The SCC<i>mec</i>III_R structure of ST239 MRSA strain 16K.

<p>GenBank accession number for SCC<i>mec</i>III_R is AB539727. The data for strain TW20 are from GenBank accession number FN433596. Homologous regions are shaded. In A, when the structure of SCC<i>mec</i>III_R was compared with SCCmercury/SCC<i>mec</i>III.1.1.1 of TW20 (upper part of figure), the SCC<i>mec</i>III core was shared by the two, but the left side regions (flanked by <i>att</i> and IS<i>431</i>) of SCC<i>mec</i>III_R and SCC<i>mec</i>III.1.1.1 showed no homology. Moreover, Strain 16K lacked SCCmercury. The <i>dcs</i>-carrying unit (marked in pink) was shared by SCC<i>mec</i>III_R, SCC<i>mec</i>IV, SCC<i>mec</i>II, and SCC<i>mec</i>I (lower part of figure). The data for strains JCSC6668, NN1, 80s-2, CA05, N315, and NCTC10442 were from GenBank accession numbers AB425823, AB245470, AB245471, AB063172, NC_002745, and AB033763, respectively. In B, the mosaic SCC<i>mec</i>III_R structure was specifically detected by multiplex PCR. Multiplex PCR detects targets: P1 and P2 in the SCC<i>mec</i>III core, P3 in the left side region (attM-pT181) of SCC<i>mec</i>III.1.1.1, P4 in the left side region (<i>dcs</i>-carrying unit) of SCC<i>mec</i>III_R, and PM1 (in an <i>orf</i>) and PM2 in SCCmercury or MES16K (PCR targets are shown in this figure [in A] and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029187#pone-0029187-g004" target="_blank">Fig. 4</a> for SCCmercury, and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029187#pone-0029187-g004" target="_blank">Fig. 4</a> for MES16K); strain 16K was negative for the <i>mer</i> operon (lacked SCCmercury). ST239/SCC<i>mec</i>III.1.1.1 MRSA strain ANS46 gave five PCR bands; three bands (P1, P2, and P3) for SCC<i>mec</i>III.1.1.1 and two bands (PM1 and PM2) for SCCmercury. In contrast, the Russian variant (strain 16K) gave different combinations of five PCR bands; three bands (P1, P2, and P4) for SCC<i>mec</i>III_R and two bands (PM1 and PM2, marked with arrows) for MES16K. PCR band P4 was shared by SCC<i>mec</i>III_R and SCC<i>mec</i>IVc (and SCC<i>mec</i>IVa, SCC<i>mec</i>II, and SCC<i>mec</i>I). The combination of P1, P2, P4, PM1, and PM2 was unique to the Russian variant (strain 16K).