Correction for Johnson et al., 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.; Ketheesan, Natkunam; Mayo, Mark; Hoffmaster, Alex R.; Elrod, Mindy G.; Wuthiekanun, Vanaporn; Tuanyok, Apichai; Norton, Robert; Currie, Bart J.; Wagner, David M.; Keim, Paul; 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.00313-16

Cited by 10 publications

(14 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For this confirmation, it was considered that they are unique continuous DNA regions absent in the available genome sequences of the published epidemic clones and longer than 10 kbp, flanked, at both sides, by homologous regions (especially those inserted immediately downstream of tRNA), and have lower (or higher) GC content compared with the rest of the genome ( Guo et al, 2017 ; Nunvar et al, 2017 ). The absence of DNA regions homologous to these unique GIs in the genomes of epidemic clones – B. cenocepacia ET12 and ST32 ( Holden et al, 2009 ; Nunvar et al, 2017 ) and B. multivorans ATCC_17616 and ATCC_BAA-247 ( Komatsu et al, 2003 ; Johnson et al, 2015 ; Johnson et al, 2016 ) – was confirmed and visualized by Progressive MAUVE whole genome pairwise alignment and ACT/Artemis ( Carver et al, 2005 ; Darling et al, 2010 ). Large DNA regions that respected those criteria but were not predicted by IslandViewer, were also manually identified and considered genuine-unique GIs.…”

Section: Methodsmentioning

confidence: 88%

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

et al. 2020

View full text Add to dashboard Cite

During chronic respiratory infections of cystic fibrosis (CF) patients, bacteria adaptively evolve in response to the nutritional and immune environment as well as influence other infecting microbes. The present study was designed to gain insights into the genetic mechanisms underlying adaptation and diversification by the two most prevalent pathogenic species of the Burkholderia cepacia complex (Bcc), B. cenocepacia and B. multivorans. Herein, we study the evolution of both of these species during coinfection of a CF patient for 4.4 years using genome sequences of 9 B. multivorans and 11 B. cenocepacia. This co-infection spanned at least 3 years following initial infection by B. multivorans and ultimately ended in the patient's death by cepacia syndrome. Both species acquired several mutations with accumulation rates of 2.08 (B. cenocepacia) and 2.27 (B. multivorans) SNPs/year. Many of the mutated genes are associated with oxidative stress response, transition metal metabolism, defense mechanisms against antibiotics, and other metabolic alterations consistent with the idea that positive selection might be driven by the action of the host immune system, antibiotic therapy and low oxygen and iron concentrations. Two orthologous genes shared by B. cenocepacia and B. multivorans were found to be under strong selection and accumulated mutations associated with lineage diversification. One gene encodes a nucleotide sugar dehydratase involved in lipopolysaccharide O-antigen (OAg) biosynthesis (wbiI). The other gene encodes a putative two-component regulatory sensor kinase protein required to sense and adapt to oxidative-and heavy metalinducing stresses. This study contributes to understanding of shared and speciesspecific evolutionary patterns of B. cenocepacia and B. multivorans evolving in the same CF lung environment.

show abstract

Section: Methodsmentioning

confidence: 88%

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

et al. 2020

View full text Add to dashboard Cite

show abstract

“…nov. are present in GenBank and consist of strains MSMB121 and MSMB43 T (which is the same type strain used in this study but is listed with an alternative BioProject strain identifier, 2002721687 [BioProject no. PRJNA239255 ]) ( 34 , 35 ) with GenBank assembly accession numbers GCA_000385525 and GCA_000959325 , respectively. A comparative genomics approach using LS-BSR ( 25 ) was also performed with the B. pseudomallei genome strain K96243 ( BPSS1165 to BPSS1184 ).…”

