Sequence specific antimicrobials
AssigneeThe Rockefeller University
InventorsDavid Bikard, Luciano Marraffini
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Abstract
Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.
Claims24
A method for selectively modifying a mixed population of bacteria, wherein the mixed population of bacteria comprises at least a first and a second bacterial species, comprising:
- (a) contacting the mixed population of bacteria with packaged, recombinant phagemids that are packaged in phage capsids, wherein the packaged phagemids comprise a clustered regularly interspaced short palindromic repeats (CRISPR) system comprising i) a type II CRISPR-associated enzyme and ii) two or more crRNA guides that target different chromosomal sequences in bacterial cells of the second bacterial species and,
- (b) producing the crRNA guides in the bacterial cells of the second bacterial species, wherein the crRNA guides comprise i) a first crRNA guide complementary to a first target chromosomal sequence in the bacterial cells of the second bacterial species and ii) a second crRNA guide complementary to a second target chromosomal sequence in the bacterial cells of the second bacterial species, wherein the second target chromosomal sequence is different from the first target chromosomal sequence;
- and wherein:
- 1) the first target chromosomal sequence is comprised by a first antibiotic resistance gene and the second target chromosomal sequence is comprised by a second antibiotic resistance gene,
- 2) the first target chromosomal sequence is comprised by an antibiotic resistance gene and the second target chromosomal sequence is comprised by a virulence gene, or
- 3) the first target chromosomal sequence is comprised by a first virulence gene and the second target chromosomal sequence is comprised by a second virulence gene;
- wherein the expressed type II CRISPR-associated enzyme cleaves the first and second target chromosomal sequences at the target sites of the crRNA guides in the bacterial cells of the second bacterial species,
- wherein the first and second bacterial species are different and are selected from Streptococcus, Staphylococcus, Clostridium, Bacillus, Salmonella, Helicobacter pylori, Neisseria gonorrhoeae, Neisseria meningitidis, and Escherichia coli, and
- wherein the growth of the bacterial cells of the first bacterial species in the mixed population is not inhibited, and wherein at least 50% of the bacterial cells of the second bacterial species are killed.
Dependencies are inferred from the claim text.