emm Typing Overview and Guidelines

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

You can submit a sequence that doesn't match 100% with any of the emm sequences in CDC's database.

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

These sequences are usually linked to M protein genes rather than the similar mrp or enn genes. For this reason, using alternative primers for obtaining emm sequence is discouraged.

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.

View MLST primers for S. pyogenes.