Exploiting CRISPR-cas nucleases to produce sequence-specific antimicrobials

Nature Biotechnology

Volumn 32, Issue 11, 2014, Pages 1146-1150

  Bikard, David ^a,d   Euler, Chad W ^a   Jiang, Wenyan ^a   Nussenzweig, Philip M ^a   Goldberg, Gregory W ^a   Duportet, Xavier ^b,c   Fischetti, Vincent A ^a   Marraffini, Luciano A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b INRIA ROCQUENCOURT   (France)

^c Massachusetts Institute of Technology Cambridge   (United States)

^d INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; ENZYME INHIBITION; GENES; POPULATION STATISTICS;

ANTIBIOTIC RESISTANCE; ANTIBIOTIC RESISTANCE GENES; BACTERIAL POPULATION; CELLULAR PATHWAY; GROWTH FUNCTIONS; MICROBIAL POPULATIONS; SEQUENCE-SPECIFIC MANNER; STAPHYLOCOCCUS AUREUS;

ANTIBIOTICS;

ANTIBIOTIC AGENT; NUCLEASE; ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; ANTIMICROBIAL THERAPY; ARTICLE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIOPHAGE; BIOGENESIS; CONTROLLED STUDY; CRISPR CAS SYSTEM; DNA SEQUENCE; ESCHERICHIA COLI; FLOW CYTOMETRY; HOSPITAL INFECTION; HUMAN; IN VIVO STUDY; MICROBIAL COMMUNITY; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; POISSON DISTRIBUTION; PRIORITY JOURNAL; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PYOGENES; SURVIVAL RATE; ANIMAL; DRUG EFFECTS; GENETICS; NUCLEOTIDE SEQUENCE; PLASMID; SYNTHESIS; VIRULENCE;

ANIMALS; ANTI-INFECTIVE AGENTS; BACTERIOPHAGES; BASE SEQUENCE; CRISPR-CAS SYSTEMS; DRUG RESISTANCE, MICROBIAL; MICE; PLASMIDS; STAPHYLOCOCCUS AUREUS; VIRULENCE;

EID: 84983142945     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3043     Document Type: Article

References (30)

1. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
2. 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. USA 109, E2579-E2586 (2012).
3. Diep, B.A. et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367, 731-739 (2006).
4. Weigel, L.M. et al. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302, 1569-1571 (2003).
5. Round, J.L. et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 332, 974-977 (2011).
6. Mazmanian, S.K., Round, J.L. & Kasper, D.L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620-625 (2008).
7. Dethlefsen, L., Huse, S., Sogin, M.L. & Relman, D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280 (2008).
8. Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607 (2011).
9. Gomaa, A.A. et al. Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 5, e00928-e00913 (2014).
10. 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).
11. Melnikov, A.A., Tchernov, A.P., Fodor, I. & Bayev, A.A. Lambda phagemids and their transducing properties. Gene 28, 29-35 (1984).
12. 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).
13. Grice, E.A. et al. Topographical and temporal diversity of the human skin microbiome. Science 324, 1190-1192 (2009).
14. Lowy, F.D. Staphylococcus aureus infections. N. Engl. J. Med. 339, 520-532 (1998).
15. Horinouchi, S. & Weisblum, B. Nucleotide sequence and functional map of pC194, a plasmid that specifies inducible chloramphenicol resistance. J. Bacteriol. 150, 815-825 (1982).
16. Kreiswirth, B.N. et al. The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature 305, 709-712 (1983).
17. 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).
18. Baba, T., Bae, T., Schneewind, O., Takeuchi, F. & Hiramatsu, K. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. J. Bacteriol. 190, 300-310 (2008).
19. Charpentier, E. et al. Novel cassette-based shuttle vector system for gram-positive bacteria. Appl. Environ. Microbiol. 70, 6076-6085 (2004).
20. Ubukata, K., Nonoguchi, R., Matsuhashi, M. & Konno, M. Expression and inducibility in Staphylococcus aureus of the mecA gene, which encodes a methicillin-resistant S. aureus-specific penicillin-binding protein. J. Bacteriol. 171, 2882-2885 (1989).
21. Isnard, C., Malbruny, B., Leclercq, R. & Cattoir, V. Genetic basis for in vitro and in vivo resistance to lincosamides, streptogramins A, and pleuromutilins (LSAP Phenotype) in Enterococcus faecium. Antimicrob. Agents Chemother. 57, 4463-4469 (2013).
22. Kugelberg, E. et al. Establishment of a superficial skin infection model in mice by using Staphylococcus aureus and Streptococcus pyogenes. Antimicrob. Agents Chemother. 49, 3435-3441 (2005).
23. Pastagia, M. et al. A novel chimeric lysin shows superiority to mupirocin for skin decolonization of methicillin-resistant and-sensitive Staphylococcus aureus strains. Antimicrob. Agents Chemother. 55, 738-744 (2011).
24. Agarwal, R. & Roy, K. Intracellular delivery of polymeric nanocarriers: a matter of size, shape, charge, elasticity and surface composition. Ther. Deliv. 4, 705-723 (2013).
25. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41, 7429-7437 (2013).
26. Qi, L.S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183 (2013).
27. McDougal, L.K. et al. Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: establishing a national database. J. Clin. Microbiol. 41, 5113-5120 (2003).
28. Bae, T., Baba, T., Hiramatsu, K. & Schneewind, O. Prophages of Staphylococcus aureus Newman and their contribution to virulence. Mol. Microbiol. 62, 1035-1047 (2006).
29. Goldberg, G.W., Jiang, W., Bikard, D. & Marraffini, L.A. Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature doi: 10.1038/nature13637 (31 August 2014).
30. Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).