Genes significantly associated with animal and human isolates belonging to the ST398 lineage.

*<p>For each gene, isolates with ambiguous microarray result were excluded from the analysis and from P-value calculation. For this reason, percentages are not necessarily calculated relative to the total no. of isolates.</p>**<p>P-values were calculated for each gene using a two-tailed Fisher's exact test and corrected for multiple testing using the Holm-Bonferroni method. Inf, positive infinite.</p

Dendrogram (UPGMA method, circular representation) based on the results of DNA microarrays study (172 genes only) of the 105 MSSA CC398 strains and the 53 MRSA CC398 isolated in France.

<p>For each of the 172 genes, the average of the results of all the strains corresponding to the same <i>spa</i> type was calculated. Each group of strains is represented by the corresponding <i>spa</i> type. s<i>pa</i> types corresponding to MRSA strains are colored in red.</p

Dendrogram (UPGMA method, squared representation) based on the homology degree of the <i>spa-types</i> of the 105 MSSA CC398 strains and the 53 MRSA CC398 isolated in France.

<p>The homology between the repeats of the strains is of 76%. <i>spa</i>CC: <i>spa</i> clonal complex. s<i>pa types</i> corresponding to MRSA strains are colored in red.</p

Phylogenic tree with 158 <i>S. aureus</i> CC398 strains (modified <i>Parsimony</i> method, circular representation), based on the analysis of 319 genes and alleles by DNA microarrays.

<p>Since the PCR analysis of the <i>agr</i> alleles confirmed that all the strains were <i>agr</i> 1, the analysis of the results of DNA microarrays concerned only 319 genes and alleles. MSSA group is subdivided in <i>bla−</i> and <i>bla+</i> clusters, and MRSA group in SCC<i>mec</i> IV and SCC<i>mec</i> V clusters.</p

Description of the studied populations, corresponding used methods, and objectives.

*<p>The 10 strains isolated from infective endocarditis are included in the 89 strains from infections.</p>†<p>The belonging of the strains to CC398 was confirmed by MLST in case of discrepancies between previous typing techniques. All strains were isolated in mainland France.</p

Nature and number of infections caused by 89 MSSA CC398 strains collected in mainland France between 1999 and 2011.

<p>Disseminated infections are defined by the presence of septic metastasis in at least 2 noncontiguous organs (by opposition to bloodstream infections). Infections classified as infective endocarditis correspond to bloodstream infections with infective endocarditis and without any other septic metastasis.</p

Frequency of antibiotic resistance of 105 MSSA CC398 strains of human origin isolated between 1999 and 2011 in mainland France.

<p>Frequency of antibiotic resistance of 105 MSSA CC398 strains of human origin isolated between 1999 and 2011 in mainland France.</p

Whole genome sequence based analysis of divergence of ST291 and ST398.

<p>Maximum-parsimony tree of the two ST291 isolates (HT20040853 and ST20090964) and 89 CC398 isolates based on 12,735 SNPs total SNPs. The tree was rooted with MRSA252 (ST36), the closest non-CC398 available out-group. The scale indicates the number of SNP differences.</p

MLST based CC398 phylogeny.

<p>Maximum parsimony analysis of the concatenated allelic sequences from the 43 CC398 sequence types and rooted using MRSA252 (ST36). The cluster containing ST398 is highlighted in light grey and the ST291 cluster is dark grey. The scale indicates the number of SNP differences.</p

Diversity in <i>S. aureus</i> CC398 genome content.

<p>Comparison of the genome content of the livestock- and human-associated <i>S. aureus</i> CC398s with the two ST291s. Reference genomes are in A) S0385 the livestock associated CC398, and in B) ST398NM01/71193 the human associated CC398. Presented are analysis of ST398NM01/71193 (purple), S0385 (cyan), HT20040853 (blue) and ST20090964 (red), compared to the references. The outer circle in A represent the distribution of the 7,800 SNPs differentiating both ST291s from the SO385 reference genome.</p