DOI QR코드

DOI QR Code

CRISPR/Cas 시스템 기술을 활용한 고위험성 식중독 세균 신속 검출을 위한 바이오센서 개발

Development of Biosensors for Rapid Detection of Foodborne Pathogenic Bacteria using CRISPR/Cas

  • Seon Yeong Jo (Department of Food Science and Technology, Chung-Ang University) ;
  • Jong Pil Park (Department of Food Science and Technology, Chung-Ang University)
  • 투고 : 2023.07.25
  • 심사 : 2023.08.11
  • 발행 : 2023.10.30

초록

Rapid and accurate detection of pathogenic bacteria is crucial for various applications, including public health and food safety. However, existing bacteria detection techniques have several drawbacks as they are inconvenient and require time-consuming procedures and complex machinery. Recently, the precision and versatility of CRISPR/Cas system has been leveraged to design biosensors that offer a more efficient and accurate approach to bacterial detection compared to the existing techniques. Significant research has been focused on developing biosensors based on the CRISPR/Cas system which has shown promise in efficiently detecting pathogenic bacteria or virus. In this review, we present a biosensor based on the CRISPR/Cas system that has been specifically developed to overcome these limitations and detect different pathogenic bacteria effectively including Vibrio parahaemolyticus, Salmonella, E. coli O157:H7, and Listeria monocytogenes. This biosensor takes advantage of the CRISPR/Cas system's precision and versatility for more efficiently accurately detecting bacteria compared to the previous techniques. The biosensor has potential to enhance public health and ensure food safety as the biosensor's design can revolutionize method of detecting pathogenic bacteria. It provides a rapid and reliable method for identifying harmful bacteria and it can aid in early intervention and preventive measures, mitigating the risk of bacterial outbreaks and their associated consequences. Further research and development in this area will lead to development of even more advanced biosensors capable of detecting an even broader range of bacterial pathogens, thereby significantly benefiting various industries and helping in safeguard human health

키워드

과제정보

이 연구는 2023년 식품의약품안전처 지원 과제(21153MFDS605)에 의해 수행됐으며, 이에 감사드립니다.

참고문헌

  1. Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., Nakata, A., Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol., 169, 5429-5433 (1987).  https://doi.org/10.1128/jb.169.12.5429-5433.1987
  2. Jansen, R., Embden, J.D.V., Gaastra, W., Schouls, L.M., Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol., 43, 1565-1575 (2002).  https://doi.org/10.1046/j.1365-2958.2002.02839.x
  3. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., Charpentier, E., A programmable dual-RNA-guided DNA Endonuclease in adaptive bacterial immunity. Science, 337, 816-821 (2012).  https://doi.org/10.1126/science.1225829
  4. Mojica, F.J., Diez-Villasenor, C.S., Garcia-Martinez, J., Soria, E., Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol., 60, 174-182 (2005).  https://doi.org/10.1007/s00239-004-0046-3
  5. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A., Horvath, P., CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315, 1709-1712 (2007).  https://doi.org/10.1126/science.1138140
  6. Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., Kaplan, M., Iavarone, A.T., Charpentier, E., Nogales, E., Doudna, J.A., Structures of Cas9 Endonucleases reveal RNA-mediated conformational activation. Science, 343, 1247997 (2014). 
  7. Lou, J., Wang, B., Li, J., Ni, P., Jin, Y., Chen, S., Xi, Y., Zhang, R., Duan, G., The CRISPR-Cas system as a tool for diagnosing and treating infectious diseases. Mol. Biol. Rep., 49, 11301-11311 (2022).  https://doi.org/10.1007/s11033-022-07752-z
  8. Lee, S., Kim, Y.Y., Ahn, H.J., Systemic delivery of CRISPR/Cas9 to hepatic tumors for cancer treatment using altered tropism of lentiviral vector. Biomaterials, 272, 120793 (2021). 
  9. Qiao, Z., Fu, Y., Lei, C., Li, Y., Advances in antimicrobial peptides-based biosensing methods for detection of foodborne pathogens: A review. Food Control, 112, 107116 (2020). 
  10. Velusamy, V., Arshak, K., Korostynska, O., Oliwa, K., Adley, C., An overview of foodborne pathogen detection: In the perspective of biosensors. Biotechnol. Adv., 28, 232-254 (2010).  https://doi.org/10.1016/j.biotechadv.2009.12.004
  11. Sassolas, A., Leca-Bouvier, B.D., Blum, L.J., DNA Biosensors and Microarrays. Chem. Rev., 108, 109-139 (2008).  https://doi.org/10.1021/cr0684467
  12. Wolcott, M.J., Advances in nucleic acid-based detection methods. Clin. Microbiol. Rev., 5, 370-386 (1992).  https://doi.org/10.1128/CMR.5.4.370
  13. Scheler, O., Glynn, B., Kurg, A., Nucleic acid detection technologies and marker molecules in bacterial diagnostics. Expert Rev. Mol. Diagn., 14, 489-500 (2014).  https://doi.org/10.1586/14737159.2014.908710
  14. Zhao, Y., Chen, F., Li, Q., Wang, L., Fan, C., Isothermal amplification of nucleic acids. Chem. Rev., 115, 12491-12545 (2015).  https://doi.org/10.1021/acs.chemrev.5b00428
  15. Chakraborty, J., Chaudhary, A.A., Khan, S.U.D., Rudayni, H.A., Rahaman, S.M., Sarkar, H., CRISPR/Cas-based biosensor as a new age detection method for pathogenic bacteria. ACS omega, 7, 39562-39573 (2022).  https://doi.org/10.1021/acsomega.2c04513
  16. Garneau, J. E., Dupuis, M. E., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadan, A.H., Moineau, S., The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature, 468, 67-71 (2010).  https://doi.org/10.1038/nature09523
  17. Hille, F., Charpentier, E., CRISPR-Cas: biology, mechanisms and relevance. Philos. Trans. R. Soc. B: Biol. Sci., 371, 20150496 (2016). 
  18. McGinn, J., Marraffini, L.A., Molecular mechanisms of CRISPR-Cas spacer acquisition. Nat. Rev. Microbiol., 17, 7-12 (2019).  https://doi.org/10.1038/s41579-018-0071-7
  19. Ishino, Y., Krupovic, M., Forterre, P., History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. J. Bacteriol., 200, 10-1128 (2018). 
  20. Carte, J., Wang, R., Li, H., Terns, R. M., Terns, M.P., Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev., 22, 3489-3496 (2008).  https://doi.org/10.1101/gad.1742908
  21. East-Seletsky, A., O'Connell, M.R., Burstein, D., Knott, G.J., Doudna, J.A., RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell, 66, 373-383 (2017).  https://doi.org/10.1016/j.molcel.2017.04.008
  22. Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Snijders, A.P., Dickman, M.J., Makarova, K.S., Koonin, E.V., Van Der Oost, J., Small CRISPR RNAs guide antiviral defense in prokaryotes. Science, 321, 960-964 (2008).  https://doi.org/10.1126/science.1159689
  23. Karvelis, T., Gasiunas, G., Young, J., Bigelyte, G., Silanskas, A., Cigan, M., Siksnys, V., Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biol., 16, 1-13 (2015).  https://doi.org/10.1186/s13059-014-0572-2
  24. Liu, T.Y., Doudna, J.A., Chemistry of class 1 CRISPR-Cas effectors: binding, editing, and regulation. J. Biol. Chem., 295, 14473-14487 (2020).  https://doi.org/10.1074/jbc.REV120.007034
  25. Murugan, K., Babu, K., Sundaresan, R., Rajan, R., Sashital, D.G., The revolution continues: newly discovered systems expand the CRISPR-Cas toolkit. Mol. Cell, 68, 15-25 (2017).  https://doi.org/10.1016/j.molcel.2017.09.007
  26. Mohanraju, P., Makarova, K.S., Zetsche, B., Zhang, F., Koonin, E.V., Van der Oost, J., Diverse evolutionary roots and mechanistic variations of theCRISPR-Cas systems. Science, 353, aad5147 (2016). 
  27. Koonin, E.V., Makarova, K.S., Origins and evolution of CRISPR-Cas systems. Philos. Trans. R. Soc. B: Biol. Sci., 374, 20180087 (2019). 
  28. Hidalgo-Cantabrana, C., Barrangou, R., Characterization and applications of type I CRISPR-Cas systems. Biochem. Soc. Trans., 48, 15-23 (2020).  https://doi.org/10.1042/BST20190119
  29. Makarova, K.S., Wolf, Y.I., Iranzo, J., Shmakov, S.A., Alkhnbashi, O.S., Brouns, S.J.J., Charpentier, E., Cheng, D., Haft, D.H., Horvath, P., Moineau, S., Mojica, F.J.M., Scott, D., Shah, S.A., Siksnys, V., Terns, M.P., Venclovas, C, White, M.F., Yakunin, A.F., Yan, W., Zhang, F., Garrett, R.A., Backofen, R., Van der oost, J., Barrangou, R., Koonin, E. V., Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol., 18, 67-83 (2020).  https://doi.org/10.1038/s41579-019-0299-x
  30. Wang, M., Zhang, R., Li, J., CRISPR/Cas systems redefine nucleic acid detection: principles and methods. Biosens. Bioelectron., 165, 112430 (2020). 
  31. Li, Y., Li, S., Wang, J., Liu, G., CRISPR/Cas systems towards next-generation biosensing. Trends Biotechnol., 37, 730-743 (2019).  https://doi.org/10.1016/j.tibtech.2018.12.005
  32. Mukama, O., Wu, J., Li, Z., Liang, Q., Yi, Z., Lu, X., Liu, Y., Liu, Y., Hussain, M., Makafe, G.G., Liu, J., Xu, N., Zeng, L., An ultrasensitive and specific point-of-care CRISPR/Cas12 based lateral flow biosensor for the rapid detection of nucleic acids. Biosens. Bioelectron., 159, 112143 (2020). 
  33. Gootenberg, J.S., Abudayyeh, O.O., Kellner, M.J., Joung, J., Collins, J.J., Zhang, F., Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science, 360, 439-444 (2018).  https://doi.org/10.1126/science.aaq0179
  34. Kellner, M.J., Koob, J.G., Gootenberg, J.S., Abudayyeh, O.O., Zhang, F., SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat. Protoc., 14, 2986-3012 (2019).  https://doi.org/10.1038/s41596-019-0210-2
  35. Thompson, F.L., Iida, T., Swings, J., Biodiversity of Vibrios. Microbiol. Mol. Biol. Rev., 68, 403-431 (2004).  https://doi.org/10.1128/MMBR.68.3.403-431.2004
  36. Donovan, T.J., Van Netten, P., Culture media for the isolation and enumeration of pathogenic Vibrio species in foods and environmental samples. Int. J. Food Microbiol., 26, 77-91 (1995).  https://doi.org/10.1016/0168-1605(95)00015-C
  37. Parte, A.C., Carbasse, J.S., Meier-Kolthoff, J.P., Reimer, L.C., Goker, M., List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol., 70, 5607-5612 (2020).  https://doi.org/10.1099/ijsem.0.004332
  38. Baker-Austin, C., Oliver, J.D., Alam, M., Ali, A., Waldor, M.K., Qadri, F., Martinez-Urtaza, J., Vibrio spp. Infections. Nat. Rev. Dis. Primers., 4, 1-19 (2018). 
  39. Wu, H., Chen, Y., Yang, Q., Peng, C., Wang, X., Zhang, M., Qian, S., Xu, J., Wu, J., A reversible valve-assisted chip coupling with integrated sample treatment and CRISPR/Cas12a for visual detection of Vibrio parahaemolyticus. Biosens. Bioelectron., 188, 113352 (2021). 
