Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

Abstract

ObjectivesGenome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce the delay between pathogen sampling and data generation is single molecule sequencing. An example of this technology, which is undergoing evaluation through an early access programme, is the Oxford Nanopore MinION.MethodsWe undertook a feasibility study on six clinically significant pathogens, comparing the MinION to the Illumina MiSeq and PacBio RSII platforms. Genomic DNA was prepared and sequenced using the MinION as instructed by the manufacturer, and Illumina MiSeq and PacBio sequencing was performed using established methods.ResultsAn evaluation of the accuracy of the MinION based on sequencing of an MRSA isolate showed that error rates were higher in the MinION reads, but provided an even coverage across the entire genome length. The MinION detected all of the expected carbapenemases and ESBL genes in five Gram-negative isolates and the mecA gene in an MRSA isolate.ConclusionsThe MinION can detect the presence of acquired resistance genes, but improvements in accuracy are needed so that antimicrobial resistance associated with mutations in chromosomal genes can be identified.

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

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Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

“…Despite the relatively high error rate, MinION reads are suitable for de novo assembly of complete genomes (15,16,17,18), scaffolding NGS contigs (19), metagenomic studies (20,21), and realtime epidemiological investigations (22,23). The main advantages of the MinION platform over NGS technologies are the long reads (there is no theoretical limit of read length), the low investment cost per device, portability, and the flexible run and reduced turnaround time (22,24). Plasmids R16a and IP40a (R40a) (25) were isolated in the Pasteur Institute from abscess and urine samples collected in 1966 (St-Antoine Hospital, Paris, France) and 1969 (Necker Hospital, Paris, France), respectively.…”

Séquençage de l’ADN par nanopores

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