Number of repeat units of six VNTR loci in four clones obtained from pandemic <i>Vibrio parahaemolyticus</i> strains VpKX and PMC57.5 and mutation rates after prolonged in vitro culturing.

<p>Mutat rate: Mutation rate (x 10⁴).</p

Phylogenetic tree of the mutants from the populations of the four different clones obtained after serial subculturing of pandemic <i>V. parahaemolyticus</i>.

<p>Tree was obtained by MST-Manhattan. The founder of each cluster is indicated above the clusters.</p

Frequency of observed and expected mutants according to a geometric distribution, with 1, 2, 3, or 4 repeat unit changes for each of the clones examined.

<p>The expected frequency of mutants according to geometric distribution is shown in bold italics.</p

Frequency of mutants with increasing differences in the number of repeat units.

<p>Black bars correspond to percent of predicted mutants. Combined bars correspond to percentage of observed mutants, white sections of bars correspond to deletions and gray to insertions.</p

Phylogenetic trees for KX-1 population obtained by MST-Manhattan (A) and MST categorical (B).

<p>Each circle corresponds to the different cluster of mutants. Numbers in the lines correspond to the differences in VNTRs repeat units between clusters.</p

Phylogenetic tree of native isolates of pandemic <i>V. parahaemolyticus</i> obtained worldwide.

<p>Phylogenetic tree generated by MST-Manhattan for native isolates obtained from southern Chile (blue) northern Chile (red), Southeast Asia (brown) and Tokyo (yellow).</p

Mutation rates of VNTRs of pandemic <i>V parahaemolyticus,</i> in relation to the number of repeats in each VNTR.

<p>White circles correspond to the mutation rates observed for any VNTR, circles in black correspond to the mutation rates observed for VNTR1 in the different clones. The best fit equation for VNTR1 was y = 0.1736×–1.1245 (R² = 0.9674) while that for all the VNTRs was y =  0.1598×– 0.7923 (R² = 0.8052).</p

Multidimensional Scaling (MDS) plots from bacterial community composition observed in 72 sputum samples.

<p>Bubbles indicate relative abundances of the 4 most prevalent OTUs in the cohort: <i>P</i>. <i>aeruginosa</i> in green, <i>S</i>. <i>aureus</i> in orange, alpha-hemolytic <i>Streptococcus</i> (<i>Streptococcus</i> -1) in yellow, <i>R</i>. <i>mucilaginosa</i> in blue. 2D Stress values are given in each plot and reveal moderate stress. <b>(A)</b> Merged bubble plots from all four dominant OTUs, coloured bubbles indicating the individual abundances. <i>P</i>. <i>aeruginosa</i> as well as <i>S</i>. <i>aureus</i> have priority, whereas the abundances for <i>R</i>. <i>mucilaginosa</i> and alpha-hemolytic <i>Streptococcus</i> are in the background. (<b>B)</b> Individual MDS plots for each dominant OTU. Numbers indicate individual patients. Letters are according the order of sputum collection.</p

Comparison of prevalence of bacteria in the cohort identified by deep sequencing (NGS, grey bars) and cultivation for classical diagnostics (black bars).

<p>OTUs are listed on the left according their occurrence observed with deep sequencing. Bacteria present in >50% of all samples were categorized as highly prevalent, bacteria detectable in more than 10% of the cases were considered moderately prevalent and those observed in less than 10% of the cases were categorized as bacteria with low prevalence. Categorization follows detection rates by deep sequencing. For precise identification of bacteria see Table C in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117436#pone.0117436.s001" target="_blank">S1 File</a>. Only 71 sputum samples were taken into account (no data from cultivation for sample #20B). * Streptococcus-1 was compared with alpha-hemolytic streptococci.</p

Multidimensional Scaling (MDS) plots from bacterial community composition observed in 72 sputum samples with superimposed host factors.

<p>For a better orientation in the plot, relative abundances of <i>S</i>. <i>aureus</i> are indicated as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117436#pone.0117436.g001" target="_blank">Fig. 1B</a> (orange circles). <b>(A)</b> Age of patients superimposed on the previous MDS plot calculated for the community compositions of 72 sputum samples. Four age classes were defined for the cohort according to the statistical quartils. Symbols indicate the age of the patient at the time point of sputum collection. <b>(B)</b> Lung function of patients superimposed on the previous MDS plot defined for the community compositions of 72 sputum samples. Four classes of lung functions were calculated according to the statistical quartils of FEV₁ values measured for the patients on the day of sputum collection. Symbols indicate the four classes and samples without associated FEV₁ values. <b>(C)</b> CFTR mutations of patients superimposed on the previous MDS plot calculated for the community compositions of 72 sputum samples. Three classes of identified genotypes were determined for the cohort. Partly or completely unknown genotypes are accordingly labelled representing a fourth class.</p