Skip to main content
Log in

CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance

  • Review Article
  • Published:
BioDrugs Aims and scope Submit manuscript

Abstract

Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system’s potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. de Kraker MEA, Stewardson AJ, Harbarth S. Will 10 million people die a year due to antimicrobial resistance by 2050? PLOS Med. 2016;13: e1002184.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet Lond Engl. 2022;399:629–55.

    Article  Google Scholar 

  3. Murray, C. J. L. et al.Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet Lond Engl. 2022;399:629–55.

  4. Chung M, Yeh I, Sung L, Wu M, Chao Y, Ng I, et al. Enhanced integration of large DNA into E. coli chromosome by CRISPR/Cas9. Biotechnol Bioeng. 2017;114:172–83.

    Article  CAS  PubMed  Google Scholar 

  5. Tao S, Chen H, Li N, Liang W. The application of the CRISPR-Cas system in antibiotic resistance. Infect Drug Resist. 2022;15:4155–68.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Shetty VP, Akshay SD, Rai P, Deekshit VK. Integrons as the potential targets for combating multidrug resistance in Enterobacteriaceae using CRISPR- Cas9 technique. J Appl Microbiol. 2023;134: lxad137.

    Article  PubMed  Google Scholar 

  7. Wu Z-Y, Huang Y-T, Chao W-C, Ho S-P, Cheng J-F, Liu P-Y. Reversal of carbapenem-resistance in Shewanella algae by CRISPR/Cas9 genome editing. J Adv Res. 2019;18:61–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Lin DM, Koskella B, Lin HC. Phage therapy: an alternative to antibiotics in the age of multi-drug resistance. World J Gastrointest Pharmacol Ther. 2017;8:162–73.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Janik E, Niemcewicz M, Ceremuga M, Krzowski L, Saluk-Bijak J, Bijak M. Various aspects of a gene editing system—crispr–cas9. Int J Mol Sci. 2020;21:9604.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. He Y-Z, Kuang X, Long T-F, Li G, Ren H, He B, et al. Re-engineering a mobile-CRISPR/Cas9 system for antimicrobial resistance gene curing and immunization in Escherichia coli. J Antimicrob Chemother. 2022;77:74–82.

    Article  CAS  Google Scholar 

  11. Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR. CRISPR/Cas9 system: a bacterial tailor for genomic engineering. Genet Res Int. 2018. https://doi.org/10.1155/2018/3797214.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Kim J-S, Cho D-H, Park M, Chung W-J, Shin D, Ko KS, et al. CRISPR/Cas9-mediated re-sensitization of antibiotic-resistant Escherichia coli harboring extended-spectrum β-lactamases. J Microbiol Biotechnol. 2016;26:394–401.

    Article  CAS  PubMed  Google Scholar 

  13. Mojica FJ, Díez-Villaseñor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol. 2000;36:244–6.

    Article  CAS  PubMed  Google Scholar 

  14. Jansen R, van Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43:1565–75.

    Article  CAS  PubMed  Google Scholar 

  15. Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc B Biol Sci. 2016;371:20150496.

    Article  Google Scholar 

  16. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nat Struct Mol Biol. 2014;21:528–34.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Le Rhun A, Escalera-Maurer A, Bratovič M, Charpentier E. CRISPR-Cas in Streptococcus pyogenes. RNA Biol. 2019;16:380–9.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Teng M, Yao Y, Nair V, Luo J. Latest advances of virology research using CRISPR/Cas9-based gene-editing technology and its application to vaccine development. Viruses. 2021;13:779.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Koonin EV, Makarova KS, Zhang F. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol. 2017;37:67–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353: aaf5573.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Alduhaidhawi AHM, AlHuchaimi SN, Al-Mayah TA, Al-Ouqaili MT, Alkafaas SS, Muthupandian S, et al. Prevalence of CRISPR-cas systems and their possible association with antibiotic resistance in Enterococcus faecalis and Enterococcus faecium collected from hospital wastewater. Infect Drug Resist. 2022;15:1143–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL. Comparative analysis of the orphan CRISPR2 locus in 242 Enterococcus faecalis strains. PLoS One. 2015;10: e0138890.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Hullahalli K, Rodrigues M, Nguyen UT, Palmer K. An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition. MBio. 2018. https://doi.org/10.1128/mbio.00414-18.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Burley KM, Sedgley CM. CRISPR-Cas, a prokaryotic adaptive immune system, in endodontic, oral, and multidrug-resistant hospital-acquired Enterococcus faecalis. J Endod. 2012;38:1511–5.

