Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics

Themoula Charalampous, Hollian Richardson, Gemma L. Kay, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J. Turner, John Wain, Richard M. Leggett, David M. Livermore, Justin O’Grady
doi: https://doi.org/10.1101/387548
Themoula Charalampous
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hollian Richardson
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gemma L. Kay
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rossella Baldan
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
2CIDR, King’s College London, St Thomas’ Hospital, Westminster Bridge Road, London, UK, SE1 7EH.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher Jeanes
3Microbiology Department, Norwich and Norfolk University Hospital, Conley Ln, Norwich, UK, NR4 7GJ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Duncan Rae
3Microbiology Department, Norwich and Norfolk University Hospital, Conley Ln, Norwich, UK, NR4 7GJ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sara Grundy
3Microbiology Department, Norwich and Norfolk University Hospital, Conley Ln, Norwich, UK, NR4 7GJ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel J. Turner
4Oxford Nanopore Technologies, Gosling Building, Oxford Science Park, Edmund Halley Rd, Oxford, UK, OX4 4DQ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John Wain
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
5Quadram Institute Bioscience, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard M. Leggett
6Earlham Institute, Norwich Research Park, Conley Ln, Norwich, UK, NR4 7UZ
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David M. Livermore
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
7AMRHAI, Public Health England, 61 Colindale Ave, London, NW9 5EQ.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Justin O’Grady
1Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UQ.
5Quadram Institute Bioscience, Norwich Research Park, Colney Ln, Norwich, UK, NR4 7UA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: justin.ogrady@quadram.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Lower respiratory infections (LRIs) accounted for three million deaths worldwide in 2016, the leading infectious cause of mortality. The “gold standard” for investigation of bacterial LRIs is culture, which has poor sensitivity and is too slow to guide early antibiotic therapy. Metagenomic sequencing potentially could replace culture, providing rapid, sensitive and comprehensive results. We developed a metagenomics pipeline for the investigation of bacterial LRIs using saponin-based host DNA depletion combined with rapid nanopore sequencing. The first iteration of the pipeline was tested on respiratory samples from 40 patients. It was then refined to reduce turnaround and increase sensitivity, before testing a further 41 samples. The refined method was 96.6% concordant with culture for detection of pathogens and could accurately detect resistance genes with a turnaround time of six hours. This study demonstrates that nanopore metagenomics can rapidly and accurately characterise bacterial LRIs when combined with efficient human DNA depletion.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted August 09, 2018.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
Themoula Charalampous, Hollian Richardson, Gemma L. Kay, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J. Turner, John Wain, Richard M. Leggett, David M. Livermore, Justin O’Grady
bioRxiv 387548; doi: https://doi.org/10.1101/387548
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
Themoula Charalampous, Hollian Richardson, Gemma L. Kay, Rossella Baldan, Christopher Jeanes, Duncan Rae, Sara Grundy, Daniel J. Turner, John Wain, Richard M. Leggett, David M. Livermore, Justin O’Grady
bioRxiv 387548; doi: https://doi.org/10.1101/387548

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2430)
  • Biochemistry (4791)
  • Bioengineering (3333)
  • Bioinformatics (14684)
  • Biophysics (6640)
  • Cancer Biology (5172)
  • Cell Biology (7429)
  • Clinical Trials (138)
  • Developmental Biology (4367)
  • Ecology (6874)
  • Epidemiology (2057)
  • Evolutionary Biology (9926)
  • Genetics (7346)
  • Genomics (9533)
  • Immunology (4558)
  • Microbiology (12686)
  • Molecular Biology (4948)
  • Neuroscience (28348)
  • Paleontology (199)
  • Pathology (809)
  • Pharmacology and Toxicology (1392)
  • Physiology (2024)
  • Plant Biology (4504)
  • Scientific Communication and Education (977)
  • Synthetic Biology (1299)
  • Systems Biology (3917)
  • Zoology (726)