Occurrence and distribution of the 34 PCR-TTGE bands observed among the <i>Aeromonas</i> population.

a<p>Bold type indicates bands which were successfully sequenced (GenBank accession numbers JX014439-JX014453 and JX453432-JX453445).</p>b<p>Bold type indicates that all patterns with the corresponding band showed heterogeneity.</p>c<p>Bold and italics, bands only found in one taxon; bold and underlined, bands found in all representatives of a taxon for taxa including more than one strain (bold, italics and underlined combined for band 38 in <i>A. sobria</i>).</p

Time-kill kinetics of different NaCl concentrations against <i>P. aeruginosa</i> isolate Pa71.

<p>3% NaCl solution (orange line, filled triangles), 5% NaCl solution - corresponding to the MBC value (violet line, dash), 7% NaCl solution (red line, filled circles), and 10% NaCl solution (green line, filled squares). Control (blue line, filled lozenges) was not exposed to NaCl. Time-kill curves of 15% (not shown) and 10% NaCl solution were similar.</p

Distribution of the 171 strains (n = 148) and clones (n = 23) of <i>O. intermedium</i>/<i>O. ciceri</i> identified from the litterature and databases according to the habitat.

<p>The figure has been constructed from data presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376.s003" target="_blank">Tables S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376.s004" target="_blank">S2</a>.</p

Schematic representation of I-<i>Ceu</i>I-restricted DNA fragment sizes for <i>Aeromonas</i> spp. strains with 10 <i>rrn</i> operons.

<p>Data were given for the 142 <i>A. veronii</i>, <i>A. hydrophila</i>, <i>A. aquariorum</i>, <i>A. caviae</i> and <i>A. salmonicida</i> strains with 10 <i>rrn</i> operons with the aim to illustrate interspecific variability between the 5 taxa and the intraspecific variability for the 3 main species. I-<i>Ceu</i>I-restricted DNA fragments were numbered in size descending order; the size of the largest fragment 1 was not measured (as discussed in the text). A to F, size distribution for fragments 2 to 7, respectively. Fragment mean sizes (in kilobases) were indicated in the corresponding tables according to the species and by a blue line in the corresponding scheme A to F. Standard deviation values (SD) and coefficient of variation (CV) were indicated in kb and %, respectively, in the corresponding tables according to the species except for species with less than 10 representatives; +/−1 SD were represented by black dotted lines and +/−2 SD by red dotted lines in the corresponding scheme A to F. Schematic representations for the 3 smallest fragments with mean size lower than 97 kb (mean size and SD of 93.7±23 kb, 66.7±9.1 kb and 40.5±7.5 kb, respectively) were not presented here because they were not informative.</p

Activity of 7% and 10% NaCl solution against preformed biofilm for three strongly adherent isolates.

<p>7% (green bars) and 10% (violet bars) NaCl solution was tested against preformed biofilm for the three <i>P. aeruginosa</i> CF isolates Pa28, Pa29, and Pa31. Results are expressed as percentage of biofilm viability compared to non-exposed control after 24 h of NaCl exposure.</p

Number of <i>rrn</i> operons and PCR-TTGE patterns for the 195 <i>Aeromonas</i> strains of the study.

<p>Results are presented according to the structure of the population observed in multilocus phylogenetic analysis (MLPA). Unrooted maximum-likelihood tree was based on concatenated sequences of five housekeeping genes (<i>gltA</i>, <i>gyrB</i>, <i>rpoB</i>, <i>tsf</i> and <i>zipA</i> genes), as described in Roger <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046268#pone.0046268-Roger1" target="_blank">[13]</a>. Only type and references strains are indicated within clades on the tree. The horizontal lines show genetic distance, the scale bar indicating the number of substitutions per nucleotide position. The numbers at the nodes are support values estimated with 100 bootstrap replicates. Only bootstrap values >70 are indicated on the tree. When all members of a clade shared identical features, the common <i>rrn</i> operon number and/or PCR-TTGE pattern was indicated. * The <i>A. caviae</i> clade included the type strain <i>A. caviae</i> CECT 838^T displaying an external position to other members of the <i>A. caviae</i> clade in the tree.</p

Characteristics of the 49 <i>O. intermedium</i> strains of human origin included in this study presented according to MLST results.

<p>CC, clonal complex; ST, sequence type; Fr, France; USA, United States of America; CF, Cystic Fibrosis. Strains marked by * or ** were isolated in the same patient.</p><p>^a For each locus, each different allele was assigned an arbitrary number;</p><p>^b 46-bp atypical insertion described in Teyssier et al. 2003 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083376#pone.0083376-Teyssier1" target="_blank">[9]</a>.</p

Comparison of NaCl Minimal Inhibitory Concentration (MIC), Minimal Bactericidal Concentration (MBC) and Killing quotient (KQ) distributions for subgroups of <i>P. aeruginosa</i> CF isolates according to mucoid characteristic, antimicrobial susceptibility pattern, ability to form biofilm and patient under HTS treatment.

<p>MIC₅₀ and MIC₉₀ values were defined as the lowest concentration of NaCl at which 50% and 90% of the isolates were inhibited, respectively.</p>a<p>Only isolates exhibiting MBC values within tested range were considered.</p>b<p>5 isolates recovered in one patient.</p>c<p>isolates were randomly selected.</p>d<p>Comparison of MIC, MBC and KQ distribution between subgroups was performed with Mann-Whitney’s test, with the exception of the evaluation depending on biofilm producer groups, assessed by the Kruskal-Wallis’ test, and Spearman correlation coefficient (Rs) when Kruskal-Wallis’ test was positive. A <i>P</i> value ≤0.05 was considered to reflect significance and was indicated in bold type.</p><p>ND, not determined either because only one isolate or one patient was included in the sub-population, or because one isolate exhibiting a MBC value within the tested range.</p

Minimum-Spanning (MS) tree for 64 strains of <i>O. intermedium</i> and type strain of <i>O. ciceri</i> based on MLST data.

<p>The tree was based on the allelic profiles. Each circle corresponds to a sequence type (ST). The number given in the circle corresponds to the ST designation. The number given near the circle corresponds to the number of isolates forming the ST. Shading areas indicate the clonal complexes (CC68, CC74, CC76, CC91, CC93 and CC96). (A) MS tree depending on the clinical (red circles) or environmental origin (green circles) of the strains. (B) MS tree depending on the geographical origin of the strains.</p

NaCl Minimal Inhibitory Concentration (MIC), Minimal Bactericidal Concentration (MBC) and Killing quotient (KQ) distributions for the 85 CF isolates and the 4 reference strains of <i>P. aeruginosa.</i>

<p>MIC₅₀ and MIC₉₀ values were defined as the lowest concentration of NaCl at which 50% and 90% of the isolates were inhibited, respectively.</p>a<p>Only isolates exhibiting MBC values within tested range were considered.</p