Optimized vector for delivery in microbial populations

Patent metadata

Field	Value
Publication number	US-10808254-B2
Application number	US-201916527762-A
Country	US
Kind code	B2
Filing date	Jul 31, 2019
Priority date	Feb 3, 2017
Publication date	Oct 20, 2020
Grant date	Oct 20, 2020

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

The invention claimed is:

1. An engineered bacteriophage or packaged phagemid, for DNA delivery into Escherichia coli strains, wherein said engineered bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34); and CTGCAG (SEQ ID NO: 37) corresponding to restriction enzymes encoded by Escherichia coli strains.

2. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein the bacteriophage or packaged phagemid further has been genetically engineered to remove the restriction sites AACNNNNNNGTGC (SEQ ID NO: 2); CACNNNNGTAY (SEQ ID NO: 3); AACNNNNCTTT (SEQ ID NO: 4); and GGTCTC (SEQ ID NO: 36).

3. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein the bacteriophage or packaged phagemid further has been genetically engineered to remove the restriction AACNNNNNNGTGC (SEQ ID NO: 2) and GGTCTC (SEQ ID NO: 36).

4. An engineered bacteriophage or packaged phagemid, for DNA delivery into Escherichia coli strains, wherein said engineered bacteriophage or packaged phagemid is selected from the group consisting of:
(i) a bacteriophage or packaged phagemid that has been genetically engineered to remove the following restriction sites: CACNNNNNNNNCTGG (SEQ ID NO: 1), AACNNNNNNGTGC (SEQ ID NO: 2); and, GAAABCC (SEQ ID NO: 34);
(ii) a bacteriophage or packaged phagemid that has been genetically engineered to remove the restriction sites: CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34) and GGTCTC (SEQ ID NO: 36); and
(iii) a bacteriophage or packaged phagemid that has been genetically engineered to remove the restriction sites CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34) and GCCGGC (SEQ ID NO: 38) wherein said restriction sites correspond to restriction enzymes encoded by Escherichia coli strains.

5. The engineered bacteriophage or packaged phagemid of claim 4 , wherein said bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34) and AACNNNNNNGTGC (SEQ ID NO: 2) corresponding to restriction enzymes encoded by Escherichia coli strains.

6. The engineered bacteriophage or packaged phagemid of claim 4 , wherein said bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34) and GGTCTC (SEQ ID NO: 36) corresponding to restriction enzymes encoded by Escherichia coli strains.

7. The engineered bacteriophage or packaged phagemid of claim 4 , wherein said bacteriophage or packaged phagemid has been genetically engineered to remove the restriction sites CACNNNNNNNNCTGG (SEQ ID NO: 1); GAAABCC (SEQ ID NO: 34) and GCCGGC (SEQ ID NO: 38) corresponding to restriction enzymes encoded by Escherichia coli strains.

8. The engineered bacteriophage or packaged phagemid of claim 1 , wherein the Escherichia coli strain is a STEC strain.

9. The engineered bacteriophage or packaged phagemid of claim 4 , wherein the Escherichia coli strain is a