Nanopore sequencing can now provide
- Rapid identification of markers of antimicrobial resistance - results can be seen minutes after starting the experiment
- Analysis into whether antimicrobial resistance genes are in plasmids or integrated into the chromosome, using genome assembly
- Rapid species identification and characterisation of bacteria
- Portable analyses – the MinION weighs 100g and is powered by USB
- Simple, rapid end to end workflows – library prep is ten minutes with the latest kit, analytical workflows from Oxford Nanopore and the nanopore community
- Low cost to access the technology - $1,000 for a MinION starter pack
Antimicrobial resistance: the problem
The threat of pathogens developing resistance to antibiotics was recently summarised in the O’Neill Review on Antimicrobial resistance, which reported that:
“Without policies to stop the worrying spread of AMR, today's already large 700,000 deaths every year would become an extremely disturbing 10 million every year [by 2050], more people than currently die from cancer.”
At the root of the issue is the overuse, or unnecessary use of antibiotics, both in humans and in animals. This unnecessary use speeds up the development of drug resistance.
What can be done about the rise of antimicrobial resistance?
The O’Neill report notes that to reduce the overuse of antibiotics, a ‘step-change’ is needed in technologies that can identify pathogens. This would be used to aid decisions on whether to give antibiotics, and if so which ones to choose.
“I call on the governments of the richest countries to mandate now that by 2020, all antibiotic prescriptions will need to be informed by up-to-date surveillance information and a rapid diagnostic test wherever one exists.”
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 these data, enabling users to determine the presence of markers of antimicrobial resistance more rapidly than with traditional culturing methods. As more data is generated, over time, the user has the ability to generate sufficient data for genome assembly using long reads, which provides the ability to assess whether antimicrobial resistance genes are integrated into the chromosome or present in plasmids. Building on the coverage allows variant detection.Publications related to real-time analysis
Rapid taxonomy of bacteria within the sample
Rapid identification of organisms in the sample is also possible using a number of tools. Oxford Nanopore provides a dedicated workflow 'WIMP: Bacteria, Virus and Fungi', which gives real-time species identification and characterisation, aiding research into building a full micro-organism profile. Further workflows in development will enable species identification based on barcode of life sequence clusters, or the presence of antimicrobial markers in pathogens within a sample.Publications related to AMR research
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 even further.
The speed and simplicity of the workflow allows single samples to be analysed when required rather than considering batch testing of samples. Barcoding is available however when required.
Real-time data analysis means that workflows can be streamlined: sequencing can be stopped when an answer is been reached – perhaps a presence of a particular bacterium with resistance – allowing you to move on to the next experiment.Publications related to WIMP
The MinION weighs under 100g and can fit in a pocket. It is powered by the USB port on a laptop and is uniquely transportable into the field. With library preparation possible using only a minimum of equipment, field-based analysis labs have been setup in remote destinations. Oxford Nanopore is also preparing to release automated sample and library preparation devices to simplify the workflow even further.Publications related to portability
How are others using the MinION to address antimicrobial resistance?
What's in my pot (WIMP)
'What's in my pot' (WIMP) is a workflow that enables MinION users to identify bacteria, fungi, viruses or archea 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.
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.