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. 2001 May;45(5):1323-36.
doi: 10.1128/AAC.45.5.1323-1336.2001.

Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus

T Ito  1 , Y Katayama, K Asada, N Mori, K Tsutsumimoto, C Tiensasitorn, K Hiramatsu
Affiliations

Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus

T Ito et al. Antimicrob Agents Chemother. 2001 May.

Erratum in

  • Antimicrob Agents Chemother 2001 Dec;45(12):3677

Abstract

The beta-lactam resistance gene mecA of Staphylococcus aureus is carried by a novel mobile genetic element, designated staphylococcal cassette chromosome mec (SCCmec), identified in the chromosome of a Japanese methicillin-resistant S. aureus (MRSA) strain. We now report identification of two additional types of mecA-carrying genetic elements found in the MRSA strains isolated in other countries of the world. There were substantial differences in the size and nucleotide sequences between the elements and the SCCmec. However, new elements shared the chromosomal integration site with the SCCmec. Structural analysis of the new elements revealed that they possessed all of the salient features of the SCCmec: conserved terminal inverted repeats and direct repeats at the integration junction points, conserved genetic organization around the mecA gene, and the presence of cassette chromosome recombinase (ccr) genes responsible for the movements of SCCmec. The elements, therefore, were considered to comprise the SCCmec family of staphylococcal mobile genetic elements together with the previously identified SCCmec. Among 38 epidemic MRSA strains isolated in 20 countries, 34 were shown to possess one of the three typical SCCmec elements on the chromosome. Our findings indicated that there are at least three distinct MRSA clones in the world with different types of SCCmec in their chromosome.

