Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

The co-transfer of plasmid-borne colistin-resistant genes mcr-1 and mcr-3.5, the carbapenemase gene blaNDM-5 and the 16S methylase gene rmtB from Escherichia coli

(2019) Haiyan Long et al.   Scientific Reports

New insights into culture negative endophthalmitis by unbiased next generation sequencing

(2019) Dhanshree Deshmukh et al.   Scientific Reports

Biofilm contamination of high‐touched surfaces in intensive care units: epidemiology and potential impacts

(2019) D.M. Costa et al.   LETTERS IN APPLIED MICROBIOLOGY

Whole-genome-based analysis reveals multiclone Serratia marcescens outbreaks in a non-Neonatal Intensive Care Unit setting in a tertiary care hospital in India

(2019) Anusha Rohit et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Genome Analysis of Shigella flexneri Serotype 3b Strain SFL1520 Reveals Significant Horizontal Gene Acquisitions Including a Multidrug Resistance Cassette

(2019) Pawan Parajuli et al.   Genome Biology and Evolution

Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy

(2019) Lindsay R. Kalan et al.   Cell Host & Microbe

Nanopore sequencing: Review of potential applications in functional genomics

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

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

(2019) Steve Miller et al.   GENOME RESEARCH

Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries

(2019) Santiago-Rodriguez et al.   Genes

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

(2019) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

(2019) Heike Sichtig et al.   Nature Communications

Resolution of dynamic MDR structures among the plasmidome of Salmonella using MinION single-molecule, long-read sequencing

(2018) Ruichao Li et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

OUP accepted manuscript

(2018)   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebral Spinal Fluid Diagnostics

(2018) Patricia J Simner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics

(2018) B. Hirsch et al.   VIRCHOWS ARCHIV

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

(2018) Nicholas D Sanderson et al.   BMC GENOMICS

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

(2018) Natacha Couto et al.   Scientific Reports

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

(2018) Wei Gu et al.   Annual Review of Pathology-Mechanisms of Disease

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

(2018) Pranita D. Tamma et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Next generation sequencing-based gene panel tests for the management of solid tumors

(2018) Masayuki Nagahashi et al.   CANCER SCIENCE

Genome-based prediction of bacterial antibiotic resistance

(2018) Michelle Su et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer

(2018) Sae Ashikawa et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

(2018) Jun Cheng et al.   Annals of Clinical Microbiology and Antimicrobials

Whole Genome Sequencing of Influenza A and B Viruses With the MinION Sequencer in the Clinical Setting: A Pilot Study

(2018) Kazuo Imai et al.   Frontiers in Microbiology

MinION-based long-read sequencing and assembly extends theCaenorhabditis elegansreference genome

(2017) John R. Tyson et al.   GENOME RESEARCH

MinION as part of a biomedical rapidly deployable laboratory

(2017) Mathias C. Walter et al.   JOURNAL OF BIOTECHNOLOGY

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

(2017) Jamie K. Lemon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Microbiology and Antimicrobial Challenges of Prosthetic Joint Infection

(2017) Douglas R. Osmon   JOURNAL OF THE AMERICAN ACADEMY OF ORTHOPAEDIC SURGEONS

Introducing the Microbiome into Precision Medicine

(2017) Thomas M. Kuntz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans )

(2017) Ruibang Luo et al.   G3-Genes Genomes Genetics

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

(2017) J. Goordial et al.   Frontiers in Microbiology

Metagenomics: The Next Culture-Independent Game Changer

(2017) Jessica D. Forbes et al.   Frontiers in Microbiology

Campylobacter fetus meningitis confirmed by a 16S rRNA gene analysis using the MinION nanopore sequencer, South Korea, 2016

(2017) Jangsup Moon et al.   Emerging Microbes & Infections

Community characteristics of the gut microbiomes of competitive cyclists

(2017) Lauren M. Petersen et al.   Microbiome

Nanopore DNA Sequencing and Genome Assembly on the International Space Station

(2017) Sarah L. Castro-Wallace et al.   Scientific Reports

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

(2016) M. P. Francino   Frontiers in Microbiology

Oxford Nanopore MinION Sequencing and Genome Assembly

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

The Human Microbiome and the Future Practice of Medicine

(2015) David A. Relman   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

(2015) Kim Judge et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Next-Generation Sequencing for Infectious Disease Diagnosis and Management

(2015) Martina I. Lefterova et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics

(2015) Brittany Goldberg et al.   mBio

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY