Minimum spanning tree of the 1681 <i>S. aureus</i> isolates typed by MLVA.

<p>Clustering of MLVA profiles was done using a categorical coefficient. In the minimum spanning tree the MLVA types are displayed as circles. The size of each circle indicates the number of isolates with this particular type. Thick solid lines connect types that differ in a single VNTR locus and a thin solid connects types that differ in 2 VNTR loci. The color of the halo surrounding the MLVA types denote types that belong to the same complex. MLVA complexes were assigned if 2 neighboring types did not differ in more than 1 VNTR locus and if at least 5 types fulfilled this criterion. MLVA complexes are also indicated in characters e.g. MC8 denotes MLVA complex 8.</p

Schematic map of the genome of <i>S. aureus</i> strain N315, indicating the positions of the VNTR loci used in MLVA.

<p>Schematic map of the genome of <i>S. aureus</i> strain N315, indicating the positions of the VNTR loci used in MLVA.</p

List of primers used for MLVA of <i>S. aureus</i>.

1<p>Fluorescent dyes are indicated by a character. F, FAM; N, NED; V, VIC; P, PET.</p>2<p>Coordinates in NC_002745.</p>3<p>Unlabeled version of the primer VNTR61_02, used to reduce the fluorescence signal in the MLVA (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005082#s2" target="_blank">Materials and Methods</a>).</p

Minimum spanning tree of 1304 <i>S. aureus</i> isolates typed by PFGE.

<p>The PFGE types are displayed as circles. Clustering was performed using the Pearson correlation coefficient and a 2% optimization setting. The resulting similarity matrix was used to construct a minimum spanning tree using a 10% similarity bin size. Related PFGE grouped and this is denoted by the double circle (compacted complexes). The MLVA complex is denoted as the color of the circles (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005082#pone-0005082-g002" target="_blank">figure 2</a>) and is also indicated in characters.</p

Space-time SpaType clusters found in isolates collected from 15 hospitals during the time period January–October 2008.

1<p>MT, MLVA type.</p

Characteristics of MLVA complexes found among 1681 <i>S. aureus</i> isolates.

1<p>DI, diversity index.</p

Properties of the VNTR loci used for MLVA of 1681 <i>S. aureus</i> isolates.

1<p>DI, Simpson's index of diversity.</p

Concordance of the grouping obtained by MLVA and by MLST.

<p>A minimum spanning tree was constructed based on MLVA data of 40 isolates for which MLST had already been performed. The circles represent the MLVA types and the numbers in the circles represent the STs. The numbers displayed between types denote the number of VNTR loci that differ between these types. The colors represent the MLST clonal complexes. The white circles are STs that have not been assigned to a particular clonal complex. Only single locus or double locus MLVA variants are connected by lines. The size of each circle indicates the number of isolates with this particular MLVA type.</p

Discriminatory power of MLVA, <i>spa</i>-sequence typing and PFGE for <i>S. aureus.</i>

<p>Diversity is plotted as the number of types versus the percentage of isolates. To obtain the plot the list of typing results was first sorted by frequency and the percentage of isolates versus the number of types was determined. The plot only shows the results for the 529 <i>S. aureus</i> isolates that were analyzed by all 3 methods.</p

Minimum spanning tree of 882 <i>S. aureus</i> isolates typed by <i>spa</i>-sequence typing.

<p>The SpaTypes are displayed as circles. For description of the symbols, lines etc. see legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005082#pone-0005082-g002" target="_blank">figure 2</a>. Clustering was performed using the Bionumerics spa-plugin with a conservative alignment setting of 100% and 0% maximum duplication length. Halos surrounding SpaTypes indicate related SpaTypes.</p