    Article  PubMed  Google Scholar 

  25. Hullahalli K, Rodrigues M, Palmer KL. Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations. Elife. 2017;6: e26664.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Gholizadeh P, Aghazadeh M, Ghotaslou R, Rezaee MA, Pirzadeh T, Cui L, et al. Role of CRISPR-Cas system on antibiotic resistance patterns of Enterococcus faecalis. Ann Clin Microbiol Antimicrob. 2021;20:1–12.

    Article  Google Scholar 

  27. Zhou Y, Yang Y, Li X, Tian D, Ai W, Wang W, et al. Exploiting a conjugative endogenous CRISPR-Cas3 system to tackle multidrug-resistant Klebsiella pneumoniae. EBioMedicine. 2023;88: 104445.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 2011;30:1335–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Mousseau G, Kessing CF, Fromentin R, Trautmann L, Chomont N, Valente ST. The Tat inhibitor didehydro-cortistatin A prevents HIV-1 reactivation from latency. MBio. 2015. https://doi.org/10.1128/mbio.00465-15.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Selle K, Fletcher JR, Tuson H, Schmitt DS, McMillan L, Vridhambal GS, et al. In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials. MBio. 2020;11: e00019-20.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Yosef I, Manor M, Kiro R, Qimron U. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci. 2015;112:7267–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Wu X, Kriz AJ, Sharp PA. Target specificity of the CRISPR-Cas9 system. Quant Biol. 2014;2:59–70.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hao M, He Y, Zhang H, Liao X-P, Liu Y-H, Sun J, et al. CRISPR-Cas9-mediated carbapenemase gene and plasmid curing in carbapenem-resistant enterobacteriaceae. Antimicrob Agents Chemother. 2020;64:e00843-e920.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kyrou K, Hammond AM, Galizi R, Kranjc N, Burt A, Beaghton AK, et al. A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat Biotechnol. 2018;36:1062–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Shahriar SA, Islam MN, Chun CNW, Rahim MA, Paul NC, Uddain J, et al. Control of plant viral diseases by CRISPR/Cas9: resistance mechanisms, strategies and challenges in food crops. Plants. 2021;10:1264.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Hazafa A, Mumtaz M, Farooq MF, Bilal S, Chaudhry SN, Firdous M, et al. CRISPR/Cas9: a powerful genome editing technique for the treatment of cancer cells with present challenges and future directions. Life Sci. 2020;263: 118525.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol. 2018;3:135–49.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Hamilton TA, Pellegrino GM, Therrien JA, Ham DT, Bartlett PC, Karas BJ, et al. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nat Commun. 2019;10:4544.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Pouillot F, Chomton M, Blois H, Courroux C, Noelig J, Bidet P, et al. Efficacy of bacteriophage therapy in experimental sepsis and meningitis caused by a clone O25b:H4-ST131 Escherichia coli strain producing CTX-M-15. Antimicrob Agents Chemother. 2012;56:3568–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Aslam B, Rasool M, Idris A, Muzammil S, Alvi RF, Khurshid M, et al. CRISPR-Cas system: a potential alternative tool to cope antibiotic resistance. Antimicrob Resist Infect Control. 2020;9:131.

    Article  PubMed  PubMed Central  Google Scholar 

  41. Meeske AJ, Nakandakari-Higa S, Marraffini LA. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature. 2019;570:241–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Watanabe S, Cui B, Kiga K, Aiba Y, Tan X-E, Sato’o Y, et al. Composition and diversity of CRISPR-Cas13a systems in the genus leptotrichia. Front Microbiol. 2019. https://doi.org/10.3389/fmicb.2019.02838.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Kiga K, Tan X-E, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato’o Y, et al. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat Commun. 2020;11:2934.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wan F, Draz MS, Gu M, Yu W, Ruan Z, Luo Q. Novel strategy to combat antibiotic resistance: a sight into the combination of CRISPR/Cas9 and nanoparticles. Pharmaceutics. 2021;13:352.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pyne ME, Moo-Young M, Chung DA, Chou CP. Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli. Appl Environ Microbiol. 2015;81:5103–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Asmamaw Mengstie M. Viral Vectors for the in vivo delivery of CRISPR components: advances and challenges. Front Bioeng Biotechnol. 2022. https://doi.org/10.3389/fbioe.2022.895713.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Yang W, Yan J, Zhuang P, Ding T, Chen Y, Zhang Y, et al. Progress of delivery methods for CRISPR-Cas9. Expert Opin Drug Deliv. 2022;19:913–26.

    Article  PubMed  Google Scholar 

  48. Yip BH. Recent advances in CRISPR/Cas9 delivery strategies. Biomolecules. 2020;10:839.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Wang Y, Qi T, Liu J, Yang Y, Wang Z, Wang Y, et al. A highly specific CRISPR-Cas12j nuclease enables allele-specific genome editing. Sci Adv. 2023;9: eabo6405.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Pantoja Angles A, Ali Z, Mahfouz M. CS-cells: a CRISPR-Cas12 DNA device to generate chromosome-shredded cells for efficient and safe molecular biomanufacturing. ACS Synth Biol. 2022;11:430–40.

    Article  CAS  PubMed  Google Scholar 

  51. Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, et al. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med. 2022;8: e10381.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Rodrigues M, McBride SW, Hullahalli K, Palmer KL, Duerkop BA. Conjugative delivery of CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci. Antimicrob Agents Chemother. 2019;63:e01454-e1519.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Nguyen GT, Dhingra Y, Sashital DG. Miniature CRISPR-Cas12 endonucleases–programmed DNA targeting in a smaller package. Curr Opin Struct Biol. 2022;77: 102466.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Yeh T-K, Jean S-S, Lee Y-L, Lu M-C, Ko W-C, Lin H-J, et al. Bacteriophages and phage-delivered CRISPR-Cas system as antibacterial therapy. Int J Antimicrob Agents. 2022;59: 106475.

    Article  CAS  PubMed  Google Scholar 

  55. Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, et al. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Rep. 2021;37: 109930.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Fage C, Lemire N, Moineau S. Delivery of CRISPR-Cas systems using phage-based vectors. Curr Opin Biotechnol. 2021;68:174–80.

    Article  CAS  PubMed  Google Scholar 

  57. Deng H, Huang W, Zhang Z. Nanotechnology based CRISPR/Cas9 system delivery for genome editing: progress and prospect. Nano Res. 2019;12:2437–50.

    Article  CAS  Google Scholar 

  58. Rodríguez-Rodríguez DR, Ramírez-Solís R, Garza-Elizondo MA, Garza-Rodríguez MDL, Barrera-Saldaña HA. Genome editing: a perspective on the application of CRISPR/Cas9 to study human diseases (Review). Int J Mol Med. 2019;43:1559–74.

    PubMed  PubMed Central  Google Scholar 

  59. Givens BE, Naguib YW, Geary SM, Devor EJ, Salem AK. Nanoparticle-based delivery of CRISPR/Cas9 genome-editing therapeutics. AAPS J. 2018;20:1–22.

    Article  CAS  Google Scholar 

  60. Huang J, Zhou Y, Li J, Lu A, Liang C. CRISPR/Cas systems: Delivery and application in gene therapy. Front Bioeng Biotechnol. 2022;10: 942325.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Huang K, Zapata D, Tang Y, Teng Y, Li Y. In vivo delivery of CRISPR-Cas9 genome editing components for therapeutic applications. Biomaterials. 2022;291: 121876.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Qin W, Wang H. Delivery of CRISPR-Cas9 into mouse zygotes by electroporation. Methods Mol Biol Clifton NJ. 2019;1874:179–90.

    Article  CAS  Google Scholar 

  63. Wu Y, Battalapalli D, Hakeem MJ, Selamneni V, Zhang P, Draz MS, et al. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. J Nanobiotechnology. 2021;19:401.

    Article  PubMed  PubMed Central  Google Scholar 

  64. Dhasmana N, Ram G, McAllister KN, Chupalova Y, Lopez P, Ross HF, et al. Dynamics of antibacterial drone establishment in Staphylococcus aureus: unexpected effects of antibiotic resistance genes. MBio. 2021;12:e02083-e2121.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Abavisani M, Khayami R, Hoseinzadeh M, Kodori M, Kesharwani P, Sahebkar A. CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance. Drug Resist Updat. 2023;68: 100948.

    Article  CAS  PubMed  Google Scholar 

  66. Huemer M, Mairpady Shambat S, Brugger SD, Zinkernagel AS. Antibiotic resistance and persistence—implications for human health and treatment perspectives. EMBO Rep. 2020;21: e51034.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Senthilnathan R, Ilangovan I, Kunale M, Easwaran N, Ramamoorthy S, Veeramuthu A, et al. An update on CRISPR-Cas12 as a versatile tool in genome editing. Mol Biol Rep. 2023;50:2865–81.

    Article  CAS  PubMed  Google Scholar 

  68. Agarwal C. A review: CRISPR/Cas12-mediated genome editing in fungal cells: advancements, mechanisms, and future directions in plant-fungal pathology. Sci Prepr. 2023. https://doi.org/10.14293/S2199-1006.1.SOR.2023.0001.v1

  69. Song X, Liu C, Wang N, Huang H, He S, Gong C, et al. Delivery of CRISPR/Cas systems for cancer gene therapy and immunotherapy. Adv Drug Deliv Rev. 2021;168:158–80.

    Article  CAS  PubMed  Google Scholar 

  70. Taati Moghadam M, Amirmozafari N, Shariati A, Hallajzadeh M, Mirkalantari S, Khoshbayan A, et al. How phages overcome the challenges of drug resistant bacteria in clinical infections. Infect Drug Resist. 2020;13:45–61.

    Article  PubMed  PubMed Central  Google Scholar 

  71. Wang Z, Cui W. CRISPR-Cas system for biomedical diagnostic platforms. View. 2020;1:20200008.

    Article  Google Scholar 

  72. Tang Y, Gao L, Feng W, Guo C, Yang Q, Li F, et al. The CRISPR–Cas toolbox for analytical and diagnostic assay development. Chem Soc Rev. 2021;50:11844–69.

    Article  CAS  PubMed  Google Scholar 

  73. Padmanaban V, Ranganathan UDK. CRISPR–Cas system and its use in the diagnosis of infectious diseases. Microbiol Res. 2022;263: 127100.

    Article  CAS  PubMed  Google Scholar 

  74. Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, et al. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res. 2019;47:e83–e83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud J-B, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016;17:1–12.

    Article  Google Scholar 

  76. Yang H, Zhang Y, Teng X, Hou H, Deng R, Li J. CRISPR-based nucleic acid diagnostics for pathogens. Trends Anal Chem. 2023;160: 116980.

    Article  CAS  Google Scholar 

  77. Wang C, Liu M, Wang Z, Li S, Deng Y, He N. Point-of-care diagnostics for infectious diseases: from methods to devices. Nano Today. 2021;37: 101092.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc. 2019;14:2986–3012.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Arizti-Sanz J, Freije CA, Stanton AC, Petros BA, Boehm CK, Siddiqui S, et al. Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nat Commun. 2020;11:5921.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Bonini A, Poma N, Vivaldi F, Biagini D, Bottai D, Tavanti A, et al. A label-free impedance biosensing assay based on CRISPR/Cas12a collateral activity for bacterial DNA detection. J Pharm Biomed Anal. 2021;204: 114268.

    Article  CAS  PubMed  Google Scholar 

  81. Wang F, Wang L, Chen H, Li N, Wang Y, Li Y, et al. Rapid detection of blaKPC, blaNDM, blaOXA-48-like and blaIMP carbapenemases in enterobacterales using recombinase polymerase amplification combined with lateral flow strip. Front Cell Infect Microbiol. 2021. https://doi.org/10.3389/fcimb.2021.772966.

    Article  PubMed  PubMed Central  Google Scholar 

  82. Nguyen LT, Macaluso NC, Pizzano BLM, Cash MN, Spacek J, Karasek J, et al. A thermostable Cas12b from Brevibacillus leverages one-pot detection of SARS-CoV-2 variants of concern. MedRxiv Prepr Serv Health Sci. 2021;2021.10.15.21265066.

  83. Ge X, Meng T, Tan X, Wei Y, Tao Z, Yang Z, et al. Cas14a1-mediated nucleic acid detectifon platform for pathogens. Biosens Bioelectron. 2021;189: 113350.

    Article  CAS  PubMed  Google Scholar 

  84. Wei Y, Tao Z, Wan L, Zong C, Wu J, Tan X, et al. Aptamer-based Cas14a1 biosensor for amplification-free live pathogenic detection. Biosens Bioelectron. 2022;211: 114282.

    Article  CAS  PubMed  Google Scholar 

  85. Abavisani M, Khayami R, Hoseinzadeh M, Kodori M, Kesharwani P, Sahebkar A. CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance. Drug Resist Updat Rev Comment Antimicrob Anticancer Chemother. 2023;68: 100948.

    CAS  Google Scholar 

  86. Huang M, Zhou X, Wang H, Xing D. Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection. Anal Chem. 2018;90:2193–200.

    Article  CAS  PubMed  Google Scholar 

  87. Xiao G, Zhang S, Liang Z, Li G, Fang M, Liu Y, et al. Identification of Mycobacterium abscessus species and subspecies using the Cas12a/sgRNA-based nucleic acid detection platform. Eur J Clin Microbiol Infect Dis. 2020;39:551–8.

    Article  CAS  PubMed  Google Scholar 

  88. Duan C, Cao H, Zhang L-H, Xu Z. Harnessing the CRISPR-Cas systems to combat antimicrobial resistance. Front Microbiol. 2021. https://doi.org/10.3389/fmicb.2021.716064.

    Article  PubMed  PubMed Central  Google Scholar 

  89. Pouillot F, Chomton M, Blois H, Courroux C, Noelig J, Bidet P, et al. Efficacy of bacteriophage therapy in experimental sepsis and meningitis caused by a clone O25b: H4-ST131 Escherichia coli strain producing CTX-M-15. Antimicrob Agents Chemother. 2012;56:3568–75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Sun Q, Wang Y, Dong N, Shen L, Zhou H, Hu Y, et al. Application of CRISPR/Cas9-based genome editing in studying the mechanism of pandrug resistance in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2019;63:e00113-e119.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Wu X, Zha J, Koffas MA, Dordick JS. Reducing Staphylococcus aureus resistance to lysostaphin using CRISPR-dCas9. Biotechnol Bioeng. 2019;116:3149–59.

    Article  CAS  PubMed  Google Scholar 

  92. Ram G, Ross HF, Novick RP, Rodriguez-Pagan I, Jiang D. Conversion of staphylococcal pathogenicity islands to CRISPR-carrying antibacterial agents that cure infections in mice. Nat Biotechnol. 2018;36:971–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Park JY, Moon BY, Park JW, Thornton JA, Park YH, Seo KS. Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Sci Rep. 2017;7:44929.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Kang YK, Kwon K, Ryu JS, Lee HN, Park C, Chung HJ. Nonviral genome editing based on a polymer-derivatized CRISPR nanocomplex for targeting bacterial pathogens and antibiotic resistance. Bioconjug Chem. 2017;28:957–67.

    Article  CAS  PubMed  Google Scholar 

  95. Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol. 2014;32:1146–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Walflor HSM, Lucena ARC, Tuon FF, Medeiros LCS, Faoro H. Resensitization of fosfomycin-resistant Escherichia coli using the CRISPR system. Int J Mol Sci. 2022;23:9175.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Wan P, Cui S, Ma Z, Chen L, Li X, Zhao R, et al. Reversal of mcr-1-mediated colistin resistance in Escherichia coli by CRISPR-Cas9 system. Infect Drug Resist. 2020;13:1171–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Reuter A, Hilpert C, Dedieu-Berne A, Lematre S, Gueguen E, Launay G, et al. Targeted-antibacterial-plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity. Nucleic Acids Res. 2021;49:3584–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Tagliaferri TL, Guimarães NR, Pereira MPM, Vilela LFF, Horz H-P, Dos Santos SG, et al. Exploring the potential of CRISPR-Cas9 under challenging conditions: facing high-copy plasmids and counteracting beta-lactam resistance in clinical strains of Enterobacteriaceae. Front Microbiol. 2020;11:578.

    Article  PubMed  PubMed Central  Google Scholar 

  100. Li P, Wan P, Zhao R, Chen J, Li X, Li J, et al. Targeted elimination of blaNDM-5 gene in Escherichia coli by conjugative CRISPR-Cas9 system. Infect Drug Resist. 2022;15:1707–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Citorik RJ, Mimee M, Lu TK. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol. 2014;32:1141–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Liu H, Li H, Liang Y, Du X, Yang C, Yang L, et al. Phage-delivered sensitisation with subsequent antibiotic treatment reveals sustained effect against antimicrobial resistant bacteria. Theranostics. 2020;10:6310–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Wang T, Liu Y, Sun H-H, Yin B-C, Ye B-C. An RNA-guided Cas9 nickase-based method for universal isothermal DNA amplification. Angew Chem. 2019;131:5436–40.

