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Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season.
Xu, Yifei; Lewandowski, Kuiama; Downs, Louise O; Kavanagh, James; Hender, Thomas; Lumley, Sheila; Jeffery, Katie; Foster, Dona; Sanderson, Nicholas D; Vaughan, Ali; Morgan, Marcus; Vipond, Richard; Carroll, Miles; Peto, Timothy; Crook, Derrick; Walker, A Sarah; Matthews, Philippa C; Pullan, Steven T.
  • Xu Y; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
  • Lewandowski K; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
  • Downs LO; Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom.
  • Kavanagh J; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
  • Hender T; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
  • Lumley S; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
  • Jeffery K; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
  • Foster D; Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom.
  • Sanderson ND; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
  • Vaughan A; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom.
  • Morgan M; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
  • Vipond R; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
  • Carroll M; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
  • Peto T; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
  • Crook D; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
  • Walker AS; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
  • Matthews PC; NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.
  • Pullan ST; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1577032
ABSTRACT
BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Cross Infection / Influenza, Human / Nanopores Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.27.2000004

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Cross Infection / Influenza, Human / Nanopores Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.27.2000004