The Application of the CRISPR-Cas System in Antibiotic Resistance

References

• Kim JH, Yu D, Eom SH, et al. Synergistic antibacterial effects of chitosan-caffeic acid conjugate against antibiotic-resistant acne-related bacteria. Mar Drugs. 2017;15(6):167. doi:10.3390/md15060167
   Web of Science ®Google Scholar
• Santajit S, Indrawattana N. Mechanisms of antimicrobial resistance in ESKAPE pathogens. Biomed Res Int. 2016;2016:2475067. doi:10.1155/2016/2475067
   PubMed Web of Science ®Google Scholar
• Christaki E, Marcou M, Tofarides A. Antimicrobial resistance in bacteria: mechanisms, evolution, and persistence. J Mol Evol. 2020;88(1):26–40.
   PubMed Web of Science ®Google Scholar
• Pang Z, Raudonis R, Glick BR, Lin TJ, Cheng Z. Antibiotic resistance in Pseudomonas aeruginosa: mechanisms and alternative therapeutic strategies. Biotechnol Adv. 2019;37(1):177–192. doi:10.1016/j.biotechadv.2018.11.013
   PubMed Web of Science ®Google Scholar
• Rostock L, Driller R, Grätz S, et al. Molecular insights into antibiotic resistance - how a binding protein traps albicidin. Nat Commun. 2018;9(1):3095. doi:10.1038/s41467-018-05551-4
   Web of Science ®Google Scholar
• Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev. 2018;42(1). doi:10.1093/femsre/fux053
   Web of Science ®Google Scholar
• von Wintersdorff CJ, Penders J, van Niekerk JM, et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol. 2016;7:173. doi:10.3389/fmicb.2016.00173
   PubMed Web of Science ®Google Scholar
• Meng M, Li Y, Yao H. Plasmid-mediated transfer of antibiotic resistance genes in soil. Antibiotics. 2022;11(4). doi:10.3390/antibiotics11040525
   Web of Science ®Google Scholar
• Fogg PCM. Identification and characterization of a direct activator of a gene transfer agent. Nat Commun. 2019;10(1):595. doi:10.1038/s41467-019-08526-1
   Web of Science ®Google Scholar
• Engelstädter J, Harms K, Johnsen PJ. The evolutionary dynamics of integrons in changing environments. ISME J. 2016;10(6):1296–1307. doi:10.1038/ismej.2015.222
   PubMed Web of Science ®Google Scholar
• Koonin EV, Makarova KS. Mobile genetic elements and evolution of CRISPR-Cas systems: all the way there and back. Genome Biol Evol. 2017;9(10):2812–2825. doi:10.1093/gbe/evx192
   PubMedGoogle Scholar
• Price VJ, Huo W, Sharifi A, Palmer KL. CRISPR-Cas and restriction-modification act additively against conjugative antibiotic resistance plasmid transfer in Enterococcus faecalis. mSphere. 2016;1(3). doi:10.1128/mSphere.00064-16
   Web of Science ®Google Scholar
• Mackow NA, Shen J, Adnan M, et al. CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae. PLoS One. 2019;14(11):e0225131. doi:10.1371/journal.pone.0225131
   Web of Science ®Google Scholar
• Hille F, Charpentier E. CRISPR-Cas: biology, mechanisms and relevance. Philos Trans R Soc Lond B Biol Sci. 2016;371(1707). doi:10.1098/rstb.2015.0496
   Web of Science ®Google Scholar
• Zheng Z, Zhang Y, Liu Z, et al. The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments. ISME J. 2020;14(6):1479–1493. doi:10.1038/s41396-020-0623-5
   Web of Science ®Google Scholar
• Gholizadeh P, Ş K, Dao S, et al. How CRISPR-Cas system could be used to combat antimicrobial resistance. Infect Drug Resist. 2020;13:1111–1121. doi:10.2147/IDR.S247271
   PubMed Web of Science ®Google Scholar
• Rath D, Amlinger L, Hoekzema M, Devulapally PR, Lundgren M. Efficient programmable gene silencing by Cascade. Nucleic Acids Res. 2015;43(1):237–246. doi:10.1093/nar/gku1257
   Web of Science ®Google Scholar
• Hillary VE, Ignacimuthu S, Ceasar SA. Potential of CRISPR/Cas system in the diagnosis of COVID-19 infection. Expert Rev Mol Diagn. 2021;21(11):1179–1189. doi:10.1080/14737159.2021.1970535
   PubMed Web of Science ®Google Scholar
• Hu T, Cui Y, Qu X. Characterization and comparison of CRISPR Loci in Streptococcus thermophilus. Arch Microbiol. 2020;202(4):695–710. doi:10.1007/s00203-019-01780-3
   Web of Science ®Google Scholar
• Alkhnbashi OS, Shah SA, Garrett RA, et al. Characterizing leader sequences of CRISPR loci. Bioinformatics. 2016;32(17):i576–i585. doi:10.1093/bioinformatics/btw454
   PubMed Web of Science ®Google Scholar
• Nishimasu H, Nureki O. Structures and mechanisms of CRISPR RNA-guided effector nucleases. Curr Opin Struct Biol. 2017;43:68–78. doi:10.1016/j.sbi.2016.11.013
   Web of Science ®Google Scholar
• Mohanraju P, Makarova KS, Zetsche B, et al. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016;353(6299):aad5147. doi:10.1126/science.aad5147
   PubMed Web of Science ®Google Scholar
• Shmakov S, Abudayyeh OO, Makarova KS, et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell. 2015;60(3):385–397. doi:10.1016/j.molcel.2015.10.008
   PubMed Web of Science ®Google Scholar
• Makarova KS, Wolf YI, Alkhnbashi OS, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13(11):722–736. doi:10.1038/nrmicro3569
   PubMed Web of Science ®Google Scholar
• Kalds P, Zhou S, Cai B, et al. Sheep and goat genome engineering: from random transgenesis to the CRISPR era. Front Genet. 2019;10:750. doi:10.3389/fgene.2019.00750
   Web of Science ®Google Scholar
• Zhang Q, Doak TG, Ye Y. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Res. 2014;42(4):2448–2459. doi:10.1093/nar/gkt1262
   Web of Science ®Google Scholar
• Jackson SA, McKenzie RE, Fagerlund RD, et al. CRISPR-Cas: adapting to change. Science. 2017;356(6333). doi:10.1126/science.aal5056.
   Web of Science ®Google Scholar
• Nuñez JK, Kranzusch PJ, Noeske J, et al. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014;21(6):528–534. doi:10.1038/nsmb.2820
   PubMed Web of Science ®Google Scholar
• Nuñez JK, Lee AS, Engelman A, Doudna JA. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature. 2015;519(7542):193–198. doi:10.1038/nature14237
   PubMed Web of Science ®Google Scholar
• Plagens A, Richter H, Charpentier E, Randau L. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. FEMS Microbiol Rev. 2015;39(3):442–463. doi:10.1093/femsre/fuv019
   Web of Science ®Google Scholar
• Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev. 2015;39(3):428–441. doi:10.1093/femsre/fuv023
   PubMed Web of Science ®Google Scholar
• Le Rhun A, Escalera-Maurer A, Bratovič M, Charpentier E. CRISPR-Cas in Streptococcus pyogenes. RNA Biol. 2019;16(4):380–389. doi:10.1080/15476286.2019.1582974
   PubMed Web of Science ®Google Scholar
• 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(5):779. doi:10.3390/v13050779
   PubMed Web of Science ®Google Scholar
• Makarova KS, Zhang F, Koonin EV. SnapShot: class 1 CRISPR-Cas systems. Cell. 2017;168(5):946–946.e1. doi:10.1016/j.cell.2017.02.018
   PubMed Web of Science ®Google Scholar
• Zheng Y, Li J, Wang B, et al. Endogenous type I CRISPR-Cas: from foreign DNA defense to prokaryotic engineering. Front Bioeng Biotechnol. 2020;8:62. doi:10.3389/fbioe.2020.00062
   Web of Science ®Google Scholar
• Westra ER, van Erp PB, Künne T, et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell. 2012;46(5):595–605. doi:10.1016/j.molcel.2012.03.018
   PubMed Web of Science ®Google Scholar
• Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microb Cell Fact. 2020;19(1):172. doi:10.1186/s12934-020-01431-z
   PubMed Web of Science ®Google Scholar
• Shmakov S, Smargon A, Scott D, et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169–182. doi:10.1038/nrmicro.2016.184
   PubMed Web of Science ®Google Scholar
• Mir A, Edraki A, Lee J, Sontheimer EJ. Type II-C CRISPR-Cas9 biology, mechanism, and application. ACS Chem Biol. 2018;13(2):357–365. doi:10.1021/acschembio.7b00855
   Web of Science ®Google Scholar
• Nishimasu H, Ran FA, Hsu PD, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014;156(5):935–949. doi:10.1016/j.cell.2014.02.001
   PubMed Web of Science ®Google Scholar
• Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012;109(39):E2579–86. doi:10.1073/pnas.1208507109
   Web of Science ®Google Scholar
• Komor AC, Badran AH, Liu DR. CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell. 2017;168(1–2):20–36. doi:10.1016/j.cell.2016.10.044
   PubMed Web of Science ®Google Scholar
• Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–424. doi:10.1038/nature17946
   PubMed Web of Science ®Google Scholar
• Fu YW, Dai XY, Wang WT, et al. Dynamics and competition of CRISPR-Cas9 ribonucleoproteins and AAV donor-mediated NHEJ, MMEJ and HDR editing. Nucleic Acids Res. 2021;49(2):969–985. doi:10.1093/nar/gkaa1251
   Web of Science ®Google Scholar
• Pickar-Oliver A, Gersbach CA. The next generation of CRISPR-Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20(8):490–507. doi:10.1038/s41580-019-0131-5
   PubMed Web of Science ®Google Scholar
• Cencic R, Miura H, Malina A, et al. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage. PLoS One. 2014;9(10):e109213. doi:10.1371/journal.pone.0109213
   PubMed Web of Science ®Google Scholar
• Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv. 2018;25(1):1234–1257. doi:10.1080/10717544.2018.1474964
   PubMed Web of Science ®Google Scholar
• Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev. 2015;39(1):81–95. doi:10.1111/1574-6976.12085
   PubMed Web of Science ®Google Scholar
• Harrison E, Brockhurst MA. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol. 2012;20(6):262–267. doi:10.1016/j.tim.2012.04.003
   PubMed Web of Science ®Google Scholar
• Köstlbacher S, Collingro A, Halter T, Domman D, Horn M. Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria. Curr Biol. 2021;31(2):346–357.e3. doi:10.1016/j.cub.2020.10.030
   Web of Science ®Google Scholar
• 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(11). doi:10.1128/AAC.01454-19
   Web of Science ®Google Scholar
• Kang YK, Kwon K, Ryu JS, et al. Nonviral genome editing based on a polymer-derivatized CRISPR nanocomplex for targeting bacterial pathogens and antibiotic resistance. Bioconjug Chem. 2017;28(4):957–967. doi:10.1021/acs.bioconjchem.6b00676
   PubMed Web of Science ®Google Scholar
• Gama JA, Zilhão R, Dionisio F. Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: plasmids promote the immigration of other plasmids but repress co-colonizing plasmids. Plasmid. 2017;93:6–16. doi:10.1016/j.plasmid.2017.08.003
   Web of Science ®Google Scholar
• Reuter A, Hilpert C, Dedieu-Berne A, et al. Targeted-antibacterial-plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity. Nucleic Acids Res. 2021;49(6):3584–3598. doi:10.1093/nar/gkab126
   Web of Science ®Google Scholar
• Dong H, Xiang H, Mu D, Wang D, Wang T. Exploiting a conjugative CRISPR/Cas9 system to eliminate plasmid harbouring the mcr-1 gene from Escherichia coli. Int J Antimicrob Agents. 2019;53(1):1–8. doi:10.1016/j.ijantimicag.2018.09.017
   Web of Science ®Google Scholar
• Wang P, He D, Li B, et al. Eliminating mcr-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system. J Antimicrob Chemother. 2019;74(9):2559–2565. doi:10.1093/jac/dkz246
   PubMed Web of Science ®Google Scholar
• Chen G, Cheng D, Chen B. [Development of CRISPR technology and its application in bone and cartilage tissue engineering]. Nan Fang Yi Ke Da Xue Xue Bao. 2019 Dec 30;39(12):1515-1520. Chinese. doi:10.12122/j.issn.1673-4254.2019.12.19
   Google Scholar
• Ling X, Xie B, Gao X, et al. Improving the efficiency of precise genome editing with site-specific Cas9-oligonucleotide conjugates. Sci Adv. 2020;6(15):eaaz0051. doi:10.1126/sciadv.aaz0051
   PubMed Web of Science ®Google Scholar
• Price VJ, McBride SW, Hullahalli K, et al. Enterococcus faecalis CRISPR-Cas Is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine. mSphere. 2019;4(4). doi:10.1128/mSphere.00464-19.
   Web of Science ®Google Scholar
• Zou J, Tang Z, Yan J, et al. Dissemination of linezolid resistance through sex pheromone plasmid transfer in Enterococcus faecalis. Front Microbiol. 2020;11:1185. doi:10.3389/fmicb.2020.01185
   Web of Science ®Google Scholar
• Borges AL, Castro B, Govindarajan S, et al. Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat Microbiol. 2020;5(5):679–687. doi:10.1038/s41564-020-0691-3
   Web of Science ®Google Scholar
• Górski A, Międzybrodzki R, Borysowski J, et al. Phage as a modulator of immune responses: practical implications for phage therapy. Adv Virus Res. 2012;83:41–71.
   PubMed Web of Science ®Google Scholar
• Fage C, Lemire N, Moineau S. Delivery of CRISPR-Cas systems using phage-based vectors. Curr Opin Biotechnol. 2021;68:174–180. doi:10.1016/j.copbio.2020.11.012
   Web of Science ®Google Scholar
• Kim JS, Cho DH, Park M, et al. CRISPR/Cas9-mediated re-sensitization of antibiotic-resistant Escherichia coli harboring extended-spectrum β-Lactamases. J Microbiol Biotechnol. 2016;26(2):394–401. doi:10.4014/jmb.1508.08080
   PubMed Web of Science ®Google Scholar
• Yosef I, Manor M, Kiro R, Qimron U. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci U S A. 2015;112(23):7267–7272. doi:10.1073/pnas.1500107112
   PubMed Web of Science ®Google Scholar
• Oechslin F. Resistance development to bacteriophages occurring during bacteriophage therapy. Viruses. 2018;10(7):351. doi:10.3390/v10070351
   PubMed Web of Science ®Google Scholar
• Bikard D, Euler CW, Jiang W, et al. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol. 2014;32(11):1146–1150. doi:10.1038/nbt.3043
   PubMed Web of Science ®Google Scholar
• Lam KN, Spanogiannopoulos P, Soto-Perez P, et al. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Rep. 2021;37(5):109930. doi:10.1016/j.celrep.2021.109930
   Web of Science ®Google Scholar
• Kiga K, Tan XE, Ibarra-Chávez R, et al. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat Commun. 2020;11(1):2934. doi:10.1038/s41467-020-16731-6
   PubMed Web of Science ®Google Scholar
• Gerritzen MJH, Martens DE, Wijffels RH, Stork M. High throughput nanoparticle tracking analysis for monitoring outer membrane vesicle production. J Extracell Vesicles. 2017;6(1):1333883. doi:10.1080/20013078.2017.1333883
   PubMed Web of Science ®Google Scholar
• Collins SM, Brown AC. Bacterial outer membrane vesicles as antibiotic delivery vehicles. Front Immunol. 2021;12:733064. doi:10.3389/fimmu.2021.733064
   Web of Science ®Google Scholar
• Martora F, Pinto F, Folliero V, et al. Isolation, characterization and analysis of pro-inflammatory potential of Klebsiella pneumoniae outer membrane vesicles. Microb Pathog. 2019;136:103719. doi:10.1016/j.micpath.2019.103719
   Web of Science ®Google Scholar
• Dell’Annunziata F, Folliero V, Giugliano R, et al. Gene transfer potential of outer membrane vesicles of gram-negative bacteria. Int J Mol Sci. 2021;22(11):5985. doi:10.3390/ijms22115985
   PubMed Web of Science ®Google Scholar
• Yao X, Lyu P, Yoo K, et al. Engineered extracellular vesicles as versatile ribonucleoprotein delivery vehicles for efficient and safe CRISPR genome editing. J Extracell Vesicles. 2021;10(5):e12076. doi:10.1002/jev2.12076
   PubMed Web of Science ®Google Scholar
• Fantappiè L, de Santis M, Chiarot E, et al. Antibody-mediated immunity induced by engineered Escherichia coli OMVs carrying heterologous antigens in their lumen. J Extracell Vesicles. 2014;3(1):24015. doi:10.3402/jev.v3.24015
   PubMedGoogle Scholar
• Lu M, Xing H, Yang Z, et al. Recent advances on extracellular vesicles in therapeutic delivery: challenges, solutions, and opportunities. Eur J Pharm Biopharm. 2017;119:381–395. doi:10.1016/j.ejpb.2017.07.010
   PubMed Web of Science ®Google Scholar
• Pudlarz A, Szemraj J. Nanoparticles as carriers of proteins, peptides and other therapeutic molecules. Open Life Sci. 2018;13(1):285–298. doi:10.1515/biol-2018-0035
   Web of Science ®Google Scholar
• Givens BE, Naguib YW, Geary SM, Devor EJ, Salem AK. Nanoparticle-based delivery of CRISPR/Cas9 genome-editing therapeutics. AAPS J. 2018;20(6):108. doi:10.1208/s12248-018-0267-9
   PubMed Web of Science ®Google Scholar
• Lima R, Del Fiol FS, Balcão VM. Prospects for the use of new technologies to combat multidrug-resistant bacteria. Front Pharmacol. 2019;10:692. doi:10.3389/fphar.2019.00692
   PubMed Web of Science ®Google Scholar
• Xu X, Liu C, Wang Y, et al. Nanotechnology-based delivery of CRISPR/Cas9 for cancer treatment. Adv Drug Deliv Rev. 2021;176:113891. doi:10.1016/j.addr.2021.113891
   PubMed Web of Science ®Google Scholar
• Wan F, Draz MS, Gu M, et al. Novel strategy to combat antibiotic resistance: a sight into the combination of CRISPR/Cas9 and nanoparticles. Pharmaceutics. 2021;13(3):352. doi:10.3390/pharmaceutics13030352
   PubMed Web of Science ®Google Scholar
• Shaw DJ, Hill RE, Simpson N, et al. Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chem Sci. 2017;8(12):8384–8399. doi:10.1039/C7SC03336B
   Web of Science ®Google Scholar
• Stevenson C, Hall JP, Harrison E, Wood A, Brockhurst MA. Gene mobility promotes the spread of resistance in bacterial populations. ISME J. 2017;11(8):1930–1932. doi:10.1038/ismej.2017.42
   Web of Science ®Google Scholar
• Liu T, Liu Z, Ye Q, et al. Coupling transcriptional activation of CRISPR-Cas system and DNA repair genes by Csa3a in sulfolobus islandicus. Nucleic Acids Res. 2017;45(15):8978–8992. doi:10.1093/nar/gkx612
   Web of Science ®Google Scholar
• Serajian S, Ahmadpour E, Oliveira SMR, Pereira ML, Heidarzadeh S. CRISPR-Cas technology: emerging applications in clinical microbiology and infectious diseases. Pharmaceuticals. 2021;14(11). doi:10.3390/ph14111171
   Web of Science ®Google Scholar
• Xu Y, Li Z. CRISPR-Cas systems: overview, innovations and applications in human disease research and gene therapy. Comput Struct Biotechnol J. 2020;18:2401–2415. doi:10.1016/j.csbj.2020.08.031
   PubMed Web of Science ®Google Scholar
• Aydin S, Personne Y, Newire E, et al. Presence of Type I-F CRISPR/Cas systems is associated with antimicrobial susceptibility in Escherichia coli. J Antimicrob Chemother. 2017;72(8):2213–2218. doi:10.1093/jac/dkx137
   Web of Science ®Google Scholar
• Wang G, Song G, Xu Y. Association of CRISPR/Cas system with the drug resistance in Klebsiella pneumoniae. Infect Drug Resist. 2020;13:1929–1935. doi:10.2147/IDR.S253380
   Web of Science ®Google Scholar
• Pursey E, Dimitriu T, Paganelli FL, Westra ER, van Houte S. CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci. 2022;377(1842):20200464. doi:10.1098/rstb.2020.0464
   Web of Science ®Google Scholar
• Gophna U, Kristensen DM, Wolf YI, et al. No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. Isme j. 2015;9(9):2021–2027. doi:10.1038/ismej.2015.20
   PubMed Web of Science ®Google Scholar
• Farrag HA, Abdallah N, Shehata MMK, Awad EM. Natural outer membrane permeabilizers boost antibiotic action against irradiated resistant bacteria. J Biomed Sci. 2019;26(1):69. doi:10.1186/s12929-019-0561-6
   Web of Science ®Google Scholar
• Hawkey PM, Warren RE, Livermore DM, et al. Treatment of infections caused by multidrug-resistant Gram-negative bacteria: report of the British Society for Antimicrobial Chemotherapy/Healthcare Infection Society/British Infection Association Joint Working Party. J Antimicrob Chemother. 2018;73(suppl_3):iii2–iii78. doi:10.1093/jac/dky027
   PubMed Web of Science ®Google Scholar
• Liang WJ, Liu HY, Duan GC, et al. Emergence and mechanism of carbapenem-resistant Escherichia coli in Henan, China, 2014. J Infect Public Health. 2018;11(3):347–351. doi:10.1016/j.jiph.2017.09.020
   PubMed Web of Science ®Google Scholar
• Wang R, Liu Y, Zhang Q, et al. The prevalence of colistin resistance in Escherichia coli and Klebsiella pneumoniae isolated from food animals in China: coexistence of mcr-1 and bla(NDM) with low fitness cost. Int J Antimicrob Agents. 2018;51(5):739–744. doi:10.1016/j.ijantimicag.2018.01.023
   Web of Science ®Google Scholar
• Sheu CC, Chang YT, Lin SY, Chen YH, Hsueh PR. Infections caused by carbapenem-resistant Enterobacteriaceae: an update on therapeutic options. Front Microbiol. 2019;10:80. doi:10.3389/fmicb.2019.00080
   PubMed Web of Science ®Google Scholar
• Choi YK, Byeon EJ, Park JJ, Lee J, Seo YB. Antibiotic resistance patterns of Enterobacteriaceae isolated from patients with healthcare-associated infections. Infect Chemother. 2021;53(2):355–363. doi:10.3947/ic.2021.0030
   Web of Science ®Google Scholar
• Hao M, He Y, Zhang H, et al. CRISPR-Cas9-mediated carbapenemase gene and plasmid curing in carbapenem-resistant Enterobacteriaceae. Antimicrob Agents Chemother. 2020;64(9). doi:10.1128/AAC.00843-20.
   Web of Science ®Google Scholar
• Wang Y, Wang S, Chen W, et al. CRISPR-Cas9 and CRISPR-assisted cytidine deaminase enable precise and efficient genome editing in Klebsiella pneumoniae. Appl Environ Microbiol. 2018;84(23). doi:10.1128/AEM.01834-18.
   Web of Science ®Google Scholar
• Wan P, Cui S, Ma Z, et al. Reversal of mcr-1-mediated colistin resistance in Escherichia coli by CRISPR-Cas9 system. Infect Drug Resist. 2020;13:1171–1178. doi:10.2147/IDR.S244885
   Web of Science ®Google Scholar
• Vad-Nielsen J, Lin L, Bolund L, Nielsen AL, Luo Y. Golden gate assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes. Cell Mol Life Sci. 2016;73(22):4315–4325. doi:10.1007/s00018-016-2271-5
   Web of Science ®Google Scholar
• Feng X, Zhao D, Zhang X, Ding X, Bi C. CRISPR/Cas9 assisted multiplex genome editing technique in Escherichia coli. Biotechnol J. 2018;13(9):e1700604. doi:10.1002/biot.201700604
   PubMed Web of Science ®Google Scholar
• Wu Y, Battalapalli D, Hakeem MJ, et al. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. J Nanobiotechnology. 2021;19(1):401. doi:10.1186/s12951-021-01132-8
   Web of Science ®Google Scholar
• Bloem A, Bax HI, Yusuf E, Verkaik NJ. New-generation antibiotics for treatment of gram-positive infections: a review with focus on Endocarditis and Osteomyelitis. J Clin Med. 2021;10(8):1743. doi:10.3390/jcm10081743
   Web of Science ®Google Scholar
• Feng Z, Chakraborty D, Dewell SB, Reddy BV, Brady SF. Environmental DNA-encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis. J Am Chem Soc. 2012;134(6):2981–2987. doi:10.1021/ja207662w
   Web of Science ®Google Scholar
• Debroy S, van der Hoeven R, Singh KV, et al. Development of a genomic site for gene integration and expression in Enterococcus faecalis. J Microbiol Methods. 2012;90(1):1–8. doi:10.1016/j.mimet.2012.04.011
   Web of Science ®Google Scholar
• Boccella M, Santella B, Pagliano P, et al. Prevalence and antimicrobial resistance of Enterococcus species: a retrospective cohort study in Italy. Antibiotics. 2021;10(12). doi:10.3390/antibiotics10121552.
   Web of Science ®Google Scholar
• Alduhaidhawi AHM, AlHuchaimi SN, Al-Mayah TA, 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;15:1143–1154. doi:10.2147/IDR.S358248
   PubMed Web of Science ®Google Scholar
• Hullahalli K, Rodrigues M, Schmidt BD, et al. Comparative analysis of the orphan CRISPR2 Locus in 242 Enterococcus faecalis strains. PLoS One. 2015;10(9):e0138890. doi:10.1371/journal.pone.0138890
   Web of Science ®Google Scholar
• Hullahalli K, Rodrigues M, Nguyen UT, Palmer K. An attenuated CRISPR-Cas System in Enterococcus faecalis permits DNA acquisition. mBio. 2018;9(3). doi:10.1128/mBio.00414-18
   PubMed Web of Science ®Google Scholar
• Gholizadeh P, Aghazadeh M, Ghotaslou R, et al. Role of CRISPR-Cas system on antibiotic resistance patterns of Enterococcus faecalis. Ann Clin Microbiol Antimicrob. 2021;20(1):49. doi:10.1186/s12941-021-00455-6
   Web of Science ®Google Scholar
• 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(11):1511–1515. doi:10.1016/j.joen.2012.07.004
   Web of Science ®Google Scholar
• Hullahalli K, Rodrigues M, Palmer KL. Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations. eLife. 2017;6. doi:10.7554/eLife.26664
   Web of Science ®Google Scholar
• Gholizadeh P, Aghazadeh M, Ghotaslou R, et al. CRISPR-cas system in the acquisition of virulence genes in dental-root canal and hospital-acquired isolates of Enterococcus faecalis. Virulence. 2020;11(1):1257–1267. doi:10.1080/21505594.2020.1809329
   PubMed Web of Science ®Google Scholar
• Maikova A, Severinov K, Soutourina O. New insights into functions and possible applications of Clostridium difficile CRISPR-Cas system. Front Microbiol. 2018;9:1740. doi:10.3389/fmicb.2018.01740
   PubMed Web of Science ®Google Scholar
• Uruén C, Chopo-Escuin G, Tommassen J, Mainar-Jaime RC, Arenas J. Biofilms as promoters of bacterial antibiotic resistance and tolerance. Antibiotics. 2020;10:1. doi:10.3390/antibiotics10010001
   Web of Science ®Google Scholar
• É R, Woerther PL, Barbier F. Mechanisms of antimicrobial resistance in Gram-negative bacilli. Ann Intensive Care. 2015;5(1):61. doi:10.1186/s13613-015-0061-0
   Web of Science ®Google Scholar
• Sampson TR, Napier BA, Schroeder MR, et al. A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion. Proc Natl Acad Sci U S A. 2014;111(30):11163–11168. doi:10.1073/pnas.1323025111
   PubMed Web of Science ®Google Scholar
• Cady KC, O’Toole GA. Non-identity-mediated CRISPR-bacteriophage interaction mediated via the Csy and Cas3 proteins. J Bacteriol. 2011;193(14):3433–3445. doi:10.1128/JB.01411-10
   PubMed Web of Science ®Google Scholar
• Zegans ME, Wagner JC, Cady KC, et al. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J Bacteriol. 2009;191(1):210–219. doi:10.1128/JB.00797-08
   PubMed Web of Science ®Google Scholar
• Southern SJ, Oyston PCF. Genome editing of Francisella tularensis using (CRISPR-Cas9). J Microbiol Methods. 2020;176:106004. doi:10.1016/j.mimet.2020.106004
   Web of Science ®Google Scholar
• Schunder E, Rydzewski K, Grunow R, Heuner K. First indication for a functional CRISPR/Cas system in Francisella tularensis. Int J Med Microbiol. 2013;303(2):51–60. doi:10.1016/j.ijmm.2012.11.004
   PubMed Web of Science ®Google Scholar
• Uribe RV, Rathmer C, Jahn LJ, et al. Bacterial resistance to CRISPR-Cas antimicrobials. Sci Rep. 2021;11(1):17267. doi:10.1038/s41598-021-96735-4
   Web of Science ®Google Scholar
• Shabbir MAB, Shabbir MZ, Wu Q, et al. CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann Clin Microbiol Antimicrob. 2019;18(1):21. doi:10.1186/s12941-019-0317-x
   PubMed Web of Science ®Google Scholar
• Toro M, Cao G, Ju W, et al. Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli. Appl Environ Microbiol. 2014;80(4):1411–1420. doi:10.1128/AEM.03018-13
   Web of Science ®Google Scholar
• Touchon M, Charpentier S, Pognard D, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology. 2012;158(Pt 12):2997–3004. doi:10.1099/mic.0.060814-0
   Web of Science ®Google Scholar
• Xu Z, Li M, Li Y, et al. Native CRISPR-cas-mediated genome editing enables dissecting and sensitizing clinical multidrug-resistant P. aeruginosa. Cell Rep. 2019;29(6):1707–1717.e3. doi:10.1016/j.celrep.2019.10.006
   Web of Science ®Google Scholar
• McDonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF. CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics. 2019;20(1):105. doi:10.1186/s12864-019-5439-1
   Web of Science ®Google Scholar
• Shabbir MA, Wu Q, Shabbir MZ, et al. The CRISPR-cas system promotes antimicrobial resistance in Campylobacter jejuni. Future Microbiol. 2018;13:1757–1774. doi:10.2217/fmb-2018-0234
   Web of Science ®Google Scholar
• Liao W, Liu Y, Chen C, et al. Distribution of CRISPR-Cas systems in clinical carbapenem-resistant Klebsiella pneumoniae strains in a Chinese Tertiary hospital and its potential relationship with virulence. Microbial Drug Resist. 2020;26(6):630–636. doi:10.1089/mdr.2019.0276
   Web of Science ®Google Scholar
• Hille F, Richter H, Wong SP, et al. The biology of CRISPR-Cas: backward and forward. Cell. 2018;172(6):1239–1259. doi:10.1016/j.cell.2017.11.032
   PubMed Web of Science ®Google Scholar
• Borges AL, Davidson AR, Bondy-Denomy J. The discovery, mechanisms, and evolutionary impact of Anti-CRISPRs. Annu Rev Virol. 2017;4(1):37–59. doi:10.1146/annurev-virology-101416-041616
   Web of Science ®Google Scholar
• Basgall EM, Goetting SC, Goeckel ME, et al. Gene drive inhibition by the anti-CRISPR proteins AcrIIA2 and AcrIIA4 in Saccharomyces cerevisiae. Microbiology. 2018;164(4):464–474. doi:10.1099/mic.0.000635
   Web of Science ®Google Scholar
• Chowdhury S, Carter J, Rollins MF, et al. Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell. 2017;169(1):47–57.e11. doi:10.1016/j.cell.2017.03.012
   PubMed Web of Science ®Google Scholar
• Guo TW, Bartesaghi A, Yang H, et al. Cryo-EM structures reveal mechanism and inhibition of DNA targeting by a CRISPR-Cas surveillance complex. Cell. 2017;171(2):414–426.e12. doi:10.1016/j.cell.2017.09.006
   PubMed Web of Science ®Google Scholar
• Harrington LB, Doxzen KW, Ma E, et al. A broad-spectrum inhibitor of CRISPR-Cas9. Cell. 2017;170(6):1224–1233.e15. doi:10.1016/j.cell.2017.07.037
   PubMed Web of Science ®Google Scholar
• Pawluk A, Shah M, Mejdani M, et al. Disabling a Type I-E CRISPR-Cas nuclease with a bacteriophage-encoded Anti-CRISPR protein. mBio. 2017;8(6). doi:10.1128/mBio.01751-17.
   Web of Science ®Google Scholar
• Bondy-Denomy J, Garcia B, Strum S, et al. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature. 2015;526(7571):136–139. doi:10.1038/nature15254
   PubMed Web of Science ®Google Scholar
• Pawluk A, Staals RH, Taylor C, et al. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat Microbiol. 2016;1(8):16085. doi:10.1038/nmicrobiol.2016.85
   PubMed Web of Science ®Google Scholar
• Mahendra C, Christie KA, Osuna BA, et al. Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat Microbiol. 2020;5(4):620–629. doi:10.1038/s41564-020-0692-2
   Web of Science ®Google Scholar
• Marino ND, Pinilla-Redondo R, Csörgő B, Bondy-Denomy J. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nat Methods. 2020;17(5):471–479. doi:10.1038/s41592-020-0771-6
   PubMed Web of Science ®Google Scholar
• Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson AR. A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. mBio. 2014;5(2):e00896. doi:10.1128/mBio.00896-14
   Web of Science ®Google Scholar
• Meeske AJ, Jia N, Cassel AK, et al. A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Science. 2020;369(6499):54–59. doi:10.1126/science.abb6151
   PubMed Web of Science ®Google Scholar
• Shehreen S, Chyou TY, Fineran PC, Brown CM. Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philos Trans R Soc Lond B Biol Sci. 2019;374(1772):20180384. doi:10.1098/rstb.2018.0384
   Web of Science ®Google Scholar
• Stanley SY, Maxwell KL. Phage-Encoded Anti-CRISPR Defenses. Annu Rev Genet. 2018;52(1):445–464. doi:10.1146/annurev-genet-120417-031321
   Web of Science ®Google Scholar
• Rather IA, Kim BC, Bajpai VK, Park YH. Self-medication and antibiotic resistance: crisis, current challenges, and prevention. Saudi J Biol Sci. 2017;24(4):808–812. doi:10.1016/j.sjbs.2017.01.004
   PubMed Web of Science ®Google Scholar
• Shen S, Loh TJ, Shen H, Zheng X, Shen H. CRISPR as a strong gene editing tool. BMB Rep. 2017;50(1):20–24. doi:10.5483/BMBRep.2017.50.1.128
   Web of Science ®Google Scholar
• Ding Q, Regan SN, Xia Y, et al. Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell. 2013;12(4):393–394. doi:10.1016/j.stem.2013.03.006
   PubMed Web of Science ®Google Scholar
• Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci. 2017;7(1):21. doi:10.1186/s13578-017-0148-4
   PubMed Web of Science ®Google Scholar
• Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–442. doi:10.1126/science.aam9321
   PubMed Web of Science ®Google Scholar