A whole genome phylogeny of 136 sequenced genomes in the genus <i>Acinetobacter</i>.

<p>The phylogeny was inferred with FastTree2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287-Price1" target="_blank">[52]</a> on a single nucleotide polymorphism (SNP) matrix alignment calculated with kSNP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287-Gardner1" target="_blank">[50]</a> and filtered with noisy <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287-Dress1" target="_blank">[51]</a>. The phylogeny was rooted with <i>A. radioresistens</i>. Genomes sequenced in the current study are shown in red. Genomes in the <i>Acinetobacter calcoaceticus-baumannii</i> (<i>Acb</i>) complex are colored by clade.</p

Annotation details of lost and acquired genes in the evolution of <i>A. baumannii</i>.

*<p><i>Acb</i> = <i>Acinetobacter calcoaceticus-baumannii</i>, b = <i>baumannii</i>, n = <i>nosocomialis</i>.</p

A heatmap of blast score ratio (BSR) [<b>57</b>] values for branch specific regions in the <i>Acb</i> complex.

<p>BSR values were visualized with the multi-experiment viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287-Saeed1" target="_blank">[58]</a>. Samples were clustered using an average linkage clustering algorithm. Numbers for each feature correlate with features described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone-0054287-t001" target="_blank">Table 1</a>. Raw data values are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287.s007" target="_blank">Table S5</a>.</p

A heatmap of blast score ratio (BSR) [<b>57</b>] values for efflux pump and beta-lactamase genes identified in <i>Acinetobacter</i>.

<p>BSR values were visualized with the multi-experiment viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287-Saeed1" target="_blank">[58]</a>. Accession details for each gene are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287.s005" target="_blank">Table S3</a>, with raw data shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054287#pone.0054287.s007" target="_blank">Table S5</a>.</p

MRSA_phylogenetic_trees_data_Luxembourg

This data file contains SNP matrices used to build phylogenetic trees. The matrices are provided in both .fasta format (the input that MEGA accepts) and Excel file format. The phylogenetic trees are provided in MEGA tree session format (MEGAsoftware.net)

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

SupportingInformationS3

S3. Rooted maximum parsimony tree of C. burnetii MST genotypes (1-34 and Dugway) after Hornstra et al. (Hornstra, Priestley, et al. 2011). Whole genome sequences are mapped onto the tree and the major genomic groups of C. burnetii are identified

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

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

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