  40. Chen, X., Wang, L., He, F., Chen, G., Bai, L., He, K., Zhang, F., Xu, X., Label-free colorimetric method for detection of Vibrio parahaemolyticus by trimming the G-quadruplex DNAzyme with CRISPR/Cas12a. Anal. Chem., 93, 14300-14306 (2021).  https://doi.org/10.1021/acs.analchem.1c03468
  41. Zhang, M., Liu, C., Shi, Y., Wu, J., Wu, J., Chen, H., Selective endpoint visualized detection of Vibrio parahaemolyticus with CRISPR/Cas12a assisted PCR using thermal cycler for on-site application. Talanta, 214, 120818 (2020). 
  42. Rahman, H.S., Mahmoud, B.M., Othman, H.H., Amin, K., A review of history, definition, classification, source, transmission, and pathogenesis of salmonella: a model for human infection. JZS-A., 20, 11-19 (2018).  https://doi.org/10.17656/jzs.10730
  43. Ohl, M.E., Miller, S.I., Salmonella: a model for bacterial pathogenesis. Annu. Rev. Med., 52, 259-274 (2001).  https://doi.org/10.1146/annurev.med.52.1.259
  44. Wu, S., Yuan, J., Xu, A., Wang, L., Li, Y., Lin, J., Yue, X., Xi, X., A lab-on-a-tube biosensor combining recombinase-aided amplification and CRISRP-Cas12a with rotated magnetic extraction for Salmonella detection. Micromachines, 14, 830 (2023). 
  45. Evanko, D., Hybridization chain reaction. Nat. Methods, 1, 186 (2004). 
  46. Wang, J., Wang, D.X., Ma, J.Y., Wang, Y.X., Kong, D.M., Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction. Chem. Sci., 10, 9758-9767 (2019).  https://doi.org/10.1039/C9SC02281C
  47. Cai, Q., Shi, H., Sun, M., Ma, N., Wang, R., Yang, W., Qiao, Z., Sensitive detection of Salmonella based on CRISPR-Cas12a and the tetrahedral DNA nanostructure-mediated hyperbranched hybridization chain reaction. J. Agric. Food Chem., 70, 16382-16389 (2022).  https://doi.org/10.1021/acs.jafc.2c05831
  48. Kohler, C.D., Dobrindt, U., What defines extraintestinal pathogenic Escherichia coli?. Int. J. Med. Microbiol., 301, 642-647 (2011).  https://doi.org/10.1016/j.ijmm.2011.09.006
  49. Kaper, J.B., Nataro, J.P., Mobley, H.L., Pathogenic Escherichia coli. Nat. Rev. Microbiol., 2, 123-140 (2004).  https://doi.org/10.1038/nrmicro818
  50. Rani, A., Ravindran, V.B., Surapaneni, A., Mantri, N., Ball, A.S., Trends in point-of-care diagnosis for Escherichia coli O157:H7 in food and water. Int. J. Food Microbiol., 349, 109233 (2021). 
  51. Zhu, L., Liang, Z., Xu, Y., Chen, Z., Wang, J., Zhou, L., Ultrasensitive and rapid visual detection of Escherichia coli O157:H7 based on RAA-CRISPR/Cas12a system. Biosensors, 13, 659 (2023). 
  52. Bertrand, R., Roig, B., Evaluation of enrichment-free PCR-based detection on the rfbE gene of Escherichia coli O157-Application to municipal wastewater. Water Res., 41, 1280-1286 (2007).  https://doi.org/10.1016/j.watres.2006.11.027
  53. Bahadir, E.B., Sezginturk, M.K., Lateral flow assays: Principles, designs and labels. TrAC, Trends Anal. Chem., 82, 286-306 (2016).  https://doi.org/10.1016/j.trac.2016.06.006
  54. Melton-Celsa, A.R., Shiga toxin (Stx) classification, structure, and function. Microbiol. Spectr., 2, 2-4 (2014). 
  55. Lee, S.Y., Oh, S.W., Filteration-based LAMP-CRISPR/Cas12a system for the rapid, sensitive and visualized detection of Escherichia coli O157:H7. Talanta, 241, 123186 (2022). 
  56. Wehr, M.H., Listeria monocytogenes-a current dilemma. JAOAC., 70, 769-772 (1987). 
  57. Cossart, P., Toledo-Arana, A., Listeria monocytogenes, a unique model in infection biology: an overview. Microbes Infect., 10, 1041-1050 (2008).  https://doi.org/10.1016/j.micinf.2008.07.043
  58. Li, F., Ye, Q., Chen, M., Zhou, B., Zhang, J., Pang, R., Xue, L., Wang, J., Zeng, H., Wu, S., Zhang, Y., Ding, Y., Wu, Q., An ultrasensitive CIRSPR/Cas12a based electrochemical biosensor for Listeria monocytogenes detection. Biosens. Bioelectron., 179, 113073 (2021). 
  59. Xiao, Y., Ren, H., Wang, H., Zou, D., Liu, Y., Li, H., Hu, P., Li, Y., Liu, Z., Lu, S., A rapid and inexpensive nucleic acid detection platform for Listeria monocytogenes based on the CRISPR/Cas system. Talanta, 259, 124558 (2023). 
  60. Bonini, A., Poma, N., Vivaldi, F., Kirchhain, A., Salvo, P., Bottai, D., Tavanti, A., Di Francesco, F., Advances in biosensing: The CRISPR/Cas system as a new powerful tool for the detection of nucleic acid. J. Pharm. Biomed. Anal., 192, 113645 (2021).