Roary: Rapid large-scale prokaryote pan genome analysis

Page, Andrew J.; Cummins, Carla; Hunt, Martin; Wong, Vanessa; Reuter, Sandra; Holden, Matthew T. G.; Fookes, María; Keane, Jacqueline A.; Parkhill, Julian

doi:10.1101/019315

Cited by 339 publications

(415 citation statements)

References 10 publications

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“…Reads were assembled de novo using default parameters in unicycler (Wick, Judd, Gorrie, & Holt, ). Contigs were annotated using prokka (Seemann, ) and core genes were detected with roary (Page et al, ). clonalframeml (Didelot & Wilson, ) was used to generate a maximum likelihood phylogenetic tree accounting for recombination from the core genome alignment obtained from roary .…”

Section: Methodsmentioning

confidence: 99%

Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial‐resistant Escherichia coli on the Kenai Peninsula, Alaska

et al. 2019

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Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill‐foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal‐use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal‐use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.

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Section: Methodsmentioning

confidence: 99%

Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial‐resistant Escherichia coli on the Kenai Peninsula, Alaska

et al. 2019

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“…For computation of the phylogenetic tree, all the genomes were annotated with the Prokka pipeline (Seemann, ). The Gff files derived from Prokka were used as input files for the Roary pan‐genome pipeline (Page et al., ), which was used to identify the core genome of the strains. Alignment of the concatenated 2353 core genes was done with MAFFT (Katoh & Standley, ) and the tree was computed with FastTree (Price, Dehal, & Arkin, ).…”

Section: Methodsmentioning

confidence: 99%

Alterations of c‐di‐GMP turnover proteins modulate semi‐constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli

Cimdins

Simm

et al. 2017

MicrobiologyOpen

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Agar plate‐based biofilm of enterobacteria like Escherichia coli is characterized by expression of the extracellular matrix components amyloid curli and cellulose exopolysaccharide, which can be visually enhanced upon addition of the dye Congo Red, resulting in a red, dry, and rough (rdar) colony morphology. Expression of the rdar morphotype depends on the transcriptional regulator CsgD and occurs predominantly at ambient temperature in model strains. In contrast, commensal and pathogenic isolates frequently express the csgD‐dependent rdar morphotype semi‐constitutively, also at human host body temperature. To unravel the molecular basis of temperature‐independent rdar morphotype expression, biofilm components and c‐di‐GMP turnover proteins of seven commensal and uropathogenic E. coli isolates were analyzed. A diversity within the c‐di‐GMP signaling network was uncovered which suggests alteration of activity of the trigger phosphodiesterase YciR to contribute to (up)regulation of csgD expression and consequently semi‐constitutive rdar morphotype development.

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“…N. gonorrhoeae and N. meningitidis were subsampled to 20 genomes. Core genes ( n = 236) were identified and aligned with Roary v 3.12.0 . Approximate maximum likelihood phylogenetic analysis was performed using FastTree v 2.1.9 .…”

Section: Neisseria Gonorrhoeae: Clinical Manifestations and Originsmentioning

confidence: 99%

Applications of genomics to slow the spread of multidrug‐resistant Neisseria gonorrhoeae

Mortimer

Grad

2018

Annals of the New York Academy of Sciences

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Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.

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Roary: Rapid large-scale prokaryote pan genome analysis

Cited by 339 publications

References 10 publications

Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial‐resistant Escherichia coli on the Kenai Peninsula, Alaska

Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial‐resistant Escherichia coli on the Kenai Peninsula, Alaska

Alterations of c‐di‐GMP turnover proteins modulate semi‐constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli

Applications of genomics to slow the spread of multidrug‐resistant Neisseria gonorrhoeae

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