SGI1 deletion variants isolated from the wt form.

<p>(<b>A</b>) Schematic map of SGI1 (not in scale). ORFs are represented by arrows, resistance genes are red. DRs are shown as green and yellow rectangles. Dashed lines above the graph show the two <i>IntI1</i> integron regions. Below the graph, the directly repeated homologous tracts are shown as bars (from left to right): light blue bars: 3588–3618 bp and 13516–13546 bp, dark grey bars: 27552–27992 bp and 36824–37264 bp, black bars: 28840–29822 bp and 38300–39282 bp, purple bars: 30150–30252 bp (<i>flo</i>DRL) and 31791–31893 bp (<i>flo</i>DRR). Coordinates are according to the annotated SGI1 sequence (GenBank AF261825.2). The lettered arrows show PCR primers used for the amplification of the deletion forms (for primer sequences see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032497#pone.0032497.s003" target="_blank">Table S1</a>). Long horizontal bars below the graph represent the deleted regions between the direct repeats. Filling of bars corresponds to those of the respective direct repeats. (<b>B</b>) PCR test of the isolated A- and S-type deletion variants. The expected size of PCR products is indicated. Lanes 1–10: PCR products from total DNA of strains ST11A/2, ST14A, ST21A, ST11S/1, ST15S, ST18S, ST19S, ST20S, ST21S/1 and ST28S/1. Used primers are indicated below the picture. (<b>C</b>) PCR test of the <b>d1</b> deletion in the SGI1 variants entrapped in pJKI666. The size of the wt (primers: <i>a–b</i>) and the <b>d1</b> (primers: <i>a–c</i>) amplicon is indicated. Lanes 1–4: PCR products from plasmid DNA of entrapped SGI1 derived from strains ST1773, ST28S/1, ST21S/1 and ST21A. Primers used are indicated below the picture. (<b>D</b>) PCR test for the presence of <b>d</b><b><i>flo</i></b> SGI1 deletion variant. The wt and <b>d</b><b><i>flo</i></b> PCR products (primers: <i>h–i</i>) and their size are indicated. Lanes 1–2: PCR products from total DNA of ST1375/IP40a, lanes 3–4: ST1375 (2 parallel colonies).