Complete Genome Sequences for 59
            <i>Burkholderia</i>
            Isolates, Both Pathogenic and Near Neighbor

Johnson, Shannon L.; Bishop‐Lilly, Kimberly A.; Ladner, Jason T.; Daligault, Hajnalka E.; Davenport, Karen W.; Jaissle, J.; Frey, K. G.; Koroleva, G. I.; Bruce, David; Coyne, S. R.; Broomall, S. M.; Li, Po-E; Teshima, Hazuki; Gibbons, Henry S.; Palacios, Gustavo; Rosenzweig, C. Nicole; Redden, C. L.; Xu, Yan; Minogue, Timothy D.; Chain, Patrick

doi:10.1128/genomea.00159-15

Cited by 69 publications

(51 citation statements)

References 20 publications

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“…G+C composition values were 66.3%, 66.9%, and 65.5% for each chromosome, respectively. The number of chromosomes, their lengths, and the high G+C content are similar to previously sequenced Bcc strains (see references 2 and 3 or Bcc taxid: 87882 on http://www.ncbi.nlm.nih.gov/genome/browse/). …”

Section: Genome Announcementsupporting

confidence: 76%

Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

et al. 2016

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Section: Genome Announcementsupporting

confidence: 76%

Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

et al. 2016

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“…Reads (9–12 million reads per replicate) were trimmed using the Trimmomatic tool [59] and mapped to the B . dolosa AU0158 genome (GenBank assembly accession GCA_000959505.1) [60] using BowTie2 using very sensitive local preset settings [61]. Differentially expressed genes were identified using CuffDiff using Benjamini–Hochberg procedure to determine the q value ( p value corrected for multiple comparisons) [62].…”

Section: Methodsmentioning

confidence: 99%

An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity

et al. 2017

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Burkholderia dolosa is a member of the Burkholderia cepacia complex (BCC), which is a group of bacteria that cause chronic lung infection in patients with cystic fibrosis (CF) and can be associated with outbreaks carrying high morbidity and mortality. While investigating the genomic diversity of B. dolosa strains collected from an outbreak among CF patients, we previously identified fixL as a gene showing signs of strong positive selection. This gene has homology to fixL of the rhizobial FixL/FixJ two-component system. The goals of this study were to determine the functions of FixLJ and their role in virulence in B. dolosa. We generated a fixLJ deletion mutant and complemented controls in B. dolosa strain AU0158. Using a fixK-lacZ reporter we found that FixLJ was activated in low oxygen in multiple BCC species. In a murine pneumonia model, the B. dolosa fixLJ deletion mutant was cleared faster from the lungs and spleen than wild-type B. dolosa strain AU0158 at 7 days post infection. Interestingly, the fixLJ deletion mutant made more biofilm, albeit with altered structure, but was less motile than strain AU0158. Using RNA-seq with in vitro grown bacteria, we found ~11% of the genome was differentially expressed in the fixLJ deletion mutant relative to strain AU0158. Multiple flagella-associated genes were down-regulated in the fixLJ deletion mutant, so we also evaluated virulence of a fliC deletion mutant, which lacks a flagellum. We saw no difference in the ability of the fliC deletion mutant to persist in the murine model relative to strain AU0158, suggesting factors other than flagella caused the phenotype of decreased persistence. We found the fixLJ deletion mutant to be less invasive in human lung epithelial and macrophage-like cells. In conclusion, B. dolosa fixLJ is a global regulator that controls biofilm formation, motility, intracellular invasion/persistence, and virulence.

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“…The global B. pseudomallei collections 12,13,15,27,[50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65] and newly sequenced data used in this study are divided into a discovery dataset (1,136 isolates) and a validation dataset (875 isolates) (Extended Data Fig 1a & b). Their accession numbers are tabulated in Supplementary table 1.…”

Section: Whole-genome Sequencing Collections Mapping and Annotationmentioning

confidence: 99%

Co-evolutionary signals fromBurkholderia pseudomalleigenomics identify its survival strategies and highlight improving environmental health as prevention policy

Chewapreecha

Pensar

Chattagul

et al. 2020

Preprint

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The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and sub-tropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies, gene expression analysis, and gene knockout assays to uncover genetic markers that have been repeatedly selected through B. pseudomallei evolution. These enabled us to identify a large number of mutation pairs under co-selection in distinct genes and non-coding RNA, of which a majority (61.5%) of signals detected in the discovery dataset can be replicated in the validation dataset (totalling 2,011 genomes). Genes under co-selection are mostly conditionally expressed with marked expression correlation of gene-gene pairs found in physical stress conditions. We discovered a putative adhesin (BPSL1661) as a hub of co-selection signals and experimentally confirmed the essential role of BPSL1661 under nutrient deprivation. The gene co-selection network surrounding BPSL1661 likely offers B. pseudomallei a selective advantage to survive nutrient limited conditions. We propose that anthropogenic activities such as pre- and post-harvest crop residue burning have accelerated soil nutrient depletion and may have directly contributed to the preferential survival of B. pseudomallei over benign soil microorganisms. This is expected to lead to a consequent increase in the incidence of melioidosis should the slash-and-burn practices continue to expand.

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Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor

Cited by 69 publications

References 20 publications

Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67)

An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity

Co-evolutionary signals fromBurkholderia pseudomalleigenomics identify its survival strategies and highlight improving environmental health as prevention policy

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