Progress in applying CRISPR in pathogen detection

Infectious diseases caused by various pathogens are among the major threats to human health, and the key to controlling these diseases is the early diagnosis of pathogens. Currently, standard methods for clinical pathogen diagnosis have issues such as high cost, long processing time, and limited sensitivity, which are difficult to overcome with existing technology. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR) gene editing technology, which utilizes a programmable endonuclease-based gene editing system, has been widely applied in the fields of treatment and diagnosis. In pathogen detection, CRISPR technology offers the advantages of being fast, accurate, sensitive, and simple, enabling the detection of various pathogens early and instantly, thereby compensating for the shortcomings of existing nucleic acid detection methods. Moreover, the precise identification and characterization of mutant genes that cause virulence and drug resistance via CRISPR has further promoted its application in clinical pathogen diagnosis, providing a basis for controlling pathogen transmission and monitoring resistance. Currently, although the CRISPR/Cas system offers various advantages, there are still areas for improvement in clinical applications, including cumbersome operational processes, difficulty in achieving accurate quantitative, multiplex, and standardized detection, and reliance on specialized instruments. Therefore, continuous improvement is necessary to develop new and more convenient CRISPR-based tools for pathogen detection. This review focuses on various simplified strategies of the latest CRISPR diagnostic tools, including extraction-free, amplification-free, and integrated reactions, as well as sensitive and portable output strategies, to overcome these obstacles in clinical applications and propose the next strategic direction for providing researchers with innovative strategies for real-time pathogen diagnosis.