Whole Genome Sequencing (WGS) **Review patient criteria

Whole genome sequencing of Gram-positive organisms: VRE, MRSA, C. difficile.

Pure culture

Isolate provided on appropriate culture medium for Gram-positive 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.

Please contact us (nml.arni-rain.lnm@phac-aspc.gc.ca or 204-789-5000) for this request so that we can triage the workload.* As part of the triage, please provide answers to the following questions when requesting outbreak support:

Q1- Is this a current outbreak or a long term investigation of cases? (Reasonabletime line for outbreak cases to be reviewed by site with epidemiological-based evidence)

Q2- What is the rationale for the genomic analysis request, what scientific question/hypothesis does the health unit wish to answer?

Q3- How will the WGS report support you?

a)How will this impact outbreak management?

b)Will this lead to change in future outbreak management procedure or policy?

c)Will this report be shared with external clients?

Q4- Is this expected to garner media attention?

*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 previous isolates requested to be included in reports. If you check the urgent box on our requisition, we will follow up. WGS turnaround times can vary based on multiple factors so it is important for us to know the urgency.

*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 surveillance 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 type, date of isolation or source of case (ex. clinical sample or environmental) and should be included in the requisition.

Please consult the lab prior to requesting a test at nml.arni-rain.lnm@phac-aspc.gc.ca.

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 (SNV) analysis

AMR detection

MLST

cgMLST

21 Calendar days. Note: Turnaround times may vary based on a case by case basis.

In House Methods.
1. Petkau A, Mabon P, Siefffert C et al. SNVphyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom 2017;3:e000116.
2. Bharat A, Petkau A, Avery BP, et al. 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
3. Alcock BP, Huynh W, Chalil R, et al. 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.