The optimal standard protocols for whole-genome sequencing of antibiotic-resistant pathogenic bacteria using third-generation sequencing platforms

Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017

(2021) Ji-Yeon Hyeon et al.   Pathogens

Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination

(2020) Bas Berbers et al.   Antibiotics-Basel

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

(2019) Sarah Goldstein et al.   BMC GENOMICS

Nanopore sequencing: Review of potential applications in functional genomics

(2019) Nobuaki Kono et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

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

(2019) Nicola De Maio et al.   Microbial Genomics

The Traveler-associated High-level Ciprofloxacin-resistant Salmonella enterica Serovar Kentucky in the Republic of Korea

(2019) Ae Kyung Park et al.   Journal of Global Antimicrobial Resistance

The Epidemiology of Carbapenem-Resistant Enterobacteriaceae: The Impact and Evolution of a Global Menace

(2017) Latania K. Logan et al.   JOURNAL OF INFECTIOUS DISEASES

Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk

(2017) Célia M. Manaia   TRENDS IN MICROBIOLOGY

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance GeneblaKPC

(2016) Anna E. Sheppard et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis

(2016) Gema Lucena-Aguilar et al.   BIOPRESERVATION AND BIOBANKING

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids

(2016) Susu He et al.   mBio

DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis

(2016) Gema Lucena-Aguilar et al.   Biopreservation and Biobanking

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

(2016) Laura Becker et al.   Scientific Reports

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

(2015) Kathryn E. Holt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quality scores for 32,000 genomes

(2015) Miriam L Land et al.   Standards in Genomic Sciences

A first look at the Oxford Nanopore MinION sequencer

(2014) Alexander S. Mikheyev et al.   Molecular Ecology Resources

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Improved workflows for high throughput library preparation using the transposome-based nextera system

(2013) Sarah Lamble et al.   BMC BIOTECHNOLOGY

Rapid bacterial genome sequencing: methods and applications in clinical microbiology

(2013) C. Bertelli et al.   CLINICAL MICROBIOLOGY AND INFECTION

Characterization of integrons and their cassettes in Escherichia coli and Salmonella isolates from poultry in Korea

(2013) H. K. Dessie et al.   POULTRY SCIENCE

Systematic biases in DNA copy number originate from isolation procedures

(2013) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

(2012) Anthony P. Underwood et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC)

(2011) Elzbieta Brzuszkiewicz et al.   ARCHIVES OF MICROBIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY