Sequence specific antimicrobials

Patent metadata

Field	Value
Publication number	US-12295993-B2
Application number	US-202017088302-A
Country	US
Kind code	B2
Filing date	Nov 3, 2020
Priority date	Feb 7, 2013
Publication date	May 13, 2025
Grant date	May 13, 2025

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.

First claim

What is claimed is:

1. A method for killing targeted pathogenic bacteria in a mixed bacterial population in a subject comprising:
providing a pharmaceutical composition comprising a pharmaceutically acceptable carrier and packaged, recombinant phagemids that are packaged in phage capsids,
wherein the packaged phagemids comprise a clustered regularly interspaced short palindromic repeats (CRISPR) system,
wherein the CRISPR system comprises DNA encoding: i) a type II CRISPR-associated enzyme; and ii) a targeting RNA that targets at least one bacterial chromosome at a target site; and
contacting the bacterial population with the pharmaceutical composition by oral, parenteral, topical, nasal, or rectal administration to the subject;
wherein the contacting with the pharmaceutical composition introduces at least some of the phagemids into at least some of the bacteria in the bacterial population,
wherein subsequent to the introduction of the phagemids, the bacteria into which the phagemid is introduced expresses the targeting RNA and the type II CRISPR-associated enzyme,
wherein the expressed type II CRISPR-associated enzyme cleaves the bacterial chromosome at the target site of the targeting RNA, and
wherein the cleavage of the bacterial chromosome at the target site kills the targeted pathogenic bacteria.

2. The method of claim 1 , wherein the CRISPR-associated enzyme is a Cas9 enzyme.

3. The method of claim 2 , wherein the Cas9 enzyme is a Streptococcus pyogenes Cas9.

4. The method of claim 1 , further comprising detecting the killing of bacteria by the pharmaceutical composition.

5. The method of claim 1 , wherein the mixed bacterial population comprises a combination of bacterial species selected from the group consisting of Staphylococcus, Clostridium, Bacillus, Salmonella, Helicobacter pylori, Neisseria gonorrhoeae, Neisseria meningitidis , and Escherichia coli.

6. The method of claim 1 , wherein the targeted bacteria is a Staphylococcus.

7. The method of claim 1 , wherein the targeted bacteria is a Mycobacterium.

8. The method of claim 1 , wherein the targeted bacteria is a Pseudomonas.

Assignees

• Univ Rockefeller

Inventors

• Bikard David
• Marraffini Luciano

Classifications

• C12N2795/10371

  Demonstrated in vivo effect · CPC title

• C12N2795/10343

  viral genome or elements thereof as genetic vector · CPC title

• C12N2795/10332

  Use of virus as therapeutic agent, other than vaccine, e.g. as cytolytic agent · CPC title

• C12N2795/10331

  Uses of virus other than therapeutic or vaccine, e.g. disinfectant · CPC title

• C12Y301/00

  Hydrolases acting on ester bonds (3.1) · CPC title