Cargando…

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (...

Descripción completa

Detalles Bibliográficos
Autores principales:	De Maio, Nicola, Shaw, Liam P., Hubbard, Alasdair, George, Sophie, Sanderson, Nicholas D., Swann, Jeremy, Wick, Ryan, AbuOun, Manal, Stubberfield, Emma, Hoosdally, Sarah J., Crook, Derrick W., Peto, Timothy E. A., Sheppard, Anna E., Bailey, Mark J., Read, Daniel S., Anjum, Muna F., Walker, A. Sarah, Stoesser, Nicole
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Microbiology Society 2019
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6807382/ https://www.ncbi.nlm.nih.gov/pubmed/31483244 http://dx.doi.org/10.1099/mgen.0.000294

Ejemplares similares

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
por: Gweon, H. Soon, et al.
Publicado: (2019)

A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage
por: AbuOun, Manal, et al.
Publicado: (2021)

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
por: Shaw, Liam P., et al.
Publicado: (2021)

Genomic network analysis of environmental and livestock F-type plasmid populations
por: Matlock, William, et al.
Publicado: (2021)

A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone
por: Smith, Richard P., et al.
Publicado: (2023)

Use of whole genome sequencing of commensal Escherichia coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018
por: Stubberfield, Emma, et al.
Publicado: (2019)

Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain
por: AbuOun, Manal, et al.
Publicado: (2020)

Corrigendum: Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain
por: AbuOun, Manal, et al.
Publicado: (2021)

The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance
por: Duggett, Nicholas, et al.
Publicado: (2020)

Whole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials
por: Stubberfield, Emma, et al.
Publicado: (2021)

Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in Brachyspira hyodysenteriae, Aetiological Agent of Swine Dysentery
por: Card, Roderick M., et al.
Publicado: (2018)

A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database
por: Orlek, Alex, et al.
Publicado: (2017)

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids
por: Orlek, Alex, et al.
Publicado: (2017)

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology
por: Orlek, Alex, et al.
Publicado: (2017)

Reconciling the Potentially Irreconcilable? Genotypic and Phenotypic Amoxicillin-Clavulanate Resistance in Escherichia coli
por: Davies, Timothy J., et al.
Publicado: (2020)

Isolation of the human-associated bla (CTX-M-15)-harbouring Klebsiella pneumoniae ST307 from a tortoise in the UK
por: Foster, Geoffrey, et al.
Publicado: (2020)

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
por: Sanderson, Nicholas D., et al.
Publicado: (2020)

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
por: Sheppard, Anna E., et al.
Publicado: (2018)

Cefotaxime Resistant Escherichia coli Collected from a Healthy Volunteer; Characterisation and the Effect of Plasmid Loss
por: Kirchner, Miranda, et al.
Publicado: (2013)

Novel Inducers of the Envelope Stress Response BaeSR in Salmonella Typhimurium: BaeR Is Critically Required for Tungstate Waste Disposal
por: Appia-Ayme, Corinne, et al.
Publicado: (2011)

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania
por: Phan, H T T, et al.
Publicado: (2018)

Evaluation of methods for detecting human reads in microbial sequencing datasets
por: Bush, Stephen J., et al.
Publicado: (2020)

Flanker: a tool for comparative genomics of gene flanking regions
por: Matlock, William, et al.
Publicado: (2021)

Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193
por: Sheppard, Anna E., et al.
Publicado: (2016)

Virulence Characterization of Salmonella enterica by a New Microarray: Detection and Evaluation of the Cytolethal Distending Toxin Gene Activity in the Unusual Host S. Typhimurium
por: Figueiredo, Rui, et al.
Publicado: (2015)

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
por: Bush, Stephen J, et al.
Publicado: (2020)

Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals
por: Lumley, Sheila F, et al.
Publicado: (2021)

Optimized use of Oxford Nanopore flowcells for hybrid assemblies
por: Lipworth, Samuel, et al.
Publicado: (2020)

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing
por: Anson, Luke W., et al.
Publicado: (2018)

Corrigendum: Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches
por: George, Sophie, et al.
Publicado: (2018)

Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches
por: George, Sophie, et al.
Publicado: (2017)

Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage
por: Storey, Nathaniel, et al.
Publicado: (2022)

DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples
por: George, Sophie, et al.
Publicado: (2020)

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
por: Sanderson, Nicholas D., et al.
Publicado: (2023)

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, bla(KPC), in Klebsiella Species Is Elusive but Not Rare
por: Mathers, Amy J., et al.
Publicado: (2017)

Temperature and Oxygen Dependent Metabolite Utilization by Salmonella enterica Serovars Derby and Mbandaka
por: Hayward, Matthew R., et al.
Publicado: (2015)

Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis
por: Orlek, Alex, et al.
Publicado: (2023)

Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria
por: Olorunleke, Solomon O., et al.
Publicado: (2022)

Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens
por: Lopez-Garcia, Angela V., et al.
Publicado: (2023)

Corrigendum: Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens
por: Lopez-Garcia, Angela V., et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_m51spol5g9lcfsk8rdcrsmigai