Journal:

Article Title: Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus

doi: 10.1128/AAC.48.5.1823-1836.2004

Figure Lengend Snippet: Alignment of DNA sequences of DRSCC and IRSCC junctions from SCC and SCCmec elements. Shown are SCCpbp4 alignments with SCCmec types I, II, and IV and SCC12263 (A) and with SCCmec type III and SCCcap1 (B). Strains represented are isolate 2314 (SCCmec IV), ATCC 12228 (SCCpbp4), CA05 and MW2 (SCCmec IVa), 8/6-3P (SCCmec IVb), NCTC 10442 (SCCmec I), N315 (SCCmec II), 85/2082 (SCCmec III), ATCC 27844 (SCC12263), and S. aureus M (SCCcap1). DRSCC and IRSCC in the left junction were designated DRSCC-L and IRSCC-L, respectively; DRSCC and IRSCC in the right junction were designated DRSCC-R and IRSCC-R, respectively. Capital letters, nucleotides in SCC or SCCmec elements; lowercase letters, nucleotides in chromosomal regions. Black arrows, direct-repeat sequences; red arrows, inverted-repeat sequences. Asterisks indicate identical nucleotides in the comparison sequences; pairs of slashes indicate intervening omitted sequences.

Article Snippet: Sequences from coagulase-negative staphylococci were from S. epidermidis ATCC 12228 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE016744","term_id":"27316888"}} AE016744 ) ( 23 ) and S. hominis ATCC 27844 ( {"type":"entrez-nucleotide","attrs":{"text":"AB063171","term_id":"18148881"}} AB063171 ).

Techniques:

Journal:

Article Title: Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus

doi: 10.1128/AAC.48.5.1823-1836.2004

Figure Lengend Snippet: Map depicting the regions of high nucleotide sequence similarity between the left portion of SCCpbp4 (L-C region), including both ccr genes, and the left extremities of SCCmec elements and non-mec-containing SCC elements, based on the nucleotide sequences deposited in the DDBJ/EMBL/GenBank database under accession no. AY271717 (Dallas CA-MRSA strain 2314, SCCmec type IV), AB096217 (strain MR108, SCCmec type IVc), AE016744 (S. epidermidis ATCC 12228, SCCpbp4), D86934 (strain N315, SCCmec type II), AB063172 (strain CA05, SCCmec type IVa), AP004822 (strain MW2, SCCmec type IVa), AB063173 (strain 8/6-3P, SCCmec type IVb), AB063171 (S. hominis ATCC 27844, SCC12263), AB033763 (NCTC 10442, SCCmec type I), and AB037671 (S. aureus strain 82/2082, SCCmec type III). Conserved ORFs of >99 bp are indicated by solid rectangles beneath the maps of the nucleotide sequences. Arrows above the rectangles for the map of SCCpbp4 indicate the direction of transcription. Identical colors for sequences from different elements indicate regions of >90% nucleotide sequence homology. Asterisk indicates a 28-bp sequence identity with SE0039 from SCCpbp4. Vertical arrowhead indicates the junction between the left SCC element and the chromosome.

Article Snippet: Sequences from coagulase-negative staphylococci were from S. epidermidis ATCC 12228 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE016744","term_id":"27316888"}} AE016744 ) ( 23 ) and S. hominis ATCC 27844 ( {"type":"entrez-nucleotide","attrs":{"text":"AB063171","term_id":"18148881"}} AB063171 ).

Techniques: Sequencing

Journal:

Article Title: Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus

doi: 10.1128/AAC.48.5.1823-1836.2004

Figure Lengend Snippet: Map of the 57-kb SCC composite island and the ca. 19-kb SCCpbp4 element (dark blue background) inserted into the 3′ end of orfX in S. epidermidis ATCC 12228. The map shows the DRSCC's and IRSCC's that mark the boundaries of the elements, as well as ORFs of interest (light blue arrows showing direction of transcription). Yellow rectangles, IS431 elements. Horizontal rectangles above the map, homologous regions (HR) of >2 kb that have 78% (lavender) to >90% (red) sequence identity to regions in the indicated SCCmec elements. The SCC composite island spans nt 32492 through 89965, and SCCpbp4 spans nt 32492 to 51506, of GenBank accession no. AE016744. In order to emphasize the SCC-specific repeat regions, the map is not drawn to scale. Nucleotide positions of all ORFs that correspond to those in GenBank accession no. AE016744 are given in supplemental Table ​Table22 (http://www.ucch.org/daum-boyle_lab-composite_island_figures/table2.htm). Nucleotide positions of the SCC direct repeats and the newly annotated features (TPA BK001539) are detailed in Table ​Table2.2. MerR is the ca. 10-kb region encoding genes for mercury resistance, flanked by two copies of IS431 (see Fig. ​Fig.5).5). CadR is a region containing genes conferring resistance to cadmium (see Fig. ​Fig.5).5). HDE288 HR is a 5.3-kb region with 92% nucleotide identity to a region containing type 4 ccrA and ccrB genes in the SCCmec element in strain HDE288 (see Fig. ​Fig.6).6). SCCmec type IVc L-C HR is about 9 kb long, with 99 to 100% identity to the L-C region in type IVc SCCmec. The nucleotide sequence and structure of one of the three 28-bp DR-SCCcomposite island's are shown below the map, and the overlapping repeat sequences DR-SCCpbp4-R (right-pointing arrow) and IR-SCCpbp4-R (line with a diamond on the left), and IR-SCCpbp4-L (line with a Ball on the right) contained within it, are indicated. Also shown below the map are the sequence and structure of the novel SCC repeat sequence composed of overlapping DR/IR-R and IR/DR-L SCC sequences (SCC composite island-SCCpbp4 junction inverted repeat) that forms the 13-bp perfect inverted complementary repeat separated by 29 nt.

