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Peer-reviewedCC BY 4.0Journal of Clinical Microbiology

Nanopore sequencing in infectious disease diagnostics and surveillance

  • Adithi Somayaji1,2
  • Piyas Mukherjee1,2,3
  • Caroline Koch4,5
  • Clarissa Prazeres da Costa1,2,3
  • Youssef Hamway1,2,3
5 affiliations
  1. 1Institute for Medical Microbiology, Immunology and Hygiene, TUM School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
  2. 2Center for Global Health, TUM School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany
  3. 3German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
  4. 4Department of Chemistry, Molecular Science Research Hub, Imperial College London, White City Campus, London, United Kingdom
  5. 5Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, United Kingdom
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Abstract

The global burden of infectious disease is on the rise, driven by antibiotic resistance, emerging pathogens, and gaps in accessible, decentralized diagnostics. To address these demands, there is a need for the development of diagnostic platforms for detection, surveillance, or monitoring assays with quick turnaround times. Oxford Nanopore sequencing, a platform for real-time long-read third-generation sequencing, has emerged as a promising tool in this space, with the ability to detect a wide range of molecular targets, including DNA, RNA, proteins, and base modifications. Its unique advantages, including portability, scalability, and the capacity for culture-independent workflows, combined with the depth of sequencing data produced, make it especially well-suited for infectious disease diagnostics and surveillance in both clinical and field settings. In this review, we aim to critically examine recent advances in the application of nanopore sequencing for diagnosing infectious diseases caused by bacterial, viral, fungal, and parasitic agents, as well as for detecting antimicrobial resistance genes. We also compare its potential advantages over conventional diagnostic methods and explore its expanding role in tracking outbreaks, monitoring pathogens in the environment, and detecting spillover events from animals to humans. Together, these applications highlight the relevance and position of this novel technology as a tool of choice for translational medical research and clinicians in the fight against infectious diseases and for global health preparedness.

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Cite

BibTeXRIS
BibTeX
@article{somayaji2026nanopore,
  title = {{Nanopore sequencing in infectious disease diagnostics and surveillance}},
  author = {Adithi Somayaji and Piyas Mukherjee and Caroline Koch and Clarissa Prazeres da Costa and Youssef Hamway},
  journal = {Journal of Clinical Microbiology},
  year = {2026},
  month = sep,
  doi = {10.1128/jcm.00083-26},
  url = {https://doi.org/10.1128/jcm.00083-26},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Nanopore sequencing in infectious disease diagnostics and surveillance
AU  - Adithi Somayaji
AU  - Piyas Mukherjee
AU  - Caroline Koch
AU  - Clarissa Prazeres da Costa
AU  - Youssef Hamway
PY  - 2026
DA  - 2026/09/17
JO  - Journal of Clinical Microbiology
DO  - 10.1128/jcm.00083-26
UR  - https://doi.org/10.1128/jcm.00083-26
AB  - The global burden of infectious disease is on the rise, driven by antibiotic resistance, emerging pathogens, and gaps in accessible, decentralized diagnostics. To address these demands, there is a need for the development of diagnostic platforms for detection, surveillance, or monitoring assays with quick turnaround times. Oxford Nanopore sequencing, a platform for real-time long-read third-generation sequencing, has emerged as a promising tool in this space, with the ability to detect a wide range of molecular targets, including DNA, RNA, proteins, and base modifications. Its unique advantages, including portability, scalability, and the capacity for culture-independent workflows, combined with the depth of sequencing data produced, make it especially well-suited for infectious disease diagnostics and surveillance in both clinical and field settings. In this review, we aim to critically examine recent advances in the application of nanopore sequencing for diagnosing infectious diseases caused by bacterial, viral, fungal, and parasitic agents, as well as for detecting antimicrobial resistance genes. We also compare its potential advantages over conventional diagnostic methods and explore its expanding role in tracking outbreaks, monitoring pathogens in the environment, and detecting spillover events from animals to humans. Together, these applications highlight the relevance and position of this novel technology as a tool of choice for translational medical research and clinicians in the fight against infectious diseases and for global health preparedness.
SN  - 0095-1137
SN  - 1098-660X
ER  -