Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases (original) (raw)

• Centers for Disease Control and Prevention. Antibiotic Resistance Threats in the United States (2013).
• Nordmann, P., Dortet, L. & Poirel, L. Carbapenem resistance in Enterobacteriaceae: here is the storm!. Trends Mol. Med. 18, 263–272 (2012).
  Article CAS PubMed Google Scholar
• Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).
  Article CAS PubMed Google Scholar
• Garneau, J.E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010).
  Article CAS PubMed Google Scholar
• Mali, P., Esvelt, K.M. & Church, G.M. Cas9 as a versatile tool for engineering biology. Nat. Methods 10, 957–963 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602–607 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
  CAS PubMed PubMed Central Google Scholar
• Rasheed, J.K. et al. Characterization of the extended-spectrum beta-lactamase reference strain, Klebsiella pneumoniae K6 (ATCC 700603), which produces the novel enzyme SHV-18. Antimicrob. Agents Chemother. 44, 2382–2388 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Rasheed, J.K. et al. New Delhi metallo-β-lactamase-producing Enterobacteriaceae, United States. Emerg. Infect. Dis. 19, 870–878 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Bikard, D., Hatoum-Aslan, A., Mucida, D. & Marraffini, L.A. CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12, 177–186 (2012).
  Article CAS PubMed Google Scholar
• Gomaa, A.A. et al. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 5, e00928–13 (2014).
  Article PubMed PubMed Central Google Scholar
• Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1–I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Pérez-Mendoza, D. & de la Cruz, F. Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any? BMC Genomics 10, 71 (2009).
  Article PubMed PubMed Central Google Scholar
• Jacoby, G.A. Mechanisms of resistance to quinolones. Clin. Infect. Dis. 41 (suppl. 2), S120–S126 (2005).
  Article CAS PubMed Google Scholar
• Pennington, J.M. & Rosenberg, S.M. Spontaneous DNA breakage in single living Escherichia coli cells. Nat. Genet. 39, 797–802 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Hayes, F. Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301, 1496–1499 (2003).
  Article CAS PubMed Google Scholar
• Mnif, B. et al. Molecular characterization of addiction systems of plasmids encoding extended-spectrum beta-lactamases in Escherichia coli. J. Antimicrob. Chemother. 65, 1599–1603 (2010).
  Article CAS PubMed Google Scholar
• Kaper, J.B., Nataro, J.P. & Mobley, H.L. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2, 123–140 (2004).
  Article CAS PubMed Google Scholar
• Desbois, A.P. & Coote, P.J. Utility of greater wax moth larva (Galleria mellonella) for evaluating the toxicity and efficacy of new antimicrobial agents. Adv. Appl. Microbiol. 78, 25–53 (2012).
  Article CAS PubMed Google Scholar
• Sonnenburg, J.L. & Fischbach, M.A. Community health care: therapeutic opportunities in the human microbiome. Sci. Transl. Med. 3, 78ps12 (2011).
  Article PubMed PubMed Central Google Scholar
• Paddon, C.J. et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496, 528–532 (2013).
  Article CAS PubMed Google Scholar
• Duan, F. & March, J.C. Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. Proc. Natl. Acad. Sci. USA 107, 11260–11264 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Lu, T.K. & Collins, J.J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. USA 104, 11197–11202 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Lu, T.K. & Collins, J.J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. USA 106, 4629–4634 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Edgar, R., Friedman, N., Molshanski-Mor, S. & Qimron, U. Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl. Environ. Microbiol. 78, 744–751 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Seed, K.D., Lazinski, D.W., Calderwood, S.B. & Camilli, A. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494, 489–491 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233–239 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Vercoe, R.B. et al. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet. 9, e1003454 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Williams, J.J. & Hergenrother, P.J. Artificial activation of toxin-antitoxin systems as an antibacterial strategy. Trends Microbiol. 20, 291–298 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Esvelt, K.M., Smidler, A.L., Catteruccia, F. & Church, G.M. Concerning RNA-guided gene drives for the alteration of wild populations. Elife e03401 (2014).
• Datta, S., Costantino, N. & Court, D.L. A set of recombineering plasmids for Gram-negative bacteria. Gene 379, 109–115 (2006).
  Article CAS PubMed Google Scholar
• Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
  Article CAS PubMed Google Scholar
• Sikorski, R.S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27 (1989).
  CAS PubMed PubMed Central Google Scholar
• Dwyer, D.J., Kohanski, M.A., Hayete, B. & Collins, J.J. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol. Syst. Biol. 3, 91 (2007).
  Article PubMed PubMed Central Google Scholar
• Clinical and Laboratory Standards Institute. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically; Approved Standard. Seventh Edition. (Clinical and Laboratory Standards Institute, Wayne, Pennsylvania, USA, 2006).
• Chung, C.T., Niemela, S.L. & Miller, R.H. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl. Acad. Sci. USA 86, 2172–2175 (1989).
  Article CAS PubMed PubMed Central Google Scholar
• Chasteen, L., Ayriss, J., Pavlik, P. & Bradbury, A.R.M. Eliminating helper phage from phage display. Nucleic Acids Res. 34, e145 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Westwater, C. et al. Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrob. Agents Chemother. 47, 1301–1307 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Dong, D., Sutaria, S., Hwangbo, J.Y. & Chen, P. A simple and rapid method to isolate purer M13 phage by isoelectric precipitation. Appl. Microbiol. Biotechnol. 97, 8023–8029 (2013).
  Article CAS PubMed Google Scholar
• Ramarao, N., Nielsen-Leroux, C. & Lereclus, D. The insect Galleria mellonella as a powerful infection model to investigate bacterial pathogenesis. J. Vis. Exp. 4392, 10.3791/4392 (2012).