CRISPR-Cas-based Techniques for Pathogen Detection: Retrospect, Recent Advances, and Future Perspectives

Overview

Journal J Adv Res

Specialties General Medicine
Science

Date 2022 Nov 11

PMID 36367481

Authors

Tao Huang

Rui Zhang

Jinming Li

Affiliations

Soon will be listed here.

Abstract

Background: Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements.

Aim Of Review: This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation.

Key Scientific Concepts Of Review: Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.

Citing Articles

CRISPR in clinical diagnostics: bridging the gap between research and practice.

Lafi Z, Ata T, Asha S Bioanalysis. 2025; 17(4):281-290.

PMID: 39902531 PMC: 11866644. DOI: 10.1080/17576180.2025.2459520.

Developing a Versatile Arsenal: Novel Antimicrobials as Offensive Tools Against Pathogenic Bacteria.

Ma J, Lu Z Microorganisms. 2025; 13(1).

PMID: 39858940 PMC: 11767912. DOI: 10.3390/microorganisms13010172.

CRISPR/Cas system and its application in the diagnosis of animal infectious diseases.

Rasool H, Chen Q, Gong X, Zhou J FASEB J. 2024; 38(24):e70252.

PMID: 39726403 PMC: 11671863. DOI: 10.1096/fj.202401569R.

Recent Advances in CRISPR/Cas System-Based Biosensors for the Detection of Foodborne Pathogenic Microorganisms.

Xie S, Yue Y, Yang F Micromachines (Basel). 2024; 15(11).

PMID: 39597141 PMC: 11596558. DOI: 10.3390/mi15111329.

A rapid visualization method for detecting rotavirus A by combining nuclear acid sequence-based amplification with the CRISPR-Cas12a assay.

Chen Y, Wu J, Gao E, Lu Y, Qiu H J Med Microbiol. 2024; 73(10).

PMID: 39360804 PMC: 11448473. DOI: 10.1099/jmm.0.001892.

References

Guk K, Keem J, Hwang S, Kim H, Kang T, Lim E . A facile, rapid and sensitive detection of MRSA using a CRISPR-mediated DNA FISH method, antibody-like dCas9/sgRNA complex. Biosens Bioelectron. 2017; 95:67-71. DOI: 10.1016/j.bios.2017.04.016. View

Wang J, Wu L, Ren J, Qu X . Visualizing human telomerase activity with primer-modified Au nanoparticles. Small. 2011; 8(2):259-64. DOI: 10.1002/smll.201101938. View

Chang W, Liu W, Liu Y, Zhan F, Chen H, Lei H . Colorimetric detection of nucleic acid sequences in plant pathogens based on CRISPR/Cas9 triggered signal amplification. Mikrochim Acta. 2019; 186(4):243. DOI: 10.1007/s00604-019-3348-2. View

Wei Y, Yang Z, Zong C, Wang B, Ge X, Tan X . trans Single-Stranded DNA Cleavage via CRISPR/Cas14a1 Activated by Target RNA without Destruction. Angew Chem Int Ed Engl. 2021; 60(45):24241-24247. DOI: 10.1002/anie.202110384. View

Xiang Y, Zhu X, Huang Q, Zheng J, Fu W . Real-time monitoring of mycobacterium genomic DNA with target-primed rolling circle amplification by a Au nanoparticle-embedded SPR biosensor. Biosens Bioelectron. 2014; 66:512-9. DOI: 10.1016/j.bios.2014.11.021. View

Babamiri B, Salimi A, Hallaj R . A molecularly imprinted electrochemiluminescence sensor for ultrasensitive HIV-1 gene detection using EuS nanocrystals as luminophore. Biosens Bioelectron. 2018; 117:332-339. DOI: 10.1016/j.bios.2018.06.003. View

Hsieh K, Zhao G, Wang T . Applying biosensor development concepts to improve preamplification-free CRISPR/Cas12a-Dx. Analyst. 2020; 145(14):4880-4888. PMC: 7362986. DOI: 10.1039/d0an00664e. View

Zhang F, Wen Y, Guo X . CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet. 2014; 23(R1):R40-6. DOI: 10.1093/hmg/ddu125. View

Yoo H, Kim I, Kim S . Nucleic Acid Testing of SARS-CoV-2. Int J Mol Sci. 2021; 22(11). PMC: 8201071. DOI: 10.3390/ijms22116150. View

10.

Patel S, Pratap C, Jain A, Gulati A, Nath G . Diagnosis of Helicobacter pylori: what should be the gold standard?. World J Gastroenterol. 2014; 20(36):12847-59. PMC: 4177467. DOI: 10.3748/wjg.v20.i36.12847. View

11.

Cao H, Mao K, Ran F, Xu P, Zhao Y, Zhang X . Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater. Environ Sci Technol. 2022; 56(18):13245-13253. DOI: 10.1021/acs.est.2c04727. View

12.

Huang W, Yu L, Wen D, Wei D, Sun Y, Zhao H . A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection. EBioMedicine. 2020; 61:103036. PMC: 7544594. DOI: 10.1016/j.ebiom.2020.103036. View

13.

Wang B, Wang R, Wang D, Wu J, Li J, Wang J . Cas12aVDet: A CRISPR/Cas12a-Based Platform for Rapid and Visual Nucleic Acid Detection. Anal Chem. 2019; 91(19):12156-12161. DOI: 10.1021/acs.analchem.9b01526. View

14.

Qian C, Wang R, Wu H, Zhang F, Wu J, Wang L . Uracil-Mediated New Photospacer-Adjacent Motif of Cas12a To Realize Visualized DNA Detection at the Single-Copy Level Free from Contamination. Anal Chem. 2019; 91(17):11362-11366. DOI: 10.1021/acs.analchem.9b02554. View

15.

Li Y, Li S, Wang J, Liu G . CRISPR/Cas Systems towards Next-Generation Biosensing. Trends Biotechnol. 2019; 37(7):730-743. DOI: 10.1016/j.tibtech.2018.12.005. View

16.

Li S, Cheng Q, Wang J, Li X, Zhang Z, Gao S . CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 2018; 4:20. PMC: 5913299. DOI: 10.1038/s41421-018-0028-z. View

17.

Elghanian R, Storhoff J, Mucic R, LETSINGER R, Mirkin C . Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science. 1997; 277(5329):1078-81. DOI: 10.1126/science.277.5329.1078. View

18.

Lin M, Yue H, Tian T, Xiong E, Zhu D, Jiang Y . Glycerol Additive Boosts 100-fold Sensitivity Enhancement for One-Pot RPA-CRISPR/Cas12a Assay. Anal Chem. 2022; 94(23):8277-8284. DOI: 10.1021/acs.analchem.2c00616. View

19.

Ding X, Yin K, Li Z, Lalla R, Ballesteros E, Sfeir M . Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun. 2020; 11(1):4711. PMC: 7501862. DOI: 10.1038/s41467-020-18575-6. View

20.

Chen J, Ma E, Harrington L, Da Costa M, Tian X, Palefsky J . CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018; 360(6387):436-439. PMC: 6628903. DOI: 10.1126/science.aar6245. View