16S rRNA Sequencing from Clinical Material<<Return to Laboratory
Partial 16S rRNA gene PCR and sequencing from clinical material obtained from normally sterile sites.
Clinical material obtained from normally sterile body sites. This includes cerebrospinal fluid (CSF), aspirates, biopsies, and tissue. Paraffin blocks, tissue scrolls, serum, plasma, and blood culture media will not be accepted for testing. Whole blood will be accepted upon special request only. At least 0.5ml of fluid samples is required for testing, and it is preferable if all samples are supplied frozen in screw-capped tubes made of freeze-thaw and shatter resistant plastic. If uncertain about a specimen type, please contact the lab by phone or email.
Please follow standard aseptic sampling methods for collecting specimens and ensure any clinical material are in appropriate storage medium.
No further processing at the sender lab is required once specimens are collected according to the above instructions. It is preferable that all specimens be frozen after collection. If that’s not possible, then store it at refrigeration temperature (2-8ºC). Ensure samples 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.
Clinical illness with symptoms suggestive of bacterial infection or unculturable agents.
Completed Special Bacteriology requisition form detailing all patient information and relevant clinical information. If possible, attach lab results that have already been done at local or provincial laboratories.
If a test performed by the submitting lab produced a positive result for any test, it is also helpful to indicate this in the documentation including what type of test was performed. Also, if bacteria were observed in a Gram stain, please indicate this in the documentation as well.
PCR for the partial 16S rRNA gene is performed using the universal primers for the first 500 base pairs of the gene. The PCR product is sequenced and results are compared against publically-available databases (GenBank). Please note that detection of the 16S rRNA is dependent upon organisms being present in the specimen collected at detectable concentrations. Therefore, a non-detectable PCR result does not exclude the possibility of the target organism being present in the sample.
10 calendar days. Please note that during times when larger numbers of samples are received or if tests must be repeated, the turnaround time may be longer..
- Kolbert CP, Rys PN, Hopkins M, Lynch DT, Germer JJ, O’Sullivan CE, et al. 16S ribosomal DNA sequence analysis for identification of bacteria in a clinical microbiology laboratory. In: Persing DH, Tenover FD, Versalovic J, Tang Y-W, Unger ER, Relman DA, White TJ, eds. Molecular microbiology: diagnostic principles and practice. Washington, DC: ASM Press 2004. pg 361–77.
- Clinical and Laboratory Standards Institute. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing. 2018. MM18-Ed2, Volume 38, Number 15.