HISA big data in biomedicine and healthcare 2013 conference

Additional file 5. Biofilm formation by the S. suis serotype 2 (S2) and serotype 9 (S9) wild-type and agI/II -deficient mutant strains in the absence of porcine fibrinogen. Biofilm formation capacity was quantified after 24 h of incubation at 37 °C in the absence of porcine fibrinogen. Data represent the mean ± SEM from at least three independent experiments

MOESM4 of Serotype-specific role of antigen I/II in the initial steps of the pathogenesis of the infection caused by Streptococcus suis

Additional file 4. Percent hydrophobicity of the S. suis serotype 2 (S2) and serotype 9 (S9) wild-type and agI/II -deficient mutant strains. Hydrophobicity was determined using n-hexadecane and the non-encapsulated S. suis serotype 2 strain, S2ΔcpsF, included as a positive control. Data represent the mean ± SEM from at least three independent experiments

Genetic organization and predicted open reading frames of NSUI002 (clade I) and NSUI036 (clade V) regions containing a fucose utilization operon and <i>zmpC</i> genes.

<p>The region spans from position 1,054,531 to 1,219,953 in strain NSUI002, and contains 152 CDSs. In NSUI036, the region is notably smaller (83,658 bp). Differences in size are mainly due to the absence in the genome of strain NSUI036 of an approx. 83 kbp mobile genetic element (MGE), highlighted in light blue, that contains gene <i>tetO</i>. Other differences include a small MGE (highlighted in light blue) in NUI036 that contains gene <i>ermB</i>. In the conserved area, we observed a high degree of gene content conservation, with the exception of a <i>zmpC</i> gene also known as <i>iga</i>, encoding an IgA protease involved in <i>S</i>. <i>suis</i> virulence [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137760#pone.0137760.ref059" target="_blank">59</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137760#pone.0137760.ref060" target="_blank">60</a>], which is intact in NSUI036 but disrupted by a transposon insertion in strain NSUI002.</p

Complex Population Structure and Virulence Differences among Serotype 2 <i>Streptococcus suis - Fig 1 </i> Strains Belonging to Sequence Type 28

<p>A) Genome atlas of Canadian <i>S</i>. <i>suis</i> ST28 strain NSUI002. Depicted data from innermost to outermost circles represent genome size in Mbp (circle 1); percent G+C content (circle 2); GC skew (circle 3), (G-C)/(G+C) averaged over a moving window of 10,000 bp, with excess G and excess C shown in green and purple, respectively; annotated coding sequences (CDSs) encoded on the forward/direct (circle 4, red), and reverse/complementary (circle 5, blue) chromosomal strands; TBLASTN comparisons of the CDSs predicted in ST28 strains NSUI002 and 05HAS68 (circle 6, percent identity defined in the Fig), TBLASTN comparisons of ST28 strain NSUI002 and ST1 strain P1/7 (circle 7, percent identity defined in the Fig); reference genome landmarks (circle 8): ribosomal RNAs are labeled in green; mobile genetic elements are labeled in black, genes used in the <i>S</i>. <i>suis</i> MLST scheme are labeled in light blue; genes encoding resistance to antimicrobial agents are labeled in red; other genes are labeled in black. B) Venn diagram depicting unique and shared CDSs in each of the <i>S</i>. <i>suis</i> strains as identified by ortholog analysis. Each strain is represented by one color, and the number of CDSs are displayed in the same color. Numbers in the intersectional regions indicate CDSs shared by two or three strains. Since there may be more than one CDS in the same ortholog cluster, number of CDSs in the intersections are slightly different between strains C) Collinearity of the genomes of <i>S</i>. <i>suis</i> ST28 strains NSUI002 and 05HAS68. The genomes of the strains were aligned using progressiveMauve. Sequence alignments that are free of rearrangements are shown as colored local collinear blocks (LCBs). Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. Several genome rearrangements between NSUI002 and 05HAS68 are noticeable.</p

Complex Population Structure and Virulence Differences among Serotype 2 <i>Streptococcus suis - Fig 2 </i> Strains Belonging to Sequence Type 28

<p>A) Results of Bayesian analysis of recombination for the 51 ST28 <i>S</i>. <i>suis</i> strains. The names and countries of isolation of the strains are shown on the right. The colored bars denote the recombination events in the strains along the core genome. The coloring of the bars at a specific genomic location reflects the clustering of the recombination events into groups, and is unrelated to other bars at distant genomic locations. CAN: Canada, USA: United States of America; JAP: Japan; Tha: Thailand. B) Neighbor-joining phylogenetic tree depicting the relationships between the 51 ST28 <i>S</i>. <i>suis</i> strains. The tree was constructed using 1,421 SNPs identified against the core genome (see text for details). Two singletons and five distinct clades (I to V) were identified.</p

Presence of two component or standalone global regulators in the different ST28 and ST1 strains.

<p>Presence of two component or standalone global regulators in the different ST28 and ST1 strains.</p

Venn diagram depicting unique and shared ortholog gene clusters in each of the five clades defined among the <i>S</i>. <i>suis</i> strains.

<p>Numbers shown in the different sections indicate the numbers of ortholog groups. The two ST28 singletons were not included in this analysis.</p

Results of animal experimental infections.

<p><b>A)</b> Survival of mice inoculated with the different <i>S</i>. <i>suis</i> ST28 strains. All the mice in the NSUI002 and NSUI062 groups survived, while approx. 75% of the animals in the NSUI036 group died from septicemia or meningitis. Animals that received strains NSUI010 or NSUI081 showed reduced mortality compared to NSUI036. Significant differences in survival (LogRank test) are depicted in the Fig <b>Bacteremia at 24 h (B) and 48 h (C) post-infection (pi)</b>. NSUI002 and NSUI062 were isolated at lower titers than the other three strains following inoculation. The different symbols represent values from individual mice. The horizontal lines indicate the geometrical mean for each group. Significant differences in isolation from blood were noted at 24 h between NSUI036 and NSUI002 and NSUI062 and 48 h pi between NSUI002 and NSUI010, NSUI081 and NSUI036 and between NSUI062 and NSUI036 only (ANOVA on ranks, P < 0.05).</p