Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.

Golparian, Daniel; Donà, Valentina; Sánchez-Busó, Leonor; Foerster, Sunniva; Harris, Simon; Endimiani, Andrea; Low, Nicola; Unemo, Magnus (2018). Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Scientific Reports, 8(1), p. 17596. Nature Publishing Group 10.1038/s41598-018-35750-4

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Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine
05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Veterinary Bacteriology

UniBE Contributor:

Donà, Valentina; Endimiani, Andrea and Low, Nicola

Subjects:

600 Technology > 610 Medicine & health
300 Social sciences, sociology & anthropology > 360 Social problems & social services
500 Science > 570 Life sciences; biology
600 Technology > 630 Agriculture

ISSN:

2045-2322

Publisher:

Nature Publishing Group

Language:

English

Submitter:

Tanya Karrer

Date Deposited:

18 Dec 2018 10:58

Last Modified:

23 Oct 2019 21:30

Publisher DOI:

10.1038/s41598-018-35750-4

PubMed ID:

30514867

Additional Information:

Nicola Low and Magnus Unemo contributed equally to this work.

BORIS DOI:

10.7892/boris.122509

URI:

https://boris.unibe.ch/id/eprint/122509

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