Whole Genome Sequencing (WGS) **Review patient criteria
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Reference Details
Whole genome sequencing of Gram Negative organisms.
- Pneumonia
- Meningitis
- Bacteraemia
- Urinary tract infection
- Wound
Pure culture
Isolate provided on appropriate culture medium for Gram negative organisms.
Send cultures as growth on culture medium or in transport medium. Culture vessel should be leak-proof or sealed appropriately.
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.
-**For now we are asking for sites to contact us (nml.arni-rain.lnm@phac-aspc.gc.ca or 204-789-5000) for this request so that we can triage the workload.
-**It is also important that sites let us know if isolates submitted are part of an ongoing outbreak and to provide NML numbers, if applicable, (ex N24-0001) for those isolates requested to be included in reports. Our requisitions have a box for urgency which we will follow up with sites if checked, WGS turn around times can very based on multiple factors so it is import for us to know how urgent samples are.
-**We only accept WGS requests for outbreak investigations and the detection of novel or emerging AMR. At this time, we do not have the capacity to provide WGS-based passive surveillance through the ARNI Reference Services Unit. The ARNI AMR & Hospital Infections Unit is part of several surveillance networks, if more information is requested please contact nml.arni-rain.lnm@phac-aspc.gc.ca).
Completed Antimicrobial Resistance and Nosocomial Infections Requisition, clearly indicating reason for WGS (outbreak or novel/emerging AMR). Sites are encouraged to provide AST or phenotypic data for any novel/emerging AMR cases. Detailed information on your outbreak can be helpful for the interpretation of data. Such information may include, specimen date of isolation or source of case (ex. clinical sample or environmental) and should be included in the requisition.
May include phylogenetics and AMR detection. The following tests can be conducted based on consultation of the submitting lab and NML where testing is deemed appropriate:
Whole Genome Single Nucleotide Variant analysis
AMR detection
Novel resistance mechanisms
MLST
cgMLST
Plasmid detection
21 Calendar days. Note: Turnaround times may vary based on a case by case basis.
- Petkau A, Mabon P, Siefffert C et al. SNVphyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom 2017;3:e000116.
- Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Domselaar GV, Reid-Smith RJ, Mulvey MR. Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr. Microorganisms. 2022; 10(2):292. https://doi.org/10.3390/microorganisms10020292
- Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy MC, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray KL, Hoad GR, Jia B, Bhando T, Carfrae LA, Farha MA, French S, Gordzevich R, Rachwalski K, Tu MM, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko RG, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023 Jan 6;51(D1):D690-D699. doi: 10.1093/nar/gkac920. PMID: 36263822; PMCID: PMC9825576.