Анімізм (з Матэрыялаў да «Тлумачальнага слоўніка славянскай міфалогіі»)

<div><p><i>Burkholderia pseudomallei</i> is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against <i>B</i>. <i>pseudomallei</i> infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 <i>B</i>. <i>pseudomallei</i> isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in <i>B</i>. <i>pseudomallei</i> were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of <i>B</i>. <i>pseudomallei</i>. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving <i>B</i>. <i>pseudomallei</i> pathogenesis, differential virulence, and efficacy to therapeutics.</p></div

Details of isolates sequenced in current study.

<p>*genome has been sequenced previously</p><p>Details of isolates sequenced in current study.</p

Correlations of LS-BSR values with observed differential virulence in BALB/c mice.

<p>*High, intermediate and low virulence determined by intranasal challenge at ~10 colony forming units.</p><p>Correlations of LS-BSR values with observed differential virulence in BALB/c mice.</p

Annotation for unique genes identified in genomes sequenced in the current study.

<p>Annotation for unique genes identified in genomes sequenced in the current study.</p

Nucleotide variant information for re-sequencing projects conducted in current study.

<p>Nucleotide variant information for re-sequencing projects conducted in current study.</p

A heatmap of blast score ratio (BSR) values [44] calculated from a known set of virulence factors characterized in <i>B</i>. <i>pseudomallei</i> (S3 Table) with the large-scale blast score ratio (LS-BSR) pipeline [43].

<p>A maximum likelihood phylogeny was inferred on a concatenation of single nucleotide polymorphisms (SNPs) and was correlated to the heatmap.</p

A maximum likelihood phylogeny inferred from a concatenation of ~63,000 core-genome single nucleotide polymorphisms (SNPs) identified in the eleven genomes sequenced in this study, shown in red, and a reference set of genomes (S2 Table).

<p>The tree was inferred with RAxML v8 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121052#pone.0121052.ref031" target="_blank">31</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121052#pone.0121052.ref032" target="_blank">32</a>] using the ASC_GTRGAMMA model and 100 bootstrap replicates. Filled circles are placed at nodes where the bootstrap support values are >90%.</p

Plots of single nucleotide polymorphism (SNP) density and homoplasy density (HD), across the two chromosomes of the reference isolate, K96243 [30].

<p>The outer ring represents the number of informative SNPs across 1-kb genomic intervals. The inner ring indicates the number of homoplasious SNPs, as determined by a retention index (RI) value <0.5 calculated by Paup [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121052#pone.0121052.ref035" target="_blank">35</a>], divided by the total number of informative SNPs over the same 1-kb genomic interval. HD and SD values were visualized with Circos [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121052#pone.0121052.ref036" target="_blank">36</a>].</p

Soil sampling locations within the United States.

<p>Soil sampling was conducted in the states of Arizona (AZ), Louisiana (LA), and Florida (FL). Yellow circles indicate the specific locations. More location information is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143254#pone.0143254.t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143254#pone.0143254.s001" target="_blank">S1 Fig</a>.</p

Maximum parsimony analysis of <i>Burkholderia</i> MLST gene sequences (2778bp) with 1,500 bootstrap replicates.

<p>All samples in bold font are isolates from this U.S. study and are labeled with a sample ID, collection state, and collection site. PubMLST sequences are labeled with species, PubMLST number, strain ID, genomovar (when available), collection country (when available), sample type (when available), and year (when available). Only bootstrap values ≥50% were reported. This tree was rooted with <i>B</i>. <i>gladioli</i>. The most parsimonious tree had a tree length of 1479 steps, a consistency index of 0.3960, and a retention index of 0.8650. Collection state: AZ = Arizona (orange text), FL = Florida (green), LA = Louisiana (purple). The tree is drawn to scale, with branch lengths calculated using the average pathway method and are in the units of the number of changes over the whole sequence. The analysis involved 75 nucleotide sequences.</p