MES16K structure and phylogenetic tree analysis for the <i>ccrC</i> genes.

<p>The SCCmercury data for strain TW20 are from GenBank accession number FN433596. The GenBank accession number of MES16K is AB666466. Homologous regions are shaded. In A, for strain TW20, the <i>ccrC</i>-carrying unit was located within SCCmercury; the <i>ccrC</i> gene (marked in yellow) was split by the insertion of IS (IS200 family). For strain 16K, the <i>ccrC</i>-carrying unit was located within a mobile element structure MES16K, which was inserted into the <i>orf</i> (corresponding to SATW20_27600 of TW20) on the 16K genome, as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029187#pone-0029187-g002" target="_blank">Fig. 2</a>; the <i>ccrC</i> gene (marked in yellow) was intact. The attachment sequence (<i>att</i>) of MES16K showed no homology to that (<i>att</i>) of the <i>orfX</i>, SCC<i>mec</i>III.1.1.1 or SCCmercury. Arrowheads PM1 and PM2 represent PCR targets for detection of SCCmercury of ST239/SCC<i>mec</i>III.1.1.1 MRSA and MES16K of the Russian variant (strain 16K) by multiplex PCR (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029187#pone-0029187-g003" target="_blank">Fig. 3</a>). In B, the <i>ccrC</i> gene sequence of strain 16K and that of strain TW20 (expected intact <i>ccrC</i> gene sequence, obtained by excluding the inserted IS200-family sequence) were analyzed for phylogenetic diversity, as described previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029187#pone.0029187-Higuchi2" target="_blank">[36]</a>. The <i>ccrC</i> gene of strain TW20 was a novel <i>ccrC1</i> allele (named <i>ccrC1</i> allele 10) and that of strain 16K was assigned as <i>ccrC1</i> allele 3, unambiguously demonstrating evolutionary diversity between them; moreover, the <i>ccrC1</i> gene of ST398 MRSA strain S0385 was also a novel allele (named <i>ccrC1</i> allele 11).