    Article  Google Scholar 

  104. Guk K, Keem JO, Hwang SG, Kim H, Kang T, Lim E-K, et al. 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.

    Article  CAS  PubMed  Google Scholar 

  105. Wang X, Xiong E, Tian T, Cheng M, Lin W, Wang H, et al. Clustered regularly interspaced short palindromic repeats/Cas9-mediated lateral flow nucleic acid assay. ACS Nano. 2020;14:2497–508.

    Article  CAS  PubMed  Google Scholar 

  106. You Y, Zhang P, Wu G, Tan Y, Zhao Y, Cao S, et al. Highly specific and sensitive detection of Yersinia pestis by portable Cas12a-UPTLFA platform. Front Microbiol. 2021;12: 700016.

    Article  PubMed  PubMed Central  Google Scholar 

  107. Ai J-W, Zhou X, Xu T, Yang M, Chen Y, He G-Q, et al. CRISPR-based rapid and ultra-sensitive diagnostic test for Mycobacterium tuberculosis. Emerg Microbes Infect. 2019;8:1361–9.

    Article  PubMed  PubMed Central  Google Scholar 

  108. Wang Y, Liang X, Xu J, Nan L, Liu F, Duan G, et al. Rapid and ultrasensitive detection of methicillin-resistant Staphylococcus aureus based on CRISPR-Cas12a combined with recombinase-aided amplification. Front Microbiol. 2022;13: 903298.

    Article  PubMed  PubMed Central  Google Scholar 

  109. Liu X, Qiu X, Xu S, Che Y, Han L, Kang Y, et al. A CRISPR-Cas12a-assisted fluorescence platform for rapid and accurate detection of Nocardia cyriacigeorgica. Front Cell Infect Microbiol. 2022;12: 835213.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Wang Y, Ke Y, Liu W, Sun Y, Ding X. A one-pot toolbox based on Cas12a/crRNA enables rapid foodborne pathogen detection at attomolar level. Acs Sens. 2020;5:1427–35.

    Article  CAS  PubMed  Google Scholar 

  111. Lu P, Chen J, Li Z, Li Z, Zhang J, Kan B, et al. Visual identification and serotyping of toxigenic Vibrio cholerae serogroups O1 and O139 with CARID. Front Cell Infect Microbiol. 2022;12: 863435.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Xiao X, Lin Z, Huang X, Lu J, Zhou Y, Zheng L, et al. Rapid and sensitive detection of Vibrio vulnificus using CRISPR/Cas12a combined with a recombinase-aided amplification assay. Front Microbiol. 2021;12: 767315.

    Article  PubMed  PubMed Central  Google Scholar 

  113. Qiu E, Jin S, Xiao Z, Chen Q, Wang Q, Liu H, et al. CRISPR-based Detection of Helicobacter pylori in Stool Samples. Helicobacter. 2021;26: e12828.

    Article  CAS  PubMed  Google Scholar 

  114. Li C, Chen X, Wen R, Ma P, Gu K, Li C, et al. Immunocapture magnetic beads enhanced the LAMP-CRISPR/Cas12a method for the sensitive, specific, and visual detection of Campylobacter jejuni. Biosensors. 2022;12:154.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Wu H, Cao X, Meng Y, Richards D, Wu J, Ye Z, et al. DropCRISPR: a LAMP-Cas12a based digital method for ultrasensitive detection of nucleic acid. Biosens Bioelectron. 2022;211: 114377.

    Article  CAS  PubMed  Google Scholar 

  116. Schultzhaus Z, Wang Z, Stenger D. Systematic analysis, identification, and use of CRISPR/Cas13a–associated crRNAs for sensitive and specific detection of the lcrV gene of Yersinia pestis. Diagn Microbiol Infect Dis. 2021;99: 115275.

    Article  CAS  PubMed  Google Scholar 

  117. Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356:438–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Zhou J, Yin L, Dong Y, Peng L, Liu G, Man S, et al. CRISPR-Cas13a based bacterial detection platform: sensing pathogen Staphylococcus aureus in food samples. Anal Chim Acta. 2020;1127:225–33.

