SCCmec

• SCCmec is defined by the characteristics listed below:

1. It carries a mec gene complex, a ccr gene(s) (ccrAB and/or ccrC), its regulatory genes, such as mecI and mecR1, and the insertion sequence IS431.
2. It carries two site-specific recombinase homologues.
3. It has characteristic direct repeats and inverted repeats at both ends.
4. It is located at the 3’ end of orfX.

IWG-SCC commentary Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7.

J regions (previously “junkyard regions”)

• Besides the mec and ccr gene complexes, the SCCmec element also contains three so-called J regions, which constitute non-essential components of the cassette.
• J regions may carry additional antimicrobial resistance determinants.
• J1 is the region between the right chromosomal junction and the ccr complex.
• J2 is between the ccr gene complex and the mec gene complex.
• J3 is between the mec complex and the left chromosomal junction.
• Variations in the J regions within the same mec-ccr complex are used for defining SCCmec subtypes.

Description of SCCmec in two ways

Examples:

SCCmec structure examples: type I, II and III

IWG-SCC commentary Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7.

• The mec gene complex is composed of mecA, its regulatory genes, and associated insertion sequences.
• The class A mec gene complex (class A mec) is the prototype complex, which contains mecA, the complete mecR1 and mecI regulatory genes upstream of mecA, and the hypervariable region (HVR) and insertion sequence IS431 downstream of mecA.
• The class B mec gene complex is composed of mecA, a truncated mecR1 resulting from the insertion of IS1272 up- stream of mecA, and HVR and IS431 downstream of mecA.
• The class C mec gene complex contains mecA and truncated mecR1 by the insertion of IS431 upstream of mecA and HVR and IS431 downstream of mecA.

List of mecA homologues and phylogenetic relationships by maximum likelihood method

IWG-SCC commentary Antimicrob Agents Chemother 2012 Oct;56(10):4997-9.

• The ccr gene complex is composed of the ccr gene(s) and surrounding open reading frames (ORFs), several of which have unknown functions. Currently, three phylogenetically distinct ccr genes, ccrA, ccrB, and ccrC, have been identified in S. aureus with DNA sequence similarities below 50%.
• Novel ccr genes should be defined based on DNA sequence similarities of <50%, and novel al- lotypes of ccr genes should be designated if their DNA sequence similarity identities are between 50% and 85%. This convention should be followed for naming novel ccr genes.

Representation of the naming conventions for ccr genes in S. aureus.

IWG-SCC commentary

Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7.