Article Snippet: Sequences from coagulase-negative staphylococci were from S. epidermidis ATCC 12228 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE016744","term_id":"27316888"}} AE016744 ) ( 23 ) and S. hominis ATCC 27844 ( {"type":"entrez-nucleotide","attrs":{"text":"AB063171","term_id":"18148881"}} AB063171 ).

Techniques: Sequencing

Journal:

Article Title: Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus

doi: 10.1128/AAC.48.5.1823-1836.2004

Figure Lengend Snippet: (A) ClustalW alignment of the ccrB4 ORF of the SCC composite island of S. epidermidis ATCC 12228 (nt 58592 to 60,220 complement) with that of SCCmec of strain HDE288 (the pediatric clone) (nt 9184 to 10812, GenBank accession no. AF411935). The missing adenine at position 1326 (shaded dash) of the ccrB4 ORF of strain HDE288 creates a putative premature stop codon (shaded box). Open box, putative stop codon of the ccrB4 ORF of strain ATCC 12228. Asterisks indicate identical residues. SCC-CI, SCC composite island. (B) Pairwise comparison of the translated amino acid sequences from the ccrA4 and ccrB4 genes of the SCC composite island of S. epidermidis ATCC 12228 (see supplemental Table ​Table22 [http://www.ucch.org/daum-boyle_lab-composite_island_figures/table2.htm]) and of strain HDE288 SCCmec (accession no. AF411935). These strains showed 91.2% similarity and 87.2% identity for CcrA4 and 80.4% similarity and 80.1% identity for CcrB4. The pairwise alignments were performed by using the Vector NTI suite, version 8 (Informax, Inc.), with the blosum62mt2 matrix. A pairwise ClustalW alignment of the DNA sequences from the entire 5.3-kb region of homology surrounding the ccrAB4 genes of the SCC composite island of S. epidermidis ATCC 12228 (nt 57056 to 62395 complement, accession no. AE016744) and SCCmec of strain HDE288 (the pediatric clone) (nt 6986 to 12345, GenBank accession no. AF411935) is shown in supplemental Fig. ​Fig.6D6D (available at http://www.ucch.org/daum-boyle_lab-composite_island_figures/fig_6D.htm). (C) Map of the region of nucleotide conservation between the SCC composite island and strain HDE288 that encompasses the ccrA4 and ccrB4 genes, highlighting the larger size of the ccrB4 ORF in the SCC composite island (1,629 versus 1,329 bp, encoding 542 versus 453 aa, respectively; vertical line indicates premature stop codon in strain HDE288). Solid arrows, unique ORFs in the SCC composite island.

Article Snippet: Sequences from coagulase-negative staphylococci were from S. epidermidis ATCC 12228 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE016744","term_id":"27316888"}} AE016744 ) ( 23 ) and S. hominis ATCC 27844 ( {"type":"entrez-nucleotide","attrs":{"text":"AB063171","term_id":"18148881"}} AB063171 ).

Techniques: Plasmid Preparation

Journal:

Article Title: Novel Non- mecA -Containing Staphylococcal Chromosomal Cassette Composite Island Containing pbp4 and tagF Genes in a Commensal Staphylococcal Species: a Possible Reservoir for Antibiotic Resistance Islands in Staphylococcus aureus

doi: 10.1128/AAC.48.5.1823-1836.2004

Figure Lengend Snippet: Analysis of the pbp4 homolog of SCCpbp4. (A) Theoretical translation of the pbp4 homolog of S. epidermidis ATCC 12228, highlighting functional domain architecture. Shading indicates the peptidase S_1 domain, starting at aa 24 and ending at aa 304. The penicillin-binding domains, SXXK, SSN, and KTG, are boxed. (B) ClustalW alignment of the pbp4 genes of S. aureus (GenBank accession no. SAPBP4GEN) and SCCpbp4 of S. epidermidis ATCC 12228. White letters on solid background, identical residues; letters on shaded background, conservative replacements. Overall there were 46.2% similarity and 32.7% identity between the two sequences. Pairwise alignments were performed with the Vector NTI suite, version 8 (Informax, Inc.), by using the blosum62mt2 matrix. (C) Architecture of ORFs in the DNA sequences surrounding and including the pbp4 genes (solid arrows) in S. aureus strain N315 (nt 91873 to 93737; accession no. AP003131) and the SCCpbp4 element of S. epidermidis ATCC 12228. Arrows indicate ORFs and their direction of transcription.

Article Snippet: Sequences from coagulase-negative staphylococci were from S. epidermidis ATCC 12228 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE016744","term_id":"27316888"}} AE016744 ) ( 23 ) and S. hominis ATCC 27844 ( {"type":"entrez-nucleotide","attrs":{"text":"AB063171","term_id":"18148881"}} AB063171 ).

Techniques: Functional Assay, Binding Assay, Plasmid Preparation