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Figures

FIG. 1
FIG. 1
Structures of three types of SCCmec. The structures of type I SCCmec (A), type II SCCmec (B), and type III SCCmec (C) are illustrated based on the nucleotide sequences deposited in the DDBJ/EMBL/GenBank databases under accession no. AB033763 (type I), D86934 (type II), and AB037681 (type III). (a) Essential structure of SCCmec. Locations of the essential genes are illustrated. The restriction sites of HindIII and XbaI are indicated. Only the EcoRI (E) and PstI (P) restriction sites, which are inevitable for the description of probes of type II SCCmec, are indicated (in parentheses). The essential genes as well as other regions are colored based on the color of the ORFs described in panel C. The regions common to MSSA are shown in white with gray-striped bars. The regions found in S. aureus NCTC 8325 and not found in ATCC 25923 are shown in gray with striped bars. The regions common to S. aureus ATCC 25923 and not found in NCTC 8325 are shown in dark gray with cross-hatched bars. Small black asterisks signify the locus common to all three strains. Large gray asterisks signify the region common to three SCCmecs. An arrowhead signifies the location of a 15-bp sequence similar to that of N315 found between the second and the third IS431 copies of type III SCCmec. Arrows indicate the direction of Tn554 or ΨTn554. Dotted arrows indicate the transcription of direction of the ORFs located downstream of ccrB or CZ072. (b) Probes used for dot-blot hybridization. (c) ORFs in and around SCCmec. The ORFs >200 bases in size in six possible reading frames are indicated by squares. Those above the line are the ORFs that have transcription directed to the right, and those below the line have transcription directed to the left. Colored squares are the ORFs the extant gene homologues of which were found in the databases, although many of them were considered incomplete (underlined). The color corresponds to the difference in the conservation of the ORFs (or regions) in three types of SCCmec white, ORFs in three types of SCCmec with identity of more than 99%: gray, conserved in three types of SCCmec with on identity score of 47 to 92%; magenta, ORFs common to type II and type III SCCmec; yellow, ORFs common to type II and type III SCCmec; blue, ORFs unique in type I SCCmec; red, ORFs unique in type II SCCmec; green, ORFs unique in type III SCCmec. ORFX is indicated in a stippled box.
FIG. 2
FIG. 2
Boundaries of SCCmec. Nucleotide sequences around the left and right boundaries of SCCmecs of N315, NCTC 10442, 85/1940, and 85/2082 (attL and attR respectively) are aligned with the sequence around the presumptive integration site, attB, on the chromosome of MSSA strains (NCTC 8325, ATCC 25923, N315ex, 85/1940ex, and 85/2082ex). The boundary sequences of an inserted element, IE25923 (DDBJ/EMBL/GenBank accession no. AB047239), identified in an MSSA type strain, ATCC 25923, is also shown in comparison with those of SCCmec. Inverted complementary repeats IR-L and IR-R at both extremities of SCCmecs are indicated by thin arrows. Direct repeats are indicated by thick arrows. Asterisks indicate identical nucleotides in the two sequences. Consensus sequences of attBscc and inverted repeats of SCCmec are indicated below. The left- and rightmost nucleotides were each inferred to be one of the four nucleotides numbered 1 to 4 and 5 to 8, respectively, in the figure. The entire lengths of three SCCmecs were 34, 364, 53,017, and 66,896 bp. We have revised the nucleotide sequence of type II SCCmec (17). We found that 931- and 344-bp deletions had occurred in the cloned DNA fragment and a sequencing error. The 931 bp segment was deleted upstream of ORF N026, and 344 bp was deleted downstream of ORF N028 (Fig. 1). Consequently, the size of type II SCCmec changed from 51,669 bp to 53,017 bp.
FIG. 3
FIG. 3
Deduced amino acid sequences of ccr genes. (A) Deduced amino acid sequences of ccrA1, ccrA2, and ccrA3. (B) Deduced amino acid sequences of ccrB1∗, ccrB2, and ccrB3. Amino acid sequences of ccr genes were aligned by using the Pile-Up program with a GCG default scoring matrix in the Wisconsin Package (version 9.0; Genetics Computer Group). Amino acids shared by the three peptides are boxed. Large bullets indicate amino acid residues of Ccr proteins shared by site-specific recombinases of the invertase-resolvase family. Small bullets indicate amino acid substitution within the same class of amino acids. A black arrowhead indicates the presumptive serine involved in the phosphoseryl linkage of the recombinase of DNA conserved in the NH2-terminal catalytic domain of site-specific recombinases of the invertase-resolvase family (27). A white arrowhead indicates the locus of the first amino acid residue changed by an addition of adenine in the nucleotide sequence of type I SCCmec as described in the text.
FIG. 3
FIG. 3
Deduced amino acid sequences of ccr genes. (A) Deduced amino acid sequences of ccrA1, ccrA2, and ccrA3. (B) Deduced amino acid sequences of ccrB1∗, ccrB2, and ccrB3. Amino acid sequences of ccr genes were aligned by using the Pile-Up program with a GCG default scoring matrix in the Wisconsin Package (version 9.0; Genetics Computer Group). Amino acids shared by the three peptides are boxed. Large bullets indicate amino acid residues of Ccr proteins shared by site-specific recombinases of the invertase-resolvase family. Small bullets indicate amino acid substitution within the same class of amino acids. A black arrowhead indicates the presumptive serine involved in the phosphoseryl linkage of the recombinase of DNA conserved in the NH2-terminal catalytic domain of site-specific recombinases of the invertase-resolvase family (27). A white arrowhead indicates the locus of the first amino acid residue changed by an addition of adenine in the nucleotide sequence of type I SCCmec as described in the text.
FIG. 4
FIG. 4
Phylogenetic relationships among ccrA genes, ccrB genes the ORF CZ072, and three site-specific recombinases. Three site-specific recombinases that showed a high similarity to ccr genes were selected to investigate phylogenetic relationships. They were the integrase (int) of bacteriophage TP901-1 found in L. lactis (1,458 bp; DDBJ/EMBL/GenBank accession no. X85213), the site-specific recombinase (spoIVCA) found in B. subtilis (1,503 bp; DDBJ/EMBL/GenBank accession no. D32216), and the transposase (tnpX) found in the conjugative transposon Tn4451 of C. perfringens (2,124 bp; DDBJ/EMBL/GenBank accession no. U15027). The nucleotide sequences of the ccrA genes (ccrA1, ccrA2, and ccrA3), ccrB genes (ccrB1∗, ccrB2, and ccrB3), ORF CZ072, int, spoIVCA, and tnpX were aligned by using the Pile-Up program with a GCG default scoring matrix. Phylogenetic relationships were developed with the Paupsearch program by the neighbor-joining method. The tree was visualized with Tree View software. The branch length indicates the distance, which is expressed as the number of substitutions per 100 bases.
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References

    1. Archer G L, Niemeyer D M, Thanassi J A, Pucci M J. Dissemination among staphylococci of DNA sequences associated with methicillin resistance. Antimicrob Agents Chemother. 1994;38:447–454. - PMC - PubMed
    1. Archer G L, Thanassi J A, Niemeyer D M, Pucci M J. Characterization of IS1272, an insertion sequence-like element from Staphylococcus haemolyticus. Antimicrob Agents Chemother. 1996;40:924–929. - PMC - PubMed
    1. Bannam T L, Crellin P K, Rood J I. Molecular genetics of the chloramphenicol-resistance transposon Tn4451 from Clostridium perfringens: the TnpX site-specific recombinase excises a circular transposon molecule. Mol Microbiol. 1995;16:535–551. - PubMed
    1. Chikramane S G, Matthews P R, Noble W C, Stewart P R, Dubin D T. Tn554 inserts in methicillin-resistant Staphylococcus aureus from Australia and England. J Gen Microbiol. 1991;137:1303–1311. - PubMed
    1. Christiansen B, Brøndsted L, Vogensen F K, Hammer K. A resolvase-like protein is required for the site-specific integration of the temperate lactococcal bacteriophage TP901–1. J Bacteriol. 1996;178:5164–5173. - PMC - PubMed

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