Whole Genome Sequencing (WGS)
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Reference Details
Whole genome sequencing of Gram Negative organisms.
- Pneumonia
- Bacteraemia
- Meningitis
- 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.
N/A
Completed Antimicrobial Resistance and Nosocomial Infections Requisition.
Please consult lab prior to requesting test. Gram negative organisms may include but are not limited to most Enterobacterales, Acinetobacter sp., and Pseudomonas sp.
Whole Genome Single Nucleotide Variant analysis
AMR detection (where applicable)
Novel resistance mechanisms (where applicable)
Please contact us prior to isolate submission using the information below. Detailed information on your outbreak or surveillance needs and interpretation guidelines are required.
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.