Resistance genes in the plasmidomes.

<p>Heat-map analysis of resistance genes. Searches were performed on unassembled 454-pyrosequencing reads using 35 custom profile Hidden Markov Models. The gene family is shown on the x-axis and the isolate identifier is shown on the y-axis (ECO-). Black indicates that the gene was found. Employed criteria to define a gene as found: E-value = 1e-20; percent identity>92%; and percent HMM query coverage >85%.</p

Domain analysis of sequencing reads using pfam profile Hidden Markov Models.

<p>(A) Stacked bar-plot showing the number of 454 sequencing reads with hits to pfam models (E-value<1e–05). Turquoise and red colours refer to no hits and hits, respectively. Sequencing reads were conceptually translated to all six reading frames prior to searching. (B) Heat-map analysis of the domain content in the isolates (942 domains were found). The horizontal axis shows the pfam domain and the y-axis indicates the isolate. The unique pfam domain identifier is given on the horizontal axis. The colour intensity is logarithmically related to the number of sequencing reads matching the domain. The white colour indicates few reads matching a domain and colour transition to red indicates that more reads were found. Isolates are clustered after similarity. The bottom-right table indicates the number of non-redundant pfam domains per isolate; i.e., counting each domain only once. (*) The sample has likely been affected by phage-mediated DNA-degradation.</p

Distribution and properties of small cryptic plasmids.

<p>(A) Illustration of the content of small cryptic plasmids in the isolates. Circles represent plasmids and the plasmid size is shown on the y-axis in kilobases and the x-axis shows the sample ECO- identifier. (B) Neighbour-joining tree of small cryptic plasmids indicating their sequence-based relationships. Sequences were aligned with ClustalW v.2.1 and the tree was created with MEGA v.5 (default settings) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065793#pone.0065793-Tamura1" target="_blank">[35]</a>. Scale bar = substitutions per site. Support values are indicated at branches. (C and D) Sequence similarity blocks between small cryptic plasmids (violet stripes). Arrows indicate ORFs longer than 300 bp. Similarity blocks were identified with Mauve v.2.3.1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065793#pone.0065793-Darling1" target="_blank">[36]</a>, and plotted with genoPlotR v.0.8.1. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065793#pone.0065793-Guy1" target="_blank">[37]</a>. ARP = putative aminoglycoside resistance protein; T2DM = putative type II DNA- methyltransferase; RE = putative EcoVIII restriction endonuclease.</p

Plasmid characteristics and content.

a<p>Average 454 coverage is specified within parenthesis.</p><p>Abbreviations: (nd) not detected; (na) not applicable; and ∑ sum of unassigned contigs.</p

Epidemiologic strain typing and S1/PFGE plasmid profiles.

<p>(A) Total <i>E. coli</i> DNA digested with the restriction enzyme Xbal and analysed using pulse-field gel electrophoresis (PFGE). Fingerprints were analysed using BioNumerics v. 6.6. The name of the isolate and the multilocus sequence type (MLST) is indicated to the right (under ‘MLST Group’). The dendrogram to the left shows sample similarity by UPGMA clustering of PFGE patterns. The bottom scale-bar refers to size of PFGE bands in kilobases. (B) S1/PFGE analysis of extrachromosomal DNA (e.g., plasmid and phage DNA) of the ten isolates.</p

The BarA-UvrY two-component system is a virulence determinant in the urinary tract-1

<p><b>Copyright information:</b></p><p>Taken from "The BarA-UvrY two-component system is a virulence determinant in the urinary tract"</p><p>BMC Microbiology 2006;6():27-27.</p><p>Published online 10 Mar 2006</p><p>PMCID:PMC1421404.</p><p>Copyright © 2006 Tomenius et al; licensee BioMed Central Ltd.</p>rines (U1, U2 & U3). B. 1:1 mixture of and mutant was grown in the three different human urines (U1, U2 & U3) and samples were taken at the indicated time points to determine the percentage of mutant. C. The same competitions as in B. but plotted as CFU with depicted as filled diamonds and as squares

Topography AFM images of biofilms formed by UMR1 (wt), MAE52 (), MAE51 (), MAE14 (), MAE222 () and MAE619 () after growth for 24 hours on mica surfaces

<p><b>Copyright information:</b></p><p>Taken from "Roles of curli, cellulose and BapA in biofilm morphology studied by atomic force microscopy"</p><p>http://www.biomedcentral.com/1471-2180/7/70</p><p>BMC Microbiology 2007;7():70-70.</p><p>Published online 24 Jul 2007</p><p>PMCID:PMC1949822.</p><p></p

High resolution AFM images of pili-like fimbrial structures and flagella in the curli mutant MAE14 after 4 h at two different scan sizes

<p><b>Copyright information:</b></p><p>Taken from "Roles of curli, cellulose and BapA in biofilm morphology studied by atomic force microscopy"</p><p>http://www.biomedcentral.com/1471-2180/7/70</p><p>BMC Microbiology 2007;7():70-70.</p><p>Published online 24 Jul 2007</p><p>PMCID:PMC1949822.</p><p></p

The BarA-UvrY two-component system is a virulence determinant in the urinary tract-0

<p><b>Copyright information:</b></p><p>Taken from "The BarA-UvrY two-component system is a virulence determinant in the urinary tract"</p><p>BMC Microbiology 2006;6():27-27.</p><p>Published online 10 Mar 2006</p><p>PMCID:PMC1421404.</p><p>Copyright © 2006 Tomenius et al; licensee BioMed Central Ltd.</p> (110-7 and 40-6) at day 0. Urine samples and vaginal smears were collected (day 2, 5 & 7). The percentage of the mutant was determined in A. urine and B. vaginal smears

The BarA-UvrY two-component system is a virulence determinant in the urinary tract-2

<p><b>Copyright information:</b></p><p>Taken from "The BarA-UvrY two-component system is a virulence determinant in the urinary tract"</p><p>BMC Microbiology 2006;6():27-27.</p><p>Published online 10 Mar 2006</p><p>PMCID:PMC1421404.</p><p>Copyright © 2006 Tomenius et al; licensee BioMed Central Ltd.</p> day seven from the urine competitions (U1, U2 & U3) and competed against wild type in LB. Samples were taken at the indicated time points to determine the percentage of mutant. B. The same experiment as in Figure 2B but the urine was complemented with LB (see Materials & Methods)