whole_genome_Bayes

whole_genome_Baye

whole_genome_phyml

whole_genome_phym

MTBC_SNP_Bayes

MTBC_SNP_Baye

H37Rv_SNP_Bayes

H37Rv_SNP_Baye

MTBC_SNP_align_200.phy_phyml_tree

MTBC_SNP_align_200.phy_phyml_tre

Characteristics of <i>E. cloacae</i> MLST loci.

*<p>Based on the sequences of the genome strains.</p><p># Nonsynonymous synonymous to synonymous substitution ratio.</p

Anlaysis of neutrality tests of genes used to develope the MLST scheme.

<p>Tajima's D statistic <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066358#pone.0066358-Tajima1" target="_blank">[12]</a>, Fu's D and F statistic <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066358#pone.0066358-Fu1" target="_blank">[13]</a> and Ramos-Onsins & Rozas' R2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066358#pone.0066358-RamosOnsins1" target="_blank">[14]</a> were analyzed using DnaSP 5.10.1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066358#pone.0066358-Rozas1" target="_blank">[15]</a>.</p>*<p>Statistically significant (P<0.05).</p><p>ns: Non significant.</p

Primers for <i>E. cloacae</i> MLST scheme.

*<p>These primers were used for sequencing of respective amplicons.</p

Unrooted UPGMA tree of concatenated sequences from combinations of seven MLST loci.

<p>Phylogenetic analysis using concatenated MLST loci created by the STRAT2 software was performed using CLUSTAL W hosted by DNA Data Bank of Japan (<a href="https://www.ddbj.nig.ac.jp" target="_blank">https://www.ddbj.nig.ac.jp</a>). The dataset used contained only one isolate/ST to prevent bias toward a clonal population for strains with the same epidemiological history. The tree was drawn using FigTree v1.4 (<a href="http://tree.bio.ed.ac.uk/software/figtree/" target="_blank">http://tree.bio.ed.ac.uk/software/figtree/</a>). Circles indicate each clade.</p

Accession number of allele identified in this study.

<p>Accession number of allele identified in this study.</p