2460-2466
- Trzcinski, K., Bogaert, D., Wyllie, A., Chu, M.L.J.N., van der Ende, A., Bruin, J.P.. Van den Dobbelsteen, G., Veenhoven, R.H., Sanders, E.A.M. Superiority of Trans-Oral over Trans-Nasal Sampling in Detecting Streptococcus pneumoniae Colonization in Adults. PLOSone. 2013; 8(3): e60520
- Tavares, D.A., Handem, S., Carvalho, R.J., Paulo, A.C., de Lencastre, H., Hinds, J., Sá- Leão, R. Identification of Streptococcus pneumonia by real-time PCR assay targeting SP2020. Scientific Reports. 2019; 9: 3285
- Pimenta, F.C., Roundtree, A., Soysal, A., Bakir, M., du Plessis, M., Wolter, N., von Gottberg, A., McGee, L., de Gloria Cavalho, M., Beall, B. Sequential Triplex Real-Time PCR Assay for Detecting 21 Pneumococcal Capsular Serotypes that Account for a High Global Disease Burden. Journal of Clinical Microbiology. 2013; 51(2): 647-652