Deciphering Pathogens

In the field of public health, the rapid and accurate identification of pathogens is fundamental to the diagnosis as well as the prevention and control of clinical infectious diseases. It is also the most effective means of dealing with public health emergencies and controlling outbreaks. The use of traditional pathogen detection methods, such as classical microbial isolation and culture techniques, is significantly limited in clinical applications due to their complexity, time consumption, and lack of sensitivity. With the leap in molecular biology in the 20th century, various molecular diagnostic technologies and nucleic acid detection methods have gradually become important tools in the fields of public health and clinical testing. DNA sequencing technology, as one of the most important techniques in molecular biological research, has seen Sanger sequencing become the “gold standard” for the molecular diagnosis of many diseases. In 2005, with the introduction of the revolutionary pyrosequencing-based high-throughput sequencing technology by Life Sciences, Inc. (USA), companies such as Illumina (USA) and Roche (Switzerland) have continuously developed and optimized new sequencing platforms. After decades of developments, genomic sequencing has been widely applied in disease detection and research lately due to its increasing sequencing throughput, decreasing costs, speed, and high accuracy. The next-generation DNA sequencing (NGS) plays an increasingly important role in the diagnosis of infectious diseases, the prevention and control of infectious diseases, and microbial genomics. In recent years, third-generation DNA sequencing (TGS), which is characterized by single-molecule real-time sequencing and long read lengths, has seen rapid development. In 2014, Oxford Nanopore Technologies (ONT), a United Kingdom-based company, launched the first commercial portable nanopore sequencer named MinION. Subsequently, high-throughput DNA sequencing technology has broken through the limitations of traditional detection methods in terms of timeliness and sensitivity, providing a convenient and efficient approach for pathogen detection and research. This chapter, based on the development process of high-throughput sequencing technology, mainly reviews the third-generation genomic sequencing technology dominated by nanopore sequencing and its application in the detection and identification of pathogens, and discusses the prospects as well as the potential issues of the technology. We hope this chapter can inform readers on the latest research results and application samples of nanopore genomic sequencing used in pathogen detection, which may play an important role in public health risk prevention and control.