Methicillin-Resistant Staphylococcus aureus (MRSA) – Whole Genome Sequencing

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Background
This page provides information for whole genome sequencing (WGS) of Methicillin-Resistant Staphylococcus aureus to assist in outbreak/cluster investigations. PHO-approved MRSA WGS requests are referred out to the National Microbiology Lab (NML). For information regarding other testing options at PHO, refer to the following PHO webpage:

Updates

Approval from a PHO Microbiologist is required prior to submitting isolates for MRSA WGS to PHO.
MRSA typing is currently performed using whole genome sequencing WGS at the National Microbiology Laboratory (NML). PHO forwards approved isolates to NML for testing.
MRSA WGS is conducted for outbreak or cluster investigations only and is NOT for routine surveillance.

* Copie d'impression non contrôlée. Valide uniquement le jour de l'impression : 28 mai 2026.

Testing Indications

MRSA WGS is performed only upon request solely to support outbreak/cluster investigations. All requests must receive approval from a PHO Microbiologist. As part of the intake and approval process, submitters must provide relevant clinical and epidemiologic information to support assessment of the request.

Prior to submitting MRSA isolates for WGS in relation to an outbreak/cluster investigation, contact PHO Laboratory Customer Service at 416-235-6556 or 1-877-604-4567 to initiate the intake process and request approval.

Acceptance/Rejection Criteria

Pure, viable cultures AND
Identified as MRSA by standard laboratory methods AND
Suspected as being associated with an outbreak/cluster investigation, and has been assigned an outbreak or investigation number*

*Note: At least 2 unique patient isolates must be submitted as part of the typing request. Only 1 isolate per patient per outbreak/cluster will be accepted.

Any of the following will result in test rejection:

Primary specimen* (e.g. skin swab, blood, CSF)
Mixed or non-viable cultured isolate
Mislabelled or unlabelled cultured isolate
Cultured isolates for a cluster/outbreak investigation analysis without an associated outbreak or investigation number on the requisition

*Note: Primary specimens should be initially processed for bacterial culture at a community laboratory or local hospital laboratory. These will not be accepted at PHO.

Specimen Collection and Handling

Specimen Requirements

Test Requested

Required Requisition(s)

Specimen Type

Minimum Volume

Collection Kit

MRSA WGS

Reference Bacteriology Requisition

Pure bacterial culture MRSA on appropriate agar.

N/A

Solid blood agar medium (or any non-selective solid agar that supports organism growth)

Semi-solid Amies charcoal transport medium swab

Submission and Collection Notes

Label the culture container(s) with the patient’s first and last name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number. Failure to provide this information may result in rejection or testing delay.

Please be sure to complete all fields on the Reference Bacteriology Requisition including:

Test requested
Isolate information (including gram stain, catalase, oxidase)
Isolate identification
Date of primary specimen collection
Primary specimen source (mandatory)
If the primary specimen source is blood: number of consecutive blood cultures positive for the submitted isolate

Include on the requisition, the outbreak or investigation number and index case (if known).

Limitations

MRSA WGS is only performed upon request and only for outbreak/cluster investigations. At present, typing is not performed for surveillance purposes.

If a cultured isolate is submitted in a semi-solid Amies charcoal transport medium swab as opposed to a solid agar plate, the turnaround time (TAT) may be increased by a minimum of 24 hours.

Storage and Transport

Cultured isolates must be stored at 2-8°C if they cannot be shipped to PHO on the same day that the incubation is completed. Refrigerated (2-8°C) cultured isolates must be shipped to PHO on ice packs within 3 days. All cultured isolates must be shipped in accordance with the Transportation of Dangerous Good Act.

Special Instructions

It is preferred if all isolates suspected of being involved in the cluster/outbreak investigation are submitted at the same time, unless otherwise communicated and/or agreed to by the PHO Microbiologist at the time of the initial request.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Approved MRSA WGS requests are referred to the National Microbiology Laboratory (Winnipeg).

Turn-around time is 21 calendar days from receipt by National Microbiology Laboratory (NML). Turn-around times may vary by case and complexity of the outbreak/cluster investigation.

Test Methods

Whole genome single nucleotide variant (SNV) analysis is performed to determine relatedness.

Outbreak/cluster analysis is performed using WGS and isolate comparison occurs using single nucleotide variant (SNV) analyses of the sequences obtained. WGS and SNV analysis provides the highest resolution and predictive value to assign genetic relatedness compared to other phylogenetic analysis methods such as Pulse Field Gel Electrophoresis (PFGE). PFGE may infer high similarity between isolates but may overcall relatedness due to the limited number of sequence types evaluated.

Interpretation

MRSA WGS genomic analysis will be provided in an aggregated report to the requestor. Results should be used in conjunction with epidemiological data to support cluster investigation and/or management (including IPAC practices).

Reporting

Reports are issued solely to the original requestor in the form of an aggregated summary for outbreak investigation. Individual patient reports are not provided.

References

Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom. 2017;3(6):e000116. doi:10.1099/mgen.0.000116. Available from: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000116
[Accessed 22 May 2026]