Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform

Robert Chapman, Luke Jones, Alberto D’Angelo, Ahmed Suliman, Muhammad Anwar, Stefan Bagby

Research output: Contribution to journalReview articlepeer-review

4 Citations (SciVal)
17 Downloads (Pure)


Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.

Original languageEnglish
Pages (from-to)171-179
Number of pages9
Issue number2
Early online date2 Apr 2023
Publication statusPublished - 30 Apr 2023

Bibliographical note

Funding Information:
RC, AS, MA, SB: report no conflicts of interest or funding related to this work. LJ is a PhD candidate partly funded by Oxford Nanopore Technologies.


  • Antimicrobial stewardship
  • Diagnostics
  • Mycobacteria
  • Nanopore sequencing
  • Next generation sequencing
  • Respiratory tract infection
  • Tuberculosis

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine


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