Pathogen Analysis & Surveillance
Nanopore sequencing on the MinION is now established as a powerful tool for the analysis of pathogens
How is the MinION being used for pathogen analysis?
- Field based genomic surveillance, e.g. Zika/Ebola
- Identification and analysis of disease-causing pathogens and their antimicrobial resistance properties e.g. TB, influenza, E. coli, STDs
- Metagenomic analyses of complex samples that may contain pathogens
- Identification of species present in a complex mix e.g. 16S rRNA
- De novo assembly of novel species
The MinION is for Research Use Only. Oxford Nanopore has stated that it intends to seek regulatory approval for a diagnostic version of the device.
Pathogen analysis often needs: a rapid turnaround of data, simple workflows and an analysis system which can be operated outside of the traditional laboratory.
Nanopore sequencing on the MinION gives you:
Real-time data, rapid results
Nanopore sequencing data starts streaming immediately, rather than being delivered in bulk at the end of a 'run'. Real-time data streaming allows immediate analysis of the data, enabling users to perform assembly and mapping / alignment quickly, even during the experiment. Rapid identification of organisms in the sample is also possible - users recently reported identifying bacteria and markers of antimicrobial resistance within 5-10 minutes. The dedicated workflow 'WIMP Bacteria, Virus and Fungi' gives real-time species identification and characterisation.Publications on rapid identification
Preparation of sequencing libraries from genomic DNA is simple and takes about ten minutes with the latest kit. Oxford Nanopore is developing new devices to simplify this further.
Real-time data analysis means you can make your workflow more efficient. You can stop sequencing when an answer has been reached and move on to the next experiment.Publications on simple workflow
The MinION weighs under 100g and can fit in a pocket. It is powered by the USB on a laptop and is uniquely transportable into the field. The MinION has been used for scientific analyses in remote destinations including plant sequencing in a remote National Park, Zika analysis in a laboratory on a bus and species ID in a jungle in Tanzania.
New, simplified library preparation only requires standard lab materials. Oxford Nanopore is also preparing to release automated sample and library preparation devices to simplify the workflow further.Publications on transportable labs
Efficient genome assembly with long reads
The Oxford Nanopore system processes the library strands of DNA that are presented to it, regardless of their length. Users can choose long reads of kilobases to ultra-long reads of hundreds of kilobases, simplifying the data analysis workflow.Publications on long reads
How are others using the MinION to analyse pathogens?
View these publications and movies to find out more.
What's in my pot (WIMP)
'What's in my pot' (WIMP) is a workflow that enables MinION users to identify pathogens, fungi, viruses or archaea in complex samples in real time.
Analysis begins as soon as sequence data starts being streamed (a few seconds after the experiment starts). Each read of streamed sequence data is compared against a database of microbial species, and an identification is made. At the same time, WIMP plots and updates a taxonomic tree of all microorganisms found in the sample
There are various workflows and techniques that have been developed by members of the nanopore community to perform or enhance assembly and species identification that can be explored in the publications area and within the nanopore community
Real time analysis of antimicrobial resistance (ARMR)
Oxford Nanopore is developing an analysis workflow to enable researchers to characterise antimicrobial resistance. Read more https://nanoporetech.com/publications/real-time-detection-antibiotic-resistance-genes-using-oxford-nanopore-technologies
Antimicrobial resistance (AMR) is a growing problem that has been created by the overuse, or inappropriate use of antibiotic and antifungal treatments. Research effort is being deployed to understanding resistance mechanisms and to identify these characteristics in the nucleic acids of potential pathogens. The speed of nanopore sequencing experiments and the ability to analysis the data in real-time makes MinION a powerful tool for research, with potential to develop into diagnostic scenarios
How do I get started?
You can start using MinION straight away.
For a $1,000 fee you receive a MinION and starter pack of flow cells and kits. You also get access to a thriving online community of MinION users.