Section: Methodsmentioning

confidence: 99%

“…nov. strains MSMB121 and MSMB122 are KF378608 and KF378609 , respectively. The complete whole-genome sequence of the strain MSMB121 was published under GenBank accession numbers CP004095 and CP004096 ( 34 , 35 ). The assembly for MSMB43 T was published under GenBank assembly number GCA_001513745 and that for MSMB122 under SRA numbers SRR1956040 and LNPD00000000 .…”

Section: Methodsmentioning

confidence: 99%

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex

Tuanyok

Mayo

Scholz

et al. 2017

Appl Environ Microbiol

Self Cite

View full text Add to dashboard Cite

During routine screening for Burkholderia pseudomallei from water wells in northern Australia in areas where it is endemic, Gram-negative bacteria (strains MSMB43T, MSMB121, and MSMB122) with a similar morphology and biochemical pattern to B. pseudomallei and B. thailandensis were coisolated with B. pseudomallei on Ashdown's selective agar. To determine the exact taxonomic position of these strains and to distinguish them from B. pseudomallei and B. thailandensis, they were subjected to a series of phenotypic and molecular analyses. Biochemical and fatty acid methyl ester analysis was unable to distinguish B. humptydooensis sp. nov. from closely related species. With matrix-assisted laser desorption ionization–time of flight analysis, all isolates grouped together in a cluster separate from other Burkholderia spp. 16S rRNA and recA sequence analyses demonstrated phylogenetic placement for B. humptydooensis sp. nov. in a novel clade within the B. pseudomallei group. Multilocus sequence typing (MLST) analysis of the three isolates in comparison with MLST data from 3,340 B. pseudomallei strains and related taxa revealed a new sequence type (ST318). Genome-to-genome distance calculations and the average nucleotide identity of all isolates to both B. thailandensis and B. pseudomallei, based on whole-genome sequences, also confirmed B. humptydooensis sp. nov. as a novel Burkholderia species within the B. pseudomallei complex. Molecular analyses clearly demonstrated that strains MSMB43T, MSMB121, and MSMB122 belong to a novel Burkholderia species for which the name Burkholderia humptydooensis sp. nov. is proposed, with the type strain MSMB43T (American Type Culture Collection BAA-2767; Belgian Co-ordinated Collections of Microorganisms LMG 29471; DDBJ accession numbers CP013380 to CP013382).IMPORTANCE Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The genus Burkholderia consists of a diverse group of species, with the closest relatives of B. pseudomallei referred to as the B. pseudomallei complex. A proposed novel species, B. humptydooensis sp. nov., was isolated from a bore water sample from the Northern Territory in Australia. B. humptydooensis sp. nov. is phylogenetically distinct from B. pseudomallei and other members of the B. pseudomallei complex, making it the fifth member of this important group of bacteria.

show abstract

“…The de novo assembly was made with MIRA v4.0-1 ( 9 ) and CAP3 ( 10 ), which generated 23 contigs and a draft genome of 8.4 Mb. The N 50 value obtained was 574,923 bp, the genome was 95.06% of the B. gladioli ATCC 10248 reference genome size ( 11 ), and the G+C content estimated for the draft genome sequence was 68.04%. Prokka 1.12 ( 12 ) and the Rapid Annotations using Subsystem Technology (RAST) Web server ( 13 ) identified the presence of 7,155 coding sequence (CDS) regions and 7,540 genes, 76 of them for tRNA and 1 for transfer-messenger RNA (tmRNA).…”

Section: Genome Announcementmentioning

confidence: 93%

Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil

et al. 2018

View full text Add to dashboard Cite

show abstract

Correction for Johnson et al., Complete Genome Sequences for 59 Burkholderia Isolates, Both Pathogenic and Near Neighbor

Abstract: e00159-15, 2015.

Cited by 10 publications

References 0 publications

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex

Draft Genome Sequence of Burkholderia gladioli Coa14, a Bacterium with Petroleum Bioremediation Potential Isolated from Coari Lake, Amazonas, Brazil

Contact Info

Product

Resources

About