Additional file 3: of Rickettsia vini n. sp. (Rickettsiaceae) infecting the tick Ixodes arboricola (Acari: Ixodidae)

Maximum Likelihood phylogenetic tree based on the partial ompB gene including a sequence for Rickettsia vini n. sp. (DOCX 639 kb

Additional file 4: of Rickettsia vini n. sp. (Rickettsiaceae) infecting the tick Ixodes arboricola (Acari: Ixodidae)

Maximum Likelihood phylogenetic tree based on the partial htrA gene including a sequence for Rickettsia vini n. sp. (DOCX 522 kb

Dendrogram of resistant <i>E. coli</i> isolates’ PFGE profiles.

<p>Generated by cluster analysis of the Dice similarity indices in the BioNumerics fingerprinting software (optimization 1%, band matching tolerance 1%, tolerance change 1%). Isolates marked with “cip” were obtained by cultivation on ciprofloxacin and harbored PMQR genes, isolates with “ctx” represent the CTX-M-15 producing <i>E. coli</i>. “H” isolate from human, “D” isolate from dog, “C” isolate from cat.</p

Characteristics of ESBL-producing isolates from villages.

<p>All isolates were obtained on MCA-cefotaxime.</p><p>“D” – isolate from dog, “H” – isolates from human, “C” – isolate from cat. “T” in brackets means that the resistance gene was successfully transformed into competent cells, “C” in brackets means that the gene was conjugated. Plasmids were isolated and characterized from isolates in bold font. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113548#pone-0113548-t002" target="_blank">Table 2</a> for plasmid characteristics.</p><p>PG = phylogroup, Amp = ampicillin, Cef = cephalotin, Caz = ceftazidime, Amc = amoxycilin-clavulanate, Nal = nalidixic acid, Cip = ciprofloxacin, Tet = tetracycline, Sxt = trimethoprim-sulfamethoxazole, Spt = streptomycin, Sul = sulfonamides compounds, Gen = gentamicin, Chl = chloramphenicol, Cpd = cefpodoxime.</p><p>Characteristics of ESBL-producing isolates from villages.</p

Characteristics of plasmids obtained by transformation.

<p>“NT”–not typable. Note: transconjugants obtained in this study contained more than one plasmid and therefore were not used for plasmid characterization.</p><p>Characteristics of plasmids obtained by transformation.</p

Characteristics of isolates with PMQR genes.

<p>Isolates were obtained on MCA-ciprofloxacin.</p><p>For legend see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0113548#pone-0113548-t001" target="_blank">table 1</a>.</p><p>Characteristics of isolates with PMQR genes.</p

ST131GBK

Collection of annotated genomes used in the analysis of this stud

Maximum likelihood phylogeny of the ST131 core genome, with the accessory genome profile overlaid.

<p>Clades A, B and C are colour coded by branch (blue, cyan, and magenta respectively). The accessory genome is presented as a heatmap (red = high identity to blue = low identity) of pairwise Spearman correlations of the accessory gene content between each strain, such that warmer colours indicate subsets of isolates with substantially more similar gene content between them than on average between randomly chosen isolates. The colour coding to the right indicates the accessory genome cluster of each strain as determined by Kpax2.</p

Maximum likelihood phylogeny of the ST131 core genome, with gene regulatory region allele profiles overlaid.

<p>Clades A, B and C are colour coded by branch (blue, cyan, and magenta respectively). The gene regulatory region allele profiles are presented as a heatmap (red = high identity to blue = low identity) of pairwise Spearman correlations of the regulatory region alleles between each strain, such that warmer colours indicate subsets of isolates with substantially more similar regulatory region alleles between them than on average between randomly chosen isolates. The colour coding to the right indicates the accessory genome cluster of each strain as determined by Kpax2.</p

Maximum likelihood phylogeny of 228 <i>E</i>. <i>coli</i> ST131 isolates.

<p>Strains isolated from dogs and cats (domesticated animals), wild birds (avian), and cattle (livestock) are indicated by colour coding at the tips of the tree, with all other strains not colour coded being human isolates. Clades A, B and C are indicated by colour coding of the branches. The large black circles indicate statistically significant inferences of host jumps or ecological adaptations within the phylogeny as detected by AdaptML. The grey circles indicate phylogenetic inferences with > 99% bootstrap support. The names of the taxa match those in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006280#pgen.1006280.s009" target="_blank">S1 Table</a>.</p