Nanopore sequencing in infectious disease diagnostics and surveillance

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.