Golparian et al. WGS of Neisseria gonorrhoeae using MinION sequencer (Oxford Nanopore Technologies).

Antimicrobial resistant (AMR) Neisseria gonorrhoeae strains are prevalent and threaten the treatment of gonorrhoea internationally. Rapid identification and characterization of AMR gonococcal strains could ensure appropriate and even personalized treatment in the future, as well as to support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole genome sequencing is ideal to elucidate the molecular AMR determinants to predict AMR, the dissemination of the AMR determinants throughout the gonococcal population, and the emergence and dissemination of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION (Oxford Nanopore Technologies (ONT)) is a small hand-held device that in less than 1-2 days can generate bacterial genomes. However, the accuracy of ONT reads has been suboptimal for many purposes and the MinION has not been previously evaluated for N. gonorrhoeae. In the present study, we show that, using appropriate analysis pipeline, e.g., our in house-developed CLC Genomics Workbench, ONT reads can be relatively concordant with Illumina and PacBio sequences and useful for rapid phylogenomic-based molecular epidemiological investigations, prediction of decreased susceptibility or resistance to recommended therapeutic antimicrobials and, in hybrid assemblies with Illumina sequences, for producing finished reference genomes.