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Publications tagged "WIMP"

Differentiation of capripox viruses by nanopore sequencing

The genus capripoxvirus (CaPV), family Poxviridae, includes three virus species: goatpox virus (GPV), sheeppox virus (SPV) and lumpy skin disease virus (LSDV). CaPV causes disease outbreaks with con...

Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbi...

Association of Streptococcus mutans harboring bona-fide collagen binding proteins and Candida albicans with early childhood caries recurrence

Early childhood caries (ECC) recurrence occurs in approximately 40% of treated cases within one year. The association of Streptococcus mutans and Candida albicans with the onset of ECC is well known...

Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater

In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of t...

The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study

Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect o...

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial geno...

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China

The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for “Candidatus Liberibacter asiaticus (Las)”, the bacterial pathogen associated with the d...

The microbiome of Leonardo da Vinci’s drawings: a bio-archive of their history

Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic document...

Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

High throughput sequencing is currently revolutionizing the genomics field and providing new approaches to the detection and characterization of microorganisms. The objective of this study was to as...

Rapid and accurate species identification of mitis group Streptococci using the MinION Nanopore sequencer

Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and ...

Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing

Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portabil...

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an...

DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods. Performing shotgun metagenomi...

Rapid and real-time identification of fungi up to the species level with long amplicon nanopore sequencing from clinical samples

The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-2...

Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibilit...

Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics

The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior...

Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

Routine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technolog...

Diagnosis and characterization of canine distemper virus through sequencing by MinION nanopore technology

Prompt identification of the causative pathogen of an infectious disease is essential for the choice of treatment or preventive measures. In this perspective, nucleic acids purified from the brain t...

Microbiota profiling with long amplicons using nanopore sequencing: full-length 16S rRNA gene and whole rrn operon

Background: Profiling the microbiome on low biomass samples is challenging for metagenomics since these samples are prone to present DNA from other sources, such as the host or the environment. The ...

Diagnosis of plant diseases using Nanopore sequencing platform

Reliable detection and identification of plant pathogens are essential for disease control strategies. Diagnostic methods commonly used to detect plant pathogens have limitations such as requirement...

Measuring Soil Health With Nanopore Sequencing

If a farmer wants to understand the health and fertility of their soil, they could send a sample to a lab for chemical analysis. This produces useful data, including levels of: 1) nitrogen, 2) phosp...

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

We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly ...

What’s in my pot? Real-time species identification on the MinION

Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted becaus...

BioMed Central blog: Real-time surveillance with nanopore-seq

Rafal Marszalek at Genome Biology notes that “Lessons about the epidemic control are usually learned the hard way. So what have we learned from the most recent outbreaks of Ebola and other diseases,...

Oxford Nanopore MinION Applications: Kits and Tools, Genetics and Metagenomics

The Applications team at Oxford Nanopore has two overarching responsibilities: creation and development of sample and library preparation protocols for a wide variety of sample types, and undertakin...

Applications of Long-read Sequencing in Infectious Disease Genomics

Next generation sequencing technology has revolutionised the study of microbial genomics, but most large-scale studies have focused on short-read sequencing. This use of short-read sequencing has li...

A year of happy MAPping

In this talk I will cover the highs and lows of being part of the Oxford Nanopore MinION Access Programme. Our laboratory joined the MAP programme in May 2014. Soon afterwards we published the first...

Nanopore sequencing – disruptive technology in clinical microbiology?

The diagnosis of infectious diseases by culture takes at least two days: one to grow the bacteria and then, at best, one to identify pathogens and test their antimicrobial susceptibility. Meanwhile ...

Real-time identification of pathogens and antibiotic resistance profile using Oxford Nanopore sequencing

Clinical pathogen sequencing has been demonstrated to have a positive outcome on treatment of patients with unknown bacterial infection. However, widespread adoption of clinical pathogen sequencing ...

Rapid short-read sequencing and aneuploidy detection using MinION nanopore technology

MinION™ is a memory stick-sized, nanopore-based sequencer primarily designed for single-molecule sequencing of long DNA fragments (>6 kb). We developed a library preparation and data analysis met...

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

We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly ...

Real-time digital pathogen surveillance — the time is now

It is time to shake up public health surveillance. New technologies for sequencing, aided by friction-free approaches to data sharing, could have an impact on public health efforts.

MinIONs and Nanofrogs

Until today, the investigation of the biological diversity of many parts of the world has been obstructed by the inability to perform field based DNA analysis, especially in those regions where the ...

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 pati...

Yaniv Erlich: A vision for Ubiquitous Sequencing

Yaniv Erlich outlines his vision for a future where “the next goal of the revolution can be ushered in by the advent of sequencing sensors – miniaturized sequencing devices that are manufactured for...