    Article  CAS  PubMed  Google Scholar 

  119. Zhan Y, Gao X, Li S, Si Y, Li Y, Han X, et al. Development and evaluation of rapid and accurate CRISPR/Cas13-based RNA diagnostics for Pneumocystis jirovecii pneumonia. Front Cell Infect Microbiol. 2022. https://doi.org/10.3389/fcimb.2022.904485.

    Article  PubMed  PubMed Central  Google Scholar 

  120. Gao S, Liu J, Li Z, Ma Y, Wang J. Sensitive detection of foodborne pathogens based on CRISPR-Cas13a. J Food Sci. 2021;86:2615–25.

    Article  CAS  PubMed  Google Scholar 

  121. Song F, Wei Y, Wang P, Ge X, Li C, Wang A, et al. Combining tag-specific primer extension and magneto-DNA system for Cas14a-based universal bacterial diagnostic platform. Biosens Bioelectron. 2021;185: 113262.

    Article  CAS  PubMed  Google Scholar 

  122. WAI CC. Genome-wide CRISPR Screen for Host Factors Associated With Norovirus Infections in Stem Cell-derived Human Intestinal Enteroid Model [Internet]. clinicaltrials.gov; 2018 Sep. Report No.: NCT03342547. Available from: https://clinicaltrials.gov/study/NCT03342547

  123. Chinese Medical Association. Species-specific Bacterial Detector for Fast Pathogen Diagnosis of Severe Pneumonia Patients in Intensive Care Uint: a Multicentre, Randomised Controlled Trial [Internet]. clinicaltrials.gov; 2022 May. Report No.: NCT05143593. Available from: https://clinicaltrials.gov/study/NCT05143593

  124. Zhang W. Evaluation of CRISPR-based Test for the Rapid Identification of Mycobacterium Tuberculosis Complex in Pulmonary Tuberculosis Suspects [Internet]. clinicaltrials.gov; 2019 Aug. Report No.: NCT04074369. Available from: https://clinicaltrials.gov/study/NCT04074369

  125. Diagnostic trial: Human Enterovirus Infections, HEV, (NCT04535648) [Internet]. CRISPR Med. [cited 2024 Feb 22]. Available from: https://crisprmedicinenews.com/diagnostic-trial/human-enterovirus-infections-hev-nct04535648-1/

  126. Chinese Medical Association. Effect of PCR-CRISPR/Cas12a on the Early Anti-infective Schemes in Patients With Open Air Pneumonia [Internet]. clinicaltrials.gov; 2019 Nov. Report No.: NCT04178382. Available from: https://clinicaltrials.gov/study/NCT04178382

  127. Children’s Hospital of Fudan University. Establishment a Nucleic Acid Rapid Detection Technology Platform for Detecting Pathogenic Bordetella and Its Drug Resistance Genes [Internet]. clinicaltrials.gov; 2022 Sep. Report No.: NCT04535505. Available from: https://clinicaltrials.gov/study/NCT04535505

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Haihong Hao.

Ethics declarations

Ethics Approval and Consent to participate

Not applicable.

Consent for Publication

Not applicable.

Availability of Data and Materials

Not applicable.

Funding

Financial support for this study was provided by the National Natural Science Foundation of China (Grant No. 32172914), the National Key Research and Development Program (Grant No. 2021YFD1800600), and the Fundamental Research Funds for the Central Universities (Grant No. 2662022DKYJC005).

Competing Interests

All authors report no conflicts of interest.

Code Availability

Not applicable.

Author Contributions

Shahzad Rafiq contributed to the original conceptualization and initial draft of the manuscript. Muhammad AbuBakr Shabbir, Ahmed Raza, Shoaib Irshad, Andleeb Asghar, Muhammad Kashif Maan, and Mushtaq Ahmed Gondal carried out the review, editing, and validation tasks. Haihong Hao played a role in the article's conceptualization, review, editing, and supervision. All the authors have thoroughly read and unanimously agreed to the final version of the published manuscript.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rafiq, M., Shabbir, M.A., Raza, A. et al. CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance. BioDrugs 38, 387–404 (2024). https://doi.org/10.1007/s40259-024-00656-3

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40259-024-00656-3

Navigation