'USB stick' could revolutionise gene sequencing
8 Dec 2014
Newly developed nanopore DNA sequencing technology could be used to diagnose infection and detect drug-resistance at the point of clinical need, researchers claim.
The sequencing device, known as MinION, is no bigger than a USB stick and was recently used to determine the cause of antibiotic resistance in a new multi-drug resistant strain of the bacterium that causes Typhoid.
The research team used MinION to produce long sequencing reads with a methodology that does not require optimal imaging.
“This type of technology makes next generation sequencing accessible to scientists everywhere
Lead researcher Justin O’Grady
It was capable of pinpointing the exact spot in the chromosomal structure of Salmonella Typhi haplotype H58 that is home to the genes which makes it drug-resistant, the researchers said.
“The device was used to determine the position and structure of a new ’antibiotic-resistance island’,” said lead researcher Justin O’Grady, from UEA’s Norwich Medical School.
“This information can now be used to develop screening tools for the presence of this island.”
The device took 18 hours to produce the results, boasting similar accuracy to current technologies and at a fraction of the cost - roughly £650 per device, as opposed to £500,000.
“This type of technology will revolutionise the way that we characterise the rapid spread of emerging antibiotic-resistant infectious diseases,” O’Grady said.
“This analysis would previously have taken months using traditional methods, due to extensive post-sequencing lab-based analysis. By the time the results are available, they might well be irrelevant for clinical diagnostics and guiding public health interventions.”
According to O’Grady, laboratories could soon be able to access this technology, and in combination with short read sequencing, could help provide fully assembled bacterial genomes.
“MinION technology could potentially enable bacterial identification, diagnosis of infectious diseases and detection of drug-resistance at the point of clinical need,” O’Grady said.
To diagnose infection, the device would have to be presented with DNA extracted from clinical samples such as blood, sputum or urine, for example - though some pathogen DNA enrichment may be necessary for this to work well, O’Grady said.
“This type of technology makes next generation sequencing accessible to scientists everywhere,” O’Grady said.
