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Antimicrobial resis...
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Golparian, Daniel,1984-Örebro universitet,Institutionen för medicinska vetenskaper,WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology
(författare)
Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer
- Artikel/kapitelEngelska2018
Förlag, utgivningsår, omfång ...
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2018-12-04
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Nature Publishing Group,2018
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Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:oru-70622
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https://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-70622URI
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https://doi.org/10.1038/s41598-018-35750-4DOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:art swepub-publicationtype
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Funding Agencies:Orebro County Council Research Committee Foundation for Medical Research at Orebro University Hospital, Orebro, Sweden SwissTransMed initiative (Translational Research Platforms in Medicine) from the Rectors' Conference of the Swiss Universities (CRUS) 25/2013 Pathogen Informatics Group at the Wellcome Sanger Institute Wellcome Grant 098051
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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.
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Donà, ValentinaInstitute for Infectious Diseases, University of Bern, Bern, Switzerland; Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
(författare)
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Sánchez-Busó, LeonorPathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
(författare)
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Foerster, SunnivaWHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
(författare)
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Harris, SimonPathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
(författare)
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Endimiani, AndreaInstitute for Infectious Diseases, University of Bern, Bern, Switzerland
(författare)
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Low, NicolaInstitute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
(författare)
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Unemo, Magnus,1970-Örebro universitet,Institutionen för medicinska vetenskaper,Region Örebro län,WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology(Swepub:oru)muo
(författare)
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Örebro universitetInstitutionen för medicinska vetenskaper
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Scientific Reports: Nature Publishing Group8:12045-2322
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