Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms

Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.