Streptococcus pyogenes (Group A Streptococcal Disease or GAS) – Typing

Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.

Background
This page provides information on emm typing of invasive or outbreak related Group A Streptococcus (Streptococcus pyogenes; GAS) at Public Health Ontario (PHO).

This page is limited to supplementary typing information of confirmed GAS cases to assist with surveillance and cluster investigations. For information regarding routine bacterial identification and/or confirmation of cultured Streptococcus pyogenes isolates, refer instead to Bacterial cultures- Aerobic- Reference ID/Confirmation.

Updates

emm typing is now performed at Public Health Ontario’s laboratory-Toronto
Turnaround time for emm typing is now 15 business days or 21 calendar days

*Uncontrolled print copy. Valid only on day of print: 21 Nov 2024.

Testing Indications

Routine M protein gene (emm) typing is recommended for all cases of invasive GAS (iGAS) in Ontario in order to assist with disease surveillance. Cases of iGAS include:

S. pyogenes isolated from a sterile site (e.g. blood, cerebrospinal fluid, joint fluid, pleural fluid, pericardial fluid), or
S. pyogenes isolated from a non-sterile site (e.g. skin) with evidence of disease severity (e.g. necrotizing fasciitis, streptococcal toxic shock syndrome, meningitis).

emm typing may also be done for cluster investigations (this may include invasive and non-invasive GAS):

Both emm typing and detailed cluster phylogenetic analysis are available upon request for cases of GAS who are part of an outbreak investigation by a health unit if meeting the following criteria:
- Outbreak number assigned by the health unit, and
- Index case’s cultured isolate is available, and
- Isolates from other cases that are part of the outbreak are available. Note: if these were not previously submitted to PHO, the health unit should attempt to locate them at the original testing laboratory and arrange for the holding laboratory to transfer the cultured isolates to PHO with the outbreak investigation number included. And
- Discussion with PHO’s Incident and Outbreak Response Team and/or PHO Microbiologist for approval

Both emm typing and detailed cluster phylogenetic analysis are available upon request for cases of GAS who are part of a cluster (non-outbreak) investigation if meeting the following criteria:
- Temporal increase in iGAS cases in a defined geographic area or suspicion for a GAS cluster in an institution that does not meet the provincial outbreak case definitions, and
- Analysis must be pre-approved by the PHO microbiologist (contact PHO’s Laboratory Customer Service), and
- Investigation number assigned by PHO.

Acceptance/Rejection Criteria

Any of the following conditions will result in test rejection:

Primary specimen* (e.g. skin swab, blood, CSF)
Mixed or non-viable cultured isolate
Mislabelled or un-labelled cultured isolate
Cultured isolates from a non-sterile site for which the disease severity is not clearly stated on the requisition
Cultured isolates from a non-sterile site for cluster/outbreak investigation analysis without an associated outbreak or investigation number on the requisition

*Note: Only pure and viable cultured isolates are accepted for testing. Primary specimens are not processed at PHO and will be rejected. Primary specimens should be initially processed at a community laboratory or local hospital laboratory.

Specimen Collection and Handling

Specimen Requirements

Test Requested

Required Requisition(s)

Specimen Type

Minimum Volume

Collection Kit

Streptococcus pyogenes, group A strep, or GAS typing or cluster analysis

Reference Bacteriology Requisition

Pure viable cultured isolate of Streptococcus pyogenes

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
Clinical/epidemiology information
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
If applicable: outbreak or investigation number

Only submit one isolate per patient (NOT per specimen source). If the organism was isolated from multiple specimen sources, the order of preference of specimen submission is CSF first, otherwise blood, otherwise any other sterile site.

PHO does not provide swabs for primary GAS outbreak screening nor tests for GAS from primary specimens.

If the patient is part of a cluster/outbreak investigation, contact PHO’s Laboratory Customer Service at 416-235-6556/1-877-604-4567 prior to sample submission.

