Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 66,916 bioRxiv papers from 294,600 authors.

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

By 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

Posted 09 Aug 2018
bioRxiv DOI: 10.1101/387548

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.

Download data

  • Downloaded 4,777 times
  • Download rankings, all-time:
    • Site-wide: 478 out of 66,973
    • In microbiology: 11 out of 5,388
  • Year to date:
    • Site-wide: 341 out of 66,973
  • Since beginning of last month:
    • Site-wide: 3,360 out of 66,973

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News