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Commentary

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)
  • For correspondence: teruybac@juntendo.ac.jp
DOI: 10.1128/AAC.00579-09
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  • FIG. 1.
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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.

  • FIG. 2.
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    FIG. 2.

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

  • FIG. 3.
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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 ).

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  • TABLE 1.

    SCCmec types identified in S. aureus

    SCCmec typeccr gene complexamec gene complex
    I1 (A1B1)B
    II2 (A2B2)A
    III3 (A3B3)A
    IV2 (A2B2)B
    V5 (C)C2
    VI4 (A4B4)B
    VII5 (C)C1
    VIII4 (A4B4)bA
    • ↵ 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 MRSAa

    SCCmec typebReported namecMajor characteristics of J regionsdRepresentative strain(s)Reference(s) and/or accession no.e
    I (1B)IJ1, subtype 1-specific ORFs (pls); J3, dcsNCTC10442, COL 9, 18
    I.2J1, subtype 2-specific ORFs; J3, dcs and pUB110PL72 18
    II (2A)IIJ1, subtype 1-specific ORFs (kdp); J2, subtype 1-specific ORFs and Tn554; J3, dcs and pUB110N315 18
    IIbJ1, subtype 2-specific ORFs; J2, subtype 1-specific ORFs and Tn554; J3, dcsJCSC3063 7
    IIBJ1, subtype 3-specific ORFs; J2, subtype 1-specific ORFs; J3, dcs and pUB110AR05/0.1345 20
    IIEJ1, subtype 3-specific ORFs; J2, short J2 region the same as subtype 1 and Tn554; J3, dcs and pUB110AR13.1/3330.2 20
    II.4.1.1J1, subtype 4-specific ORFs; J2, subtype 1-specific ORFs and Tn554; J3, dcs and pUB110RN7170 13
    III (3A)IIIJ1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs and ΨTn554; J3, subtype 1-specific ORFs and pT18185/2082, ANS46 9, 18
    IIIAJ1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs and ΨTn554; J3, subtype 1-specific ORFs, pT181, and SCCHg carrying ccrCHU25 18
    IV (2B)IVaJ1, subtype 1-specific ORFs; J3, dcsCA05, MW2 15
    IVbJ1, subtype 2-specific ORFs; J3, dcs8/6-3P 15
    IVcJ1, subtype 3-specific ORFs; J3, dcs and Tn400181/108 16
    IVcJ1, subtype 3-specific ORFs; J3, dcs2314AY271717
    IVAJ1, subtype 3-specific ORFs; J3, dcs and pUB110cm11EU437549
    IVEJ1, subtype 3-specific ORFs; J3, subtype 2-specific ORFsAR43/3330.1 20
    IVdJ1, subtype 4-specific ORFs; J3, dcsJCSC4469 16
    IVgJ1, subtype 5-specific ORFs; J3, dcsM03-68 14
    IVhJ1, subtype 6-specific ORFs; J3, dcsEMRSA-15 17
    IViJ1, subtype 7-specific ORFs; J3, dcsJCSC6668 2
    IVjJ1, subtype 8-specific ORFs; J3, dcsJCSC6670 2
    IV (2B&5)IV variantJ1, subtype 3-specific ORFs; J3, SCC carrying ccrCZH47 6
    V (5C2)VJ1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFsWIS(WBG8318) 10
    V (5C2&5)VT, VIIJ1, subtype 2-specific ORFs; J2, sutype 2-specific ORFs; J3, SCC carrying ccrCTSGH17, PM1 3, 22
    VI (4B)VIJ1, subtype 1-specific ORFs; J3, dcsHDE288 19
    VII (5C1)5C1J1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFsJCSC6082 1
    VIII (4A)VIIIJ1, subtype 1-specific ORFs; J2, subtype 1-specific ORFs; J3, subtype 1-specific ORFsC10682, 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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    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.
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Classification of Staphylococcal Cassette Chromosome mec (SCCmec): Guidelines for Reporting Novel SCCmec Elements
Antimicrobial Agents and Chemotherapy Nov 2009, 53 (12) 4961-4967; DOI: 10.1128/AAC.00579-09

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Classification of Staphylococcal Cassette Chromosome mec (SCCmec): Guidelines for Reporting Novel SCCmec Elements
Antimicrobial Agents and Chemotherapy Nov 2009, 53 (12) 4961-4967; DOI: 10.1128/AAC.00579-09
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  • Top
  • Article
    • CHARACTERISTICS OF SCCmec ELEMENTS
    • BASIC CONCEPTS FOR THE CLASSIFICATION OF SCCmec ELEMENTS
    • EIGHT CURRENTLY ESTABLISHED SCCmec TYPES
    • CLASSIFICATION OF SCCmec TYPES INTO SUBTYPES
    • COMPOSITES OF TWO OR MORE SCC ELEMENTS
    • CLASSIFICATION OF SCC ELEMENTS THAT DO NOT CARRY mecA
    • RECOMMENDATIONS AND CONCLUSIONS
    • ACKNOWLEDGMENTS
    • REFERENCES
  • Figures & Data
  • Info & Metrics
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KEYWORDS

Chromosomes, Bacterial
DNA Transposable Elements
methicillin-resistant Staphylococcus aureus

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