Limitations

If a Streptococcus pyogenes 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 to the Transportation of Dangerous Good Act.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Streptococcus pyogenes emm typingis performed at PHO’s laboratory, Toronto location once per week for surveillance. Cluster phylogenetic analysis will require additional time and may be dependent on the size and complexity of the outbreak investigation.

Turnaround time for emm gene typing is up to 15 business days or 21 calendar days from receipt at PHO’s laboratory, Toronto location.

STAT and Critical Samples Testing

Cluster or outbreak investigation testing may be prioritized upon request. Contact PHO’s Laboratory Customer Service at 416-235-6556/1-877-604-4567 prior to sample submission.

Test Methods

emm gene typing: Typing is performed using a whole genome sequencing (WGS) method.1 This method of emm typing has been adopted by other reference laboratories including the National Microbiology Laboratory (NML)/Public Health Agency of Canada (PHAC).

Cluster phylogenetic analysis: Cluster analysis is performed using a WGS method combining emm typing, multilocus sequence typing (MLST), and single nucleotide polymorphism (SNP) analyses of the sequences obtained.2

Performance:

emm gene typing: WGS provides high resolution and predictive value to assign emm types. WGS also allows for the detection of novel/non-validated emm types and dual emm/emm-like pairs.

Cluster phylogenetic analysis: WGS provides the highest resolution and predictive value to assign genetic relatedness compared to other phylogenetic analysis methods such as Pulsed-field Gel Electrophoresis (PFGE). PFGE may infer high similarity between isolates but may overcall relatedness due to the limited number of sequence types evaluated.

Algorithm

All iGAS isolates: routine emm typing performed on submitted isolates (one isolate per patient).
Outbreak/cluster investigation isolates: emm typingperformed on submitted isolates meeting the testing indication above. Additional cluster phylogenetic analysis only available upon request.

Interpretation

The table below outlines the elements evaluated as part of the routine emm typing process at Public Health Ontario:

Test	Possible Results	Comment
16S rRNA gene analysis via WGS (for confirmation of organism identification)	Streptococcus pyogenes Not Streptococcus pyogenes Unable to sequence	Whole genome sequencing and analysis to predict S. pyogenes emm types is adapted from methods described in: Athey T et al. Group A Streptococcus typing information from short-read whole genome sequencing data. J Clin Microbiol. 2014;52(6):1871-6 and Kapatlai G et al. Whole genome sequencing of Group A Streptococcus: development and evaluation of an automated pipeline for emm gene typing. PeerJ. 2017;5:e3226.
emm Type via WGS	emm1	Whole genome sequencing and analysis to predict S. pyogenes emm types is adapted from methods described in: Athey T et al. Group A Streptococcus typing information from short-read whole genome sequencing data. J Clin Microbiol. 2014;52(6):1871-6 and Kapatai G et al. Whole genome sequencing of Group A Streptococcus: development and evaluation of an automated pipeline for emm gene typing. PeerJ. 2017;5:e3226.
emm Type via WGS	Other emm type, not emm 1 e.g. emm53	N/A
emm subtype via WGS	emm1.0 emm 53.0	N/A
M1UK genotype via WGS	Global M1UK Intermediate	“M1UK” refers to the hypervirulent emm1 genotype originally described by: Lynskey NN, et al. Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study. Lancet Infect Dis. 2019;19(11):1209-1218. “Intermediate” refers to an isolate with a partial M1UK genotype (number of alterations in brackets). “Global” genotype refers to all other non-M1UK genotypes of emm1.

Reporting

Results are reported to the ordering physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

Confirmed outbreaks from cluster investigations are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.

References

Kapatai G, Coelho J, Platt S, Chalker VJ. Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing. PeerJ. 2017 Apr 27;5:e3226. doi: 10.7717/peerj.3226.
Tagini F, Aubert B, Troillet N, Pillonel T, Praz G, Crisinel PA, Prod'hom G, Asner S, Greub G. Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections. Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1173-1180. doi: 10.1007/s10096-017-2905-z.