Key points
- Streptococcus pyogenes are classified into more than 275 emm types.
- Typing is based on sequence analysis of part of the M protein gene (emm).
- emm encodes the M virulence protein found on the cell surface.
- This hypervariable sequence is downstream of forward primer sequence, allowing for direct sequencing.
Overview
CDC uses a de novo assembly approach for whole-genome sequence-based emm subtype determination. This helps to avoid confounding of the 180-base M protein gene segment by the similar emm-like mrp and enn sequences.
Related resource: emm and emm-like genes
emm clusters
emm types are predictive of related emm type clusters that are indicative of M proteins that share important functional properties1.
See the distribution of emm-types by emm-cluster.
emm designations
Guidelines for assigning new types and subtypes
CDC maintains several databases related to unique S. pyogenes sequences:
CDC requests submissions
Assigning new types and subtypes
CDC assigns new emm types or subtypes when a defined emm segment differs from known types based on the following criteria:
- Subtype: Any change to 180-base sequence
- Type: <92% identity within first 30 codons of mature M protein
- Open reading frame interruptions: >7 codons lowers the identity score
New subtypes
New subtypes are assigned for any change relative to the 180-base sequences previously defined as emm subtypes in CDC's database.
The 180 bp subtype-encoding sequence consists of both of the following:
- The signal sequence (10 codons)
- The mature M protein (50 codons)
New types
New types are assigned for 7 or more codon changes within the first 30 codons encoding the mature M protein. A new emm type is dictated by less than 92% identity to a reference emm type.
Open reading frame interruptions
If more than 7 codons interrupt the reference open reading frame, lower the overall percentage identity score. Subtract 0.5% for each out-of-frame codon.
Protocols by typing method
CDC's Streptococcus Laboratory recommends the following protocols for S. pyogenes emm typing.
Conventional polymerase chain reaction and sequencing
Laboratories can use conventional polymerase chain reaction (PCR) and sequencing methods for emm typing.
Tip: Use the sequence immediately downstream of primer 1
Real-time PCR
Laboratories can also use a real-time PCR method to identify the top 20 emm types of S. pyogenes circulating in the United States2.
View a list of oligonucleotides used in the quadriplex real-time PCR emm typing assay.
Another real-time PCR assay targets the spy gene in order to detect S. pyogenes. View a list of primer and probe sequences:
Whole-genome sequencing
emm types can be deduced from whole-genome sequencing3.
Alternative multilocus sequencing typing primers
There are alternative multilocus sequencing typing (MLST) primers for Sanger sequencing. These primers generally lie about 40 bases further upstream than other primers documented for S. pyogenes MLST. These primers are better for obtaining the first few bases of the target sequence.
- Sanderson-Smith M, De Oliveira DM, Guglielmini J, et al. A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development. J Infect Dis. 2014;210(8):1325–38.
- Velusamy S, Jordak K, Kupor M, Chochua S, McGee L, Beall B. Sequential quadriplex real-time PCR for identifying 20 common emm types of group A Streptococcus.J Clin Microbiol. 2021;59(1):e01764–20.
- Cochua S, Metcalf BJ, Li Z, et al. Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015. mBio. 2017: 8(5):e01422-17.