Optimized vector for delivery in microbial populations

Patent metadata

Field	Value
Publication number	US-11078490-B2
Application number	US-202017017111-A
Country	US
Kind code	B2
Filing date	Sep 10, 2020
Priority date	Feb 3, 2017
Publication date	Aug 3, 2021
Grant date	Aug 3, 2021

Abstract

The present invention relates to a vector, preferably included in a delivery vehicle, comprising no more than 100, preferably no more than 10, restriction sites recognized by the restriction enzymes encoded by each bacterium of a group of bacteria of interest. The invention also relates to the use of said vector, preferably included in a delivery vehicle, as a drug, especially in the treatment of a disease in a patient in need thereof.

First claim

What is claimed:

1. An engineered bacteriophage or packaged phagemid, for DNA delivery into Klebsiella pneumoniae strains, wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove one or more of the restriction sites selected from the group consisting of CAGNNNNNNCGT (SEQ ID NO: 93); GAAYNNNNNNNCTGG (SEQ ID NO: 94); CGANNNNNNNNTGCC (SEQ ID NO: 95); ACGNNNNNGTTG (SEQ ID NO: 96) and CGCATC corresponding to restriction enzymes encoded by Klebsiella pneumoniae strains.

2. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93); GAAYNNNNNNNCTGG (SEQ ID NO: 94); CGANNNNNNNNTGCC (SEQ ID NO: 95); ACGNNNNNGTTG (SEQ ID NO: 96) and CGCATC corresponding to restriction enzymes encoded by Klebsiella pneumoniae strains.

3. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction site CAGNNNNNNCGT (SEQ ID NO: 93).

4. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction site GAAYNNNNNNNCTGG (SEQ ID NO: 94).

5. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction site CGANNNNNNNNTGCC (SEQ ID NO: 95).

6. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction site ACGNNNNNGTTG (SEQ ID NO: 96).

7. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction site CGCATC.

8. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93) and CGCATC.

9. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93), GAAYNNNNNNNCTGG (SEQ ID NO: 94) and CGCATC.

10. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93), GAAYNNNNNNNCTGG (SEQ ID NO: 94), CGANNNNNNNNTGCC (SEQ ID NO: 95) and CGCATC.

11. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites GAAYNNNNNNNCTGG (SEQ ID NO: 94) and CGCATC.

12. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CGANNNNNNNNTGCC (SEQ ID NO: 95) and CGCATC.

13. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93) and GAAYNNNNNNNCTGG (SEQ ID NO: 94).

14. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CAGNNNNNNCGT (SEQ ID NO: 93) and CGANNNNNNNNTGCC (SEQ ID NO: 95).

15. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites GAAYNNNNNNNCTGG (SEQ ID NO: 94) and CGANNNNNNNNTGCC (SEQ ID NO: 95).

16. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites GAAYNNNNNNNCTGG (SEQ ID NO: 94), CGANNNNNNNNTGCC (SEQ ID NO: 95) and CGCATC.

17. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein the bacteriophage or packaged phagemid for DNA delivery into Klebsiella pneumoniae strain is derived from a bacteriophage selected from the group consisting of AIO-2, KI4B, K16B, K19, (syn=K19), K114, K115, K121, K128, K129, KI32, K133, K135, K1106B, K1171B, K1181B, K1832B, AIO-I, AO-I, AO-2, AO-3, FC3-10, K, K11, (syn=KI1), K12, (syn=K12), K13, (syn=K13), (syn=Kl 70/11), K14, (syn=K14), K15, (syn=K15), K16, (syn=K16), K17, (syn=K17), K18, (syn=K18), K119, (syn=K19), K127, (syn=K127), K131, (syn=K131), K135, K1171B, II, VI, IX, CI-I, K14B, K18, K111, K112, K113, K116, K117, K118, K120, K122, K123, K124, K126, K130, K134, K1106B, KIi65B, K1328B, KLXI, K328, P5046, 11, 380, III, IV, VII, VIII, FC3-11, K12B, (syn=K12B), K125, (syn=K125), K142B, (syn=K142), (syn=K142B), K1181B, (syn=KI1 81), (syn=K1181B), K1765/!, (syn=K1765/1), K1842B, (syn=K1832B), K1937B, (syn=K1937B), Ll, φ28, 7, 231, 483, 490, 632, 864/100, KP01K2, Kl l, Kpn5, KP34, and JDOO1.

18. A pharmaceutical or veterinary composition, comprising an engineered bacteriophage or a packaged phagemid according to claim 1 .

19. A method of treating a subject infected with pathogenic or virulent bacteria comprising the administration of the pharmaceutical or veterinary composition of claim 18 .

20. The method of claim 19 , wherein the subject is infected with Klebsiella pneumoniae.

Assignees

• Eligo Bioscience
• Pasteur Institut

Inventors

• Decrulle Antoine
• Fernandez Rodriguez Jesus
• Duportet Xavier
• Bikard David

Classifications

• C12N15/70 Primary

  Vectors or expression systems specially adapted for E. coli · CPC title

• A61K35/76

  Viruses; Subviral particles; Bacteriophages · CPC title

• A61P31/04

  Antibacterial agents · CPC title

• C12N15/73 Primary

  Expression systems using phage (lambda) regulatory sequences · CPC title

• C12N2795/10332

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