Classification of Staphylococcal Cassette Chromosome mec (SCCmec): Guidelines for Reporting Novel SCCmec Elements

International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC)

doi:10.1128/AAC.00579-09

DOI: 10.1128/AAC.00579-09

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FIG. 1.
Basic structures of representative SCCmec elements. The structures of SCCmec elements of representative strains are illustrated based on the following nucleotide sequences deposited in databases: NCTC10442 (AB033763), N315 (D86934), 85/2082(AB037671), CA05 (AB063172), ZH47 (AM292304), WIS (AB121219), TSGH17 (AB512767), PM1 (AB462393), HDE288 (AF411935), JCSC6082 (AB373032), and C10684 (FJ390057). Red arrowheads indicate the ISS of SCC that comprise DR sequences.
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FIG. 2.
Representation of the naming conventions for ccr genes in S. aureus.
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FIG. 3.
Phylogenetic relationships among ccrA genes, ccrB genes, and ccrC genes. The nucleotide sequences of 37 ccr genes (14 ccrA genes, 14 ccrB genes, and 9 ccrC genes) (see Table S1 in the supplemental material) were aligned by using the ClustalX program. In parentheses, names of S. aureus strains carrying ccr genes are indicated. In the case of non-S. aureus strains, names of species as well as strains are indicated in parentheses. A phylogenetic tree was generated by the neighbor-joining method by creating 2,000 bootstrap replicates. The tree was visualized with TreeView software, which was obtained from the TreeView website (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html).

TABLE 1.
SCCmec types identified in S. aureus
SCCmec type ccr gene complex^a mec gene complex
I 1 (A1B1) B
II 2 (A2B2) A
III 3 (A3B3) A
IV 2 (A2B2) B
V 5 (C) C2
VI 4 (A4B4) B
VII 5 (C) C1
VIII 4 (A4B4)^b A
↵a ccr genes in the gene complex are indicated in parentheses.
↵b ccrA4B4 genes found in type VIII SCCmec were nearly identical to those in the S. epidermidis SCC-CI element and showed nucleotide identities of 89.6% and 94.5% to those found in type VI SCCmec.

TABLE 2.

SCCmec elements identified in MRSA^a

SCCmec type^b	Reported name^c	Major characteristics of J regions^d	Representative strain(s)	Reference(s) and/or accession no.^e
I (1B)	I	J1, subtype 1-specific ORFs (pls); J3, dcs	NCTC10442, COL	9, 18
	I.2	J1, subtype 2-specific ORFs; J3, dcs and pUB110	PL72	18
II (2A)	II	J1, subtype 1-specific ORFs (kdp); J2, subtype 1-specific ORFs and Tn554; J3, dcs and pUB110	N315	18
	IIb	J1, subtype 2-specific ORFs; J2, subtype 1-specific ORFs and Tn554; J3, dcs	JCSC3063	7
	IIB	J1, subtype 3-specific ORFs; J2, subtype 1-specific ORFs; J3, dcs and pUB110	AR05/0.1345	20
	IIE	J1, subtype 3-specific ORFs; J2, short J2 region the same as subtype 1 and Tn554; J3, dcs and pUB110	AR13.1/3330.2	20
	II.4.1.1	J1, subtype 4-specific ORFs; J2, subtype 1-specific ORFs and Tn554; J3, dcs and pUB110	RN7170	13
III (3A)	III	J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs and ΨTn554; J3, subtype 1-specific ORFs and pT181	85/2082, ANS46	9, 18
	IIIA	J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs and ΨTn554; J3, subtype 1-specific ORFs, pT181, and SCCHg carrying ccrC	HU25	18
IV (2B)	IVa	J1, subtype 1-specific ORFs; J3, dcs	CA05, MW2	15
	IVb	J1, subtype 2-specific ORFs; J3, dcs	8/6-3P	15
	IVc	J1, subtype 3-specific ORFs; J3, dcs and Tn4001	81/108	16
	IVc	J1, subtype 3-specific ORFs; J3, dcs	2314	AY271717
	IVA	J1, subtype 3-specific ORFs; J3, dcs and pUB110	cm11	EU437549
	IVE	J1, subtype 3-specific ORFs; J3, subtype 2-specific ORFs	AR43/3330.1	20
	IVd	J1, subtype 4-specific ORFs; J3, dcs	JCSC4469	16
	IVg	J1, subtype 5-specific ORFs; J3, dcs	M03-68	14
	IVh	J1, subtype 6-specific ORFs; J3, dcs	EMRSA-15	17
	IVi	J1, subtype 7-specific ORFs; J3, dcs	JCSC6668	2
	IVj	J1, subtype 8-specific ORFs; J3, dcs	JCSC6670	2
IV (2B&5)	IV variant	J1, subtype 3-specific ORFs; J3, SCC carrying ccrC	ZH47	6
V (5C2)	V	J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFs	WIS(WBG8318)	10
V (5C2&5)	VT, VII	J1, subtype 2-specific ORFs; J2, sutype 2-specific ORFs; J3, SCC carrying ccrC	TSGH17, PM1	3, 22
VI (4B)	VI	J1, subtype 1-specific ORFs; J3, dcs	HDE288	19
VII (5C1)	5C1	J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFs	JCSC6082	1
VIII (4A)	VIII	J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFs	C10682, BK20781	23; FJ670542

↵a SCCmec elements that satisfy the following criteria are listed as follows: entire regions of SCCmec elements have been sequenced, or the essential parts of the mec gene complex and the ccr gene complex have been fully sequenced.
↵b The first categories for classifying SCCmec elements. The combinations of the ccr gene complex and the mec gene complex carried by the elements are indicated in parentheses.
↵c The names reported in original literature are listed. Assigned numbers or names that specify these elements would be given by IWG-SCC and would be seen at the website (http://www.SCCmec.org [under construction]).
↵d Key loci are indicated in parentheses. pls, plasmin-sensitive surface protein; dcs, downstream constant segment; kdp, potassium-dependent ATPase operon.
↵e GenBank/EMBL/DDBJ accession numbers are indicated in cases of direct submission.

Additional Files

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Supplemental material

Files in this Data Supplement:

Supplemental file 1 - Table 1, listing ccrA, ccrB, and ccrC genes deposited in databases, Table 2a, comparing selected ccrA genes, and Table 2b, comparing selected ccrB genes.
Excel file, 71K.