Interactive microbial genome visualization with GView

Petkau, A.; Stuart-Edwards, Matthew; Stothard, Paul; Domselaar, Gary Van

doi:10.1093/bioinformatics/btq588

Cited by 328 publications

(270 citation statements)

References 7 publications

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“…The strains appear in the following order, from outer circle to inner: SBW25, Pf0-1, A506, F113, NCIMB11764, WH6, SS101, Q2-87, and R124. Analysis and images done using the GView server (Petkau et al 2010) proportion around the origin of replication ( Fig. 5.3a) and strain-specific genes highest in the third of the genome surrounding the terminus, consistent with previous observations that levels of synteny decrease with distance from the origin Silby et al 2009).…”

Section: Genome Organizationsupporting

confidence: 88%

“…The small core genome, representing only 45-52 % of the total proteome of each strain, highlights the extreme diversity among the strains tested and combined with phylogenomic analyses has led to the reassignment of several of the strains to other species. Here, we define a more stringent P. fluorescens core genome-that is, the set of orthologous genes common to strains that currently retain the P. fluorescens designation-in a multiway BLAST analysis via the GView server (Petkau et al 2010). Using e-value and percent identity cutoffs of 1 e -10 and 80 %, respectively, a core genome of 2,396 predicted CDSs was defined (Fig.…”

Section: Genome Organizationmentioning

confidence: 99%

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Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Seaton

Silby

2014

Genomics of Plant-Associated Bacteria

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Section: Genome Organizationsupporting

confidence: 88%

Section: Genome Organizationmentioning

confidence: 99%

Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Seaton

Silby

2014

Genomics of Plant-Associated Bacteria

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“…We conducted an analysis in PhyML using a generalized time-reversible (GTR) model of nucleotide substitution with a gamma distribution; this was repeated for 1000 bootstrap replicates. Additionally, core genes (those present among all isolates) were visualized using GView (Petkau et al, 2010). …”

Section: Methodsmentioning

confidence: 99%

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates

et al. 2016

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Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

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“…De novo assembly was performed with the A5-miseq pipeline (16), followed by annotation with the Prodigal program (version 2.60) (17) and a search of the NCBI nucleotide database for homologous sequences by use of the BLASTP program (14). A BLAST Atlases view was generated using a search for homologous sequences by use of the BLASTN program and the GView program (18). A search for the replicon type of the query contigs was performed by use of a search for sequences homologous to the amplicon sequences generated by PCR-based replicon typing (PBRT) and by use of an E value of Ͻ1EϪ10, a cover ratio of Ն90%, and the BLASTN program (19).…”

mentioning

confidence: 99%

Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

Akiba

Sekizuka

Yamashita

et al. 2016

Antimicrob Agents Chemother

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kTo determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The bla NDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: bla NDM-1 in 2 isolates, bla NDM-5 in 7 isolates, and bla NDM-7 in 5 isolates. The bla CTX-M gene was detected in 112 isolates (66.3%): bla CTX-M-15 in 108 isolates and bla CTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the bla NDM -positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.

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Interactive microbial genome visualization with GView

Cited by 328 publications

References 7 publications

Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates

Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

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