Review on Anti-Biofilm Potential of CRISPR-Cas System on Various Pathogens
Life Sciences -Biotechnology
DOI:
https://doi.org/10.22376/ijlpr.2023.13.5.L132-L145Keywords:
biofilm, biofilm-residing bacteria, CRISPR-Cas system, virulence, phages, liposomes, conjugative systems.Abstract
The development of bacterial biofilms entails regulatory as well as signalling mechanisms that regulate the shift from a mobile to astationary state of existence, the production of the extracellular polymeric matrix, and the progression of 3-dimensional biofilm formation withemphasis on how easily they may be created and how crucial they are in biological, ecological, and industrial settings, biofilms are the subject ofextensive research. Biofilms and a variety of pathogenic human disorders are frequently linked. Since bacteria in biofilms can resist antibiotics, theimmune system, and other treatments, biofilm infections are typically long-lasting. Many prokaryotes include CRISPR-associated proteins (Cas), a solidadaptable immunological system that may be programmed to damage the bacterial genomes and induce cell death. Short palindromic repeats that aregrouped and adequately spaced together make up CRISPR-Cas. In light of this, CRISPR-Cas can be seen as an exciting strategy to address andovercome antibiotic resistance. Furthermore, the CRISPR-Cas system can create "precise antimicrobials" that target bacterial infections according tospecific DNA sequences. This CRISPR-Cas technique is susceptible to drug-resistant microorganisms due to its selective targeting of the genesinvolved in biofilm formation, pathogenicity, and antibiotic resistance. However, this method requires potent vectors for the CRISPR-Cas system toaccess the bacterial genomes. As vectors, genetically engineered Phage, liposomes, and lipid-mediated nanoparticles are exciting options. Thistechnique has been used to prevent extracellular and intracellular from forming biofilms. The most current developments in creating innovations andpossible advantages of the various CRISPR-Cas delivery methods for the deliberate eradication of bacterial pathogens will be covered in this review,focussing mainly on the anti-biofilm potential, which is found to be one of the primary causes of the difficulty of irradiation of Multi-drug resistantbacteria. Additionally, each distribution system's positive aspects are highlighted, along with its challenges and potential for advancement in the future.
References
Huang H, Peng C, Peng P, Lin Y, Zhang X, Ren H. Towards the biofilm characterization and regulation in biological wastewater treatment. Appl Microbiol Biotechnol. 2019 Feb;103(3):1115-29. doi: 10.1007/s00253-018-9511-6, PMID 30483847.
Høiby N. A personal history of research on microbial biofilms and biofilm infections. Pathog Dis. 2014;70(3):205-11. doi: 10.1111/2049-632X.12165, PMID 24585728.
Gupta P, Sarkar S, Das B, Bhattacharjee S, Tribedi P. Biofilm, pathogenesis and prevention--a journey to break the wall: a review. Arch Microbiol. 2016;198(1):1-15. doi: 10.1007/s00203-015-1148-6, PMID 26377585.
Solano C, Echeverz M, Lasa I. Biofilm dispersion and quorum sensing. Curr Opin Microbiol. 2014;18:96-104. doi: 10.1016/j.mib.2014.02.008, PMID 24657330.
Kostakioti M, Hadjifrangiskou M, Hultgren SJ. Bacterial biofilms: development, dispersal, and therapeutic strategies in the dawn of the post-antibiotic era. Cold Spring Harb Perspect Med. 2013;3(4):a010306. doi: 10.1101/cshperspect.a010306, PMID 23545571.
Jamal M, Ahmad W, Andleeb S, Jalil F, Imran M, Nawaz MA et al. Bacterial biofilm and associated infections. J Chin Med Assoc. 2018;81(1):7-11. doi: 10.1016/j.jcma.2017.07.012, PMID 29042186.
Allesen-Holm M, Barken KB, Yang L, Klausen M, Webb JS, Kjelleberg S et al. A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms. Mol Microbiol. 2006;59(4):1114-28. doi: 10.1111/j.1365-2958.2005.05008.x, PMID 16430688.
Anderson GG, Moreau-Marquis S, Stanton BA, O’Toole GA. In vitro Analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells. Infect Immun. 2008;76(4):1423-33. doi: 10.1128/IAI.01373-07, PMID 18212077.
Vurukonda SSKP, Giovanardi D, Stefani E. Plant growth promoting and biocontrol activity of Streptomyces spp. as endophytes. Int J Mol Sci. 2018;19(4):952. doi: 10.3390/ijms19040952, PMID 29565834.
Kim Y, Kim H, Beuchat LR, Ryu JH. Development of non-pathogenic bacterial biofilms on stainless steel surface, inhibiting Salmonella enterica. Food Microbiol. 2018;69:136-42. doi: 10.1016/j.fm.2017.08.003, PMID 28941894.
Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol. 2020;129(2):199-211. doi: 10.1111/jam.14609, PMID 32034822.
Hurlow J, Couch K, Laforet K, Bolton L, Metcalf D, Bowler P. Clinical biofilms: a challenging frontier in wound care. Adv Wound Care. 2015;4(5):295-301. doi: 10.1089/wound.2014.0567, PMID 26005595.
Costerton JW, Lewandowski Z, DeBeer D, Caldwell D, Korber D, James G. Biofilms, the customized microniche. J Bacteriol. 1994;176(8):2137-42. doi: 10.1128/jb.176.8.2137-2142.1994, PMID 8157581.
Sleytr UBI. Basic and applied S-layer research: an overview. FEMS Microbiol Rev. 1997;20(1-2):5-12.
Lu TK, Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11197-202. doi: 10.1073/pnas.0704624104, PMID 17592147.
Sutherland IW. The biofilm matrix--an immobilized but dynamic microbial environment. Trends Microbiol. 2001 May;9(5):222-7. doi: 10.1016/s0966-842x(01)02012-1, PMID 11336839.
Shaw T, Winston M, Rupp CJ, Klapper I, Stoodley P. Commonality of elastic relaxation times in biofilms. Phys Rev Lett. 2004 Aug 27;93(9):098102. doi: 10.1103/PhysRevLett.93.098102, PMID 15447143.
Garrett TR, Bhakoo M, Zhang Z. Bacterial adhesion and biofilms on surfaces. Prog Nat Sci. 2008 Sep 1;18(9):1049-56. doi: 10.1016/j.pnsc.2008.04.001.
Marić S, Vraneš J. Characteristics and significance of microbial biofilm formation. Period Bilogorum. 2007;109:115-21.
Kumar CG, Anand SK. Significance of microbial biofilms in the food industry: a review. Int J Food Microbiol. 1998 Jun 30;42(1-2):9-27. doi: 10.1016/s0168-1605(98)00060-9, PMID 9706794.
Davey ME, O’toole GA. Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev. 2000 Dec;64(4):847-67. doi: 10.1128/MMBR.64.4.847-867.2000, PMID 11104821.
Vasudevan R. Biofilms: microbial cities of scientific significance. JMEN;1(3). doi: 10.15406/jmen.2014.01.00014.
Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW, Greenberg EP. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science. 1998 Apr 10;280(5361):295-8. doi: 10.1126/science.280.5361.295, PMID 9535661.
Federle MJ, Bassler BL. Interspecies communication in bacteria. J Clin Invest. 2003 Nov;112(9):1291-9. doi: 10.1172/JCI20195, PMID 14597753.
Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science. 1999 May 21;284(5418):1318-22. doi: 10.1126/science.284.5418.1318, PMID 10334980.
Sutherland IW. Polysaccharides for microbial exopolysaccharides. Carbohydr Polym. 1999;38(4):319-28. doi: 10.1016/S0144-8617(98)00114-3.
Otto M. Staphylococcal infections: biofilm maturation and detachment mechanisms as critical determinants of pathogenicity. Annu Rev Med. 2013;64:175-88. doi: 10.1146/annurev-med-042711-140023, PMID 22906361.
Hall-Stoodley L, Stoodley P. Evolving concepts in biofilm infections. Cell Microbiol. 2009 Jul;11(7):1034-43. doi: 10.1111/j.1462-5822.2009.01323.x, PMID 19374653.
Bjarnsholt T. The role of bacterial biofilms in chronic infections. APMIS Suppl. 2013 May;136(136):1-51. doi: 10.1111/amp.12099, PMID 23635385.
Donlan RM, Costerton JW. Biofilms: survival mechanisms of clinically relevant microorganisms. Clin Microbiol Rev. 2002 Apr;15(2):167-93. doi: 10.1128/CMR.15.2.167-193.2002, PMID 11932229.
Jensen ET, Kharazmi A, Lam K, Costerton JW, Høiby N. Human polymorphonuclear leukocyte response to Pseudomonas aeruginosa grown in biofilms. Infect Immun. 1990 Jul;58(7):2383-5. doi: 10.1128/iai.58.7.2383-2385.1990, PMID 2114367.
Moser C, Pedersen HT, Lerche CJ, Kolpen M, Line L, Thomsen K et al. Biofilms and host response - helpful or harmful. APMIS. 2017 Apr;125(4):320-38. doi: 10.1111/amp.12674, PMID 28407429.
Lewis K. Multi-drug tolerance of biofilms and persister cells. Curr Top Microbiol Immunol. 2008;322:107-31. doi: 10.1007/978-3-540-75418-3_6, PMID 18453274.
Fux CA, Costerton JW, Stewart PS, Stoodley P. Survival strategies of infectious biofilms. Trends Microbiol. 2005 Jan;13(1):34-40. doi: 10.1016/j.tim.2004.11.010, PMID 15639630.
Fauvart M, De Groote VN, Michiels J. Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J Med Microbiol. 2011 Jun;60(6):699-709. doi: 10.1099/jmm.0.030932-0. PMID 21459912.
Louwen R, Staals RH, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev. 2014 Mar;78(1):74-88. doi: 10.1128/MMBR.00039-13, PMID 24600041.
Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010 Nov 4;468(7320):67-71. doi: 10.1038/nature09523, PMID 21048762.
Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP et al. Small CRISPR RNAs guide antiviral defence in prokaryotes. Science. 2008 Aug 15;321(5891):960-4. doi: 10.1126/science.1159689, PMID 18703739.
Carte J, Wang R, Li H, Terns RM, Terns MP. Cas6 is an endoribonuclease that generates guide RNAs for invader defence in prokaryotes. Genes Dev. 2008 Dec 15;22(24):3489-96. doi: 10.1101/gad.1742908, PMID 19141480.
Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol. 2010;64:475-93. doi: 10.1146/annurev.micro.112408.134123, PMID 20528693.
Shabbir MA, Hao H, Shabbir MZ, Hussain HI, Iqbal Z, Ahmed S et al. Survival and evolution of CRISPR-Cas system in prokaryotes and its applications. Front Immunol. 2016 Sep 26;7:375. doi: 10.3389/fimmu.2016.00375, PMID 27725818.
Shabbir MA, Hao H, Shabbir MZ, Wu Q, Sattar A, Yuan Z. Bacteria vs bacteriophages: parallel Evolution of Immune Arsenals. Front Microbiol. 2016 Aug 17;7:1292. doi: 10.3389/fmicb.2016.01292, PMID 27582740.
Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569, PMID 26411297.
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 Apr 6;30(7):1335-42. doi: 10.1038/emboj.2011.41, PMID 21343909.
Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019, PMID 21460843.
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011 Mar 31;471(7340):602-7. doi: 10.1038/nature09886, PMID 21455174.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126/science.1225829, PMID 22745249.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013 Feb 15;339(6121):819-23. doi: 10.1126/science.1231143, PMID 23287718.
Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell. 2012 Feb 10;45(3):303-13. doi: 10.1016/j.molcel.2011.12.013, PMID 22227115.
Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defence and regulation. Annu Rev Genet. 2011;45:273-97. doi: 10.1146/annurev-genet-110410-132430, PMID 22060043.
Wang R, Preamplume G, Terns MP, Terns RM, Li H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure. 2011 Feb 9;19(2):257-64. doi: 10.1016/j.str.2010.11.014, PMID 21300293.
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010 Sep 10;329(5997):1355-8. doi: 10.1126/science.1192272, PMID 20829488.
Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. Regulation of dev, an operon that includes genes essential for Myxococcus Xanthus development and CRISPR-associated genes and repeats. J Bacteriol. 2007 May;189(10):3738-50. doi: 10.1128/JB.00187-07, PMID 17369305.
Nam KH, Ding F, Haitjema C, Huang Q, DeLisa MP, Ke A. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J Biol Chem. 2012 Oct 19;287(43):35943-52. doi: 10.1074/jbc.M112.382598, PMID 22942283.
Vergnaud G, Li Y, Gorgé O, Cui Y, Song Y, Zhou D et al. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA. Adv Exp Med Biol. 2007;603:327-38. doi: 10.1007/978-0-387-72124-8_30, PMID 17966429.
Rezzonico F, Smits TH, Duffy B. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. Appl Environ Microbiol. 2011 Jun;77(11):3819-29. doi: 10.1128/AEM.00177-11. PMID 21460108, PMCID PMC3127596.
Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, et al. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. mBio. 2012 Sep 25;3(5):e00279-12. doi: 10.1128/mBio.00279-12, PMID 23015740.
van der Ploeg JR. Analysis of CRISPR in Streptococcus mutants suggests the frequent occurrence of acquired immunity against infection by M102-like bacteriophages. Microbiology (Reading). 2009 Jun;155(6):1966-76. doi: 10.1099/mic.0.027508-0, PMID 19383692.
Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS, CRISPR A. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature. 2013 May 9;497(7448):254-7. doi: 10.1038/nature12048, PMID 23584588.
Louwen R, Horst-Kreft D, de Boer AG, van der Graaf L, de Knegt G, Hamersma M et al. A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome. Eur J Clin Microbiol Infect Dis. 2013 Feb;32(2):207-26. doi: 10.1007/s10096-012-1733-4, PMID 22945471.
Gunderson FF, Cianciotto NP. The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. mBio. 2013 Mar 12;4(2):e00074-13. doi: 10.1128/mBio.00074-13, PMID 23481601.
Sampson TR, Weiss DS. CRISPR-Cas systems: new players in gene regulation and bacterial physiology. Front Cell Infect Microbiol. 2014 Apr 4;4:37. doi: 10.3389/fcimb.2014.00037, PMID 24772391.
Kinnevey PM, Shore AC, Brennan GI, Sullivan DJ, Ehricht R, Monecke S et al. Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harbouring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals. Antimicrob Agents Chemother. 2013 Jan;57(1):524-31. doi: 10.1128/AAC.01689-12. PMID 23147725, PMCID PMC3535981.
Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S et al. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol. 2008;9(7):R110. doi: 10.1186/gb-2008-9-7-r110, PMID 18611278.
Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell. 2009 Nov 25;139(5):945-56. doi: 10.1016/j.cell.2009.07.040, PMID 19945378.
Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science. 2008 Dec 19;322(5909):1843-5. doi: 10.1126/science.1165771, PMID 19095942.
Stucki D, Gagneux S. Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis (Edinb). 2013 Jan;93(1):30-9. doi: 10.1016/j.tube.2012.11.002, PMID 23266261.
Wang L, Zheng W, Liu S, Li B, Jiang X. Delivery of CRISPR/Cas9 by novel strategies for gene therapy. ChemBioChem. 2019 Mar 1;20(5):634-43. doi: 10.1002/cbic.201800629, PMID 30393919.
Liang P, Xu Y, Zhang X, Ding C, Huang R, Zhang Z et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 2015 May;6(5):363-72. doi: 10.1007/s13238-015-0153-5, PMID 25894090.
Lino CA, Harper JC, Carney JP, Timlin JA. Delivering CRISPR: a review of the challenges and approaches. Drug Deliv. 2018;25(1):1234-57. doi: 10.1080/10717544.2018.1474964, PMID 29801422.
Chen Y, Batra H, Dong J, Chen C, Rao VB, Tao P. Genetic engineering of bacteriophages against infectious diseases. Front Microbiol. 2019 May 3;10:954. doi: 10.3389/fmicb.2019.00954, PMID 31130936.
Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017 Mar;15(3):169-82. doi: 10.1038/micro.2016.184, PMID 28111461.
Knott GJ, Doudna JA. CRISPR-Cas guides the future of genetic engineering. Science. 2018;361(6405):866-9. doi: 10.1126/science.aat5011, PMID 30166482.
Kiro R, Shitrit D, Qimron U. Efficient engineering of a bacteriophage genome using the IE CRISPR-Cas system. RNA Biol. 2014;11(1):42-4. doi: 10.4161/rna.27766, PMID 24457913.
Box AM, McGuffie MJ, O’Hara BJ, Seed KD. Functional Analysis of bacteriophage immunity through a Type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J Bacteriol. 2016;198(3):578-90. doi: 10.1128/JB.00747-15, PMID 26598368.
Hynes AP, Villion M, Moineau S. Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages. Nat Commun. 2014 Jul 24;5:4399. doi: 10.1038/ncomms5399, PMID 25056268.
Hupfeld M, Trasanidou D, Ramazzini L, Klumpp J, Loessner MJ, Kilcher S. A functional type II-A CRISPR-Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage. Nucleic Acids Res. 2018 Jul 27;46(13):6920-33. doi: 10.1093/nar/gky544, PMID 30053228.
Bari SMN, Walker FC, Cater K, Aslan B, Hatoum-Aslan A. Strategies for editing virulent staphylococcal phages using CRISPR-Cas10. ACS Synth Biol. 2017 Dec 15;6(12):2316-25. doi: 10.1021/acssynbio.7b00240, PMID 28885820.
Cater K, Dandu VS, Bari SM, Lackey K, Everett GF, Hatoum-Aslan A. A novel Staphylococcus Podophage encodes a unique lysin with an unusual modular design. mSphere. 2017 Mar 22;2(2):e00040-17. doi: 10.1128/mSphere.00040-17, PMID 28357414.
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 Jan;53(1):1-8. doi: 10.1016/j.ijantimicag.2018.09.017, PMID 30267758.
Ghigo JM. Natural conjugative plasmids induce bacterial biofilm development. Nature. 2001 Jul 26;412(6845):442-5. doi: 10.1038/35086581, PMID 11473319.
Hausner M, Wuertz S. High conjugation rates in bacterial biofilms as determined by quantitative in situ Analysis. Appl Environ Microbiol. 1999 Aug;65(8):3710-3. doi: 10.1128/AEM.65.8.3710-3713.1999, PMID 10427070.
Peters JM, Koo BM, Patino R, Heussler GE, Hearne CC, Qu J et al. Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi. Nat Microbiol. 2019 Feb;4(2):244-50. doi: 10.1038/s41564-018-0327-z, PMID 30617347.
Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD et al. Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria. Nat Microbiol. 2018 Sep;3(9):1043-53. doi: 10.1038/s41564-018-0216-5, PMID 30127494.
Ronda C, Chen SP, Cabral V, Yaung SJ, Wang HH. Metagenomic engineering of the mammalian gut microbiome in situ. Nat Methods. 2019 Feb;16(2):167-70. doi: 10.1038/s41592-018-0301-y, PMID 30643213.
Babic A, Berkmen MB, Lee CA, Grossman AD. Efficient gene transfer in bacterial cell chains. mBio. 2011 Mar 15;2(2):e00027-11. doi: 10.1128/mBio.00027-11, PMID 21406598.
Wolfs JM, Hamilton TA, Lant JT, Laforet M, Zhang J, Salemi LM et al. Biasing genome-editing events toward precise length deletions with an RNA-guided TevCas9 dual nuclease. Proc Natl Acad Sci U S A. 2016;113(52):14988-93. doi: 10.1073/pnas.1616343114, PMID 27956611.
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 Oct 4;10(1):4544. doi: 10.1038/s41467-019-12448-3, PMID 31586051.
Boudry P, Semenova E, Monot M, Datsenko KA, Lopatina A, Sekulovic O et al. Function of the CRISPR-Cas system of the human pathogen Clostridium difficile. mBio. 2015 Sep 1;6(5):e01112-15. doi: 10.1128/mBio.01112-15, PMID 26330515.
Gholizadeh P, Aghazadeh M, Ghotaslou R, Ahangarzadeh Rezaee M, Pirzadeh T, Köse Ş et al. CRISPR-Cas system in the acquisition of virulence genes in a dental-root canal and hospital-acquired isolates of Enterococcus faecalis. Virulence. 2020 Dec;11(1):1257-67. doi: 10.1080/21505594.2020.1809329, PMID 32930628.
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 the strain-specific anti-bacterial activity. Nucleic Acids Res. 2021 Apr 6;49(6):3584-98. doi: 10.1093/nar/gkab126, PMID 33660775.
Hou M, Sun S, Feng Q, Dong X, Zhang P, Shi B et al. Genetic editing of the virulence gene of Escherichia coli using the CRISPR system. PeerJ. 2020 Apr 6;8:e8881. doi: 10.7717/peerj.8881, PMID 32292652.
Jain A, Srivastava P. Broad host range plasmids. FEMS Microbiol Lett. 2013;348(2):87-96. doi: 10.1111/1574-6968.12241, PMID 23980652.
Oliveira PH, Touchon M, Rocha EP. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res. 2014;42(16):10618-31. doi: 10.1093/nar/gku734, PMID 25120263.
Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EP, de la Cruz F. Mobility of plasmids. Microbiol Mol Biol Rev. 2010 Sep;74(3):434-52. doi: 10.1128/MMBR.00020-10, PMID 20805406.
Pérez-Mendoza D, de la Cruz F. Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any? BMC Genomics. 2009 Feb 9;10:71. doi: 10.1186/1471-2164-10-71, PMID 19203375.
Du X, Shi B, Tang Y, Dai S, Qiao SZ. Label. Label-free dendrimer-like silica nanohybrids for traceable and controlled gene delivery. Biomaterials. 2014;35(21):5580-90. doi: 10.1016/j.biomaterials.2014.03.051, PMID 24726748.
Durfee PN, Lin YS, Dunphy DR, Muñiz AJ, Butler KS, Humphrey KR et al. Mesoporous silica nanoparticle-supported lipid bilayers (protocells) for active targeting and delivery to individual leukaemia cells. ACS Nano. 2016;10(9):8325-45. doi: 10.1021/acsnano.6b02819, PMID 27419663.
Dykman LA, Khlebtsov NG. Immunological properties of gold nanoparticles. Chem Sci. 2017;8(3):1719-35. doi: 10.1039/c6sc03631g, PMID 28451297.
Fourier K, Raemdonck K, De Smedt SC, Demeester J, Coenye T, Braeckmans K. Lipid and polymer nanoparticles for drug delivery to bacterial biofilms. J Control Release. 2014 Sep 28;190:607-23. doi: 10.1016/j.jconrel.2014.03.055, PMID 24794896.
Chakraborty T, Shaw R, Chatterjee DS, Datta DL, Sengupta DA. Review on recent advancement of therapeutic interventions in combating multi-drug resistant bacteria. Int J Life Sci Pharm Res. 2020;10(5):166-79.
Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol. 2016 Mar;34(3):328-33. doi: 10.1038/nbt.3471, PMID 26829318.
Zuri's JA, Thompson DB, Shu Y, Guilinger JP, Bessen JL, Hu JH et al. Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat Biotechnol. 2015 Jan;33(1):73-80. doi: 10.1038/nbt.3081, PMID 25357182.
Wang Y, Zhang ZT, Seo SO, Lynn P, Lu T, Jin YS et al. Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9. Biotechnol Bioeng. 2016 Dec;113(12):2739-43. doi: 10.1002/bit.26020, PMID 27240718.
Mugabe C, Halwani M, Azghani AO, Lafreniere RM, Omri A. Mechanism of enhanced activity of liposome-entrapped Aminoglycosides against resistant strains of Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2006 Jun;50(6):2016-22. doi: 10.1128/AAC.01547-05, PMID 16723560.
Halwani M, Mugabe C, Azghani AO, Lafreniere RM, Kumar A, Omri A. Bactericidal efficacy of liposomal Aminoglycosides against Burkholderia cenocepacia. J Antimicrob Chemother. 2007 Oct;60(4):760-9. doi: 10.1093/jac/dkm289, PMID 17673475.
Kim HJ, Michael Gias EL, Jones MN. The adsorption of cationic liposomes to Staphylococcus aureus biofilms. Colloids Surf A Physicochem Eng Aspects. 1999;149(1-3):561-70. doi: 10.1016/S0927-7757(98)00765-1.
Vyas SP, Sihorkar V, Dubey PK. Preparation, characterization and in vitro antimicrobial activity of metronidazole bearing lectinized liposomes for intra-periodontal pocket delivery. Pharmazie. 2001 Jul;56(7):554-60. PMID 11487975.
Jones MN, Kaszuba M, Reboiras MD, Lyle IG, Hill KJ, Song YH et al. The targeting of phospholipid liposomes to bacteria. Biochim Biophys Acta. 1994 Nov 23;1196(1):57-64. doi: 10.1016/0005-2736(94)90295-X.
Hill KJ, Kaszuba M, Creeth JE, Jones MN. Reactive liposomes encapsulate a glucose oxidase-peroxidase system with anti-bacterial activity. Biochim Biophys Acta. 1997 May 22;1326(1):37-46. doi: 10.1016/s0005-2736(97)00007-2, PMID 9188798.
Jones MN, Hill KJ, Kaszuba M, Creeth JE. Anti-bacterial reactive liposomes were encapsulating coupled enzyme systems. Int J Pharm. 1998;162(1-2):107-17. doi: 10.1016/S0378-5173(97)00418-3.
Bikard D, Barrangou R. Using CRISPR-Cas systems as antimicrobials. Curr Opin Microbiol. 2017;37:155-60. doi: 10.1016/j.mib.2017.08.005, PMID 28888103.
Jones CL, Sampson TR, Nakaya HI, Pulendran B, Weiss DS. Repression of bacterial lipoprotein production by F Francisella novicida facilitates evasion of innate immune recognition. Cell Microbiol. 2012;14(10):1531-43. doi: 10.1111/j.1462-5822.2012.01816.x, PMID 22632124.
Pavlovic G, Erbs V, André P, Sylvie J, Eisenman B, Dreyer D et al. Generation of targeted overexpressing models by CRISPR/Cas9 and need of careful validation of your knock-in line obtained by nuclease genome editing. Transgenic Res. 2016;25(2):254-5.
Li J, Shou J, Guo Y, Tang Y, Wu Y, Jia Z et al. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol. 2015;7(4):284-98. doi: 10.1093/jmcb/mjv016, PMID 25757625.
Borin JM, Avrani S, Barrick JE, Petrie KL, Meyer JR. Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. Proc Natl Acad Sci U S A. 2021;118(23):e2104592118. doi: 10.1073/pnas.2104592118, PMID 34083444.
Loh B, Gondil VS, Manohar P, Khan FM, Yang H, Leptihn S. Encapsulation and delivery of therapeutic phages. Appl Environ Microbiol. 2020;87(5):e01979-20. doi: 10.1128/AEM.01979-20, PMID 33310718.
Colom J, Cano-Sarabia M, Otero J, Cortés P, Maspoch D, Llagostera M. Liposome-encapsulated bacteriophages for enhanced oral phage therapy against Salmonella spp. Appl Environ Microbiol. 2015;81(14):4841-9. doi: 10.1128/AEM.00812-15, PMID 25956778.
Chadha P, Katare OP, Chhibber S. Liposome loaded phage cocktail: enhanced therapeutic potential in resolving Klebsiella pneumoniae mediated burn wound infections. Burns. 2017;43(7):1532-43. doi: 10.1016/j.burns.2017.03.029, PMID 28502784.
Chhibber S, Kaur J, Kaur S. Liposome entrapment of bacteriophages improves wound healing in a diabetic mouse MRSA infection. Front Microbiol. 2018;9:561. doi: 10.3389/fmicb.2018.00561, PMID 29651276.
Milo S, Hathaway H, Nzakizwanayo J, Alves DR, Esteban PP, Jones BV, et al. Prevention of encrustation and blockage of urinary catheters by Proteus mirabilis via pH-triggered release of bacteriophage. J Mater Chem B. 2017;5(27):5403-11. doi: 10.1039/c7tb01302g, PMID 32264080.
Hathaway H, Alves DR, Bean J, Esteban PP, Ouadi K, Sutton JM, et al. Poly(N-isopropyl acrylamide-co-allylamine) (PNIPAM-co-ALA) nanospheres for the thermally triggered release of bacteriophage K. Eur J Pharm Biopharm. 2015;96:437-41. doi: 10.1016/j.ejpb.2015.09.013, PMID 26423908.
Rosner D, Clark J. Formulations for bacteriophage therapy and the potential uses of immobilization. Pharmaceuticals (Basel). 2021;14(4):359. doi: 10.3390/ph14040359, PMID 33924739.
Vonasek E, Lu P, Hsieh Y-L, Nitin N. Bacteriophages immobilized on electrospun cellulose microfibers by non-specific adsorption, protein–ligand binding, and electrostatic interactions. Cellulose. 2017;24(10):4581-9. doi: 10.1007/s10570-017-1442-3.
Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP et al. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev. 2016;80(1):1-43. doi: 10.1128/MMBR.00019-15, PMID 26609051.
Marappa N, Dharumadurai D, Nooruddin T, Mohammad Abdulkader AM. Morphological, molecular characterization and biofilm inhibition effect of endophytic Frankia sp. from root nodules of Actinorhizal plant Casuarina sp. S Afr J Bot. 2020;134:72-83. doi: 10.1016/j.sajb.2020.02.039.
Singh R, Dubey AK. Isolation and characterization of a new endophytic actinobacterium Streptomyces californicus Strain ADR1 as a promising source of anti-bacterial, anti-biofilm and antioxidant metabolites. Microorganisms. 2020;8(6):929. doi: 10.3390/microorganisms8060929, PMID 32575628.
Bikard D, Barrangou R. Using CRISPR-Cas systems as antimicrobials. Curr Opin Microbiol. 2017;37:155-60. doi: 10.1016/j.mib.2017.08.005, PMID 28888103.
Jones CL, Sampson TR, Nakaya HI, Pulendran B, Weiss DS. Repression of bacterial lipoprotein production by F rancisella novicida facilitates evasion of innate immune recognition. Cell Microbiol. 2012;14(10):1531-43. doi: 10.1111/j.1462-5822.2012.01816.x, PMID 22632124.
Pavlovic G, Erbs V, André P, Sylvie J, Eisenman B, Dreyer D et al. Generation of targeted overexpressing models by CRISPR/Cas9 and need of careful validation of your knock-in line obtained by nuclease genome editing. Transgenic Res. 2016;25(2):254-5.
Li J, Shou J, Guo Y, Tang Y, Wu Y, Jia Z et al. Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9. J Mol Cell Biol. 2015;7(4):284-98. doi: 10.1093/jmcb/mjv016, PMID 25757625.
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