Rodent and eulipotyphlan partial cytochrome b sequences

FASTA file comprising 248 sequences generated during this study

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 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

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

Reactivity of human sera to VP1 proteins of chimpanzee and human polyomaviruses.

<p>Antibody reactivity was assessed against 4 chimpanzee polyomaviruses (ChPyV, PtrovPyV3, PtrovPyV4 and PtrosPyV2) and 2 human polyomaviruses (HPyV9 and JCPyV) using sera from German (n = 111) and of plasma samples from Ivorian subjects (n = 115). Samples were analysed for seroreactivity with a capsomer-based IgG ELISA using the VP1 major capsid protein of the above polyomaviruses as antigens. The spread of absorbance measurement is shown with green and red dots (representing the German and Ivorian panels, respectively). COVs are shown as solid lines within the graph (COVs of Germans/Ivorians: ChPyV: 0.057/0.034; PtrovPyV3: 0.046/0.070; PtrovPyV4: 0.038/0.012; PtrosPyV2: 0.081/0.080; HPyV9: 0.089/0.066; JCPyV: 0.047/0.079).</p

Competitive inhibition of seroreactivity between human and chimpanzee polyomaviruses.

a<p>Before ELISA, 2 µg/ml of VP1 antigen was used for pre-adsorption of antibodies from human sera.</p>b<p>not tested.</p

Sample material and polyomavirus content.

a<p>Muscle or other tissues from red colobus monkeys partly consumed by chimpanzees.</p

Branch support values for selected clades in VP1, VP2 and large T phylogenetic analyses.

a<p>Clades are designated by the same letter code as used in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003429#ppat-1003429-g001" target="_blank">Figure 1</a>.</p>b<p>Branch support values are given as posterior probabilities/bootstrap values. The corresponding phylogenetic trees are available as <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003429#ppat-1003429-g001" target="_blank">Figure 1</a> (VP1), <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003429#ppat.1003429.s006" target="_blank">Figure S6</a> (VP2) and <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003429#ppat.1003429.s007" target="_blank">Figure S7</a> (large T).</p>c<p>-: not a clade in the corresponding analysis.</p>d<p>na: not applicable, i.e., none of the novel polyomaviruses included in group g allowed for whole genome recovery.</p

Novel polyomaviruses detected in nonhuman primates.

a<p>Living conditions: w, wild; c, held in captivity; s, born in the wild but kept in a sanctuary.</p>b<p>DRC = Democratic Republic of Congo.</p