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Oxford Nanopore launches analysis workflow for antimicrobial resistance

Mon 24th April 2017

Oxford Nanopore has launched a new analytical workflow for use with its real time nanopore sequencing devices.

‘ARMA’ allows characterisation of antimicrobial resistance genes in real time. The movie below shows real time analysis of pathogen DNA using two conjoined workflows: ‘What’s in my Pot’ (WIMP) is used for taxonomic classification of pathogens in a sample, and subsequently ARMA is used for antimicrobial resistance profiling.

This WIMP-ARMA workflow is intended to make it easier for researchers interested in antimicrobial resistance to characterise their samples. The real time workflow takes advantage of long read data streaming from nanopore devices such as MinION, GridION or PromethION.

 

The problem
The rising problem of antimicrobial resistance (AMR) has been highlighted as one of the biggest challenges for public health in the coming years.  Bacteria, fungi and viruses are all evolving more resistance to existing antimicrobial agents and few new antimicrobials are being developed.  In order to stem the rise of AMR, better antimicrobial stewardship is needed so that anti-infective medicines are not given unnecessarily or where they will not be effective. Overuse of these medicines contributes to the development of new resistances.

“Antimicrobial resistance is a multi-sectoral problem, affecting human and animal health, agriculture, as well as the global environment and trade. Clean water, sustainable food production and poverty alleviation are but a few of the challenges it poses.”
WHO Director-General Dr Margaret Chan 

“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.”  O’Neill report on Antimicrobial Resistance

DNA information as a route to fighting antimicrobial resistance
The DNA sequence of bacteria, viruses or other pathogens can be used to determine their identity and whether it has resistance to antibiotics. This is essential when conducting research into the causes of drug resistance, why resistance arises and how transmission occurs.

In the future, portable, easy to use devices that return rapid results will be integral to antibiotic stewardship and the prescription of effective antimicrobial agents.
Effective, rapid, low-cost diagnostic tools are needed for guiding optimal use of antibiotics in human and animal medicine, and such tools should be easily integrated into clinical, pharmacy and veterinary practices. Evidence-based prescribing and dispensing should be the standard of care.” WHO action plan

Read more about using nanopore sequencing for research into pathogens and antimicrobial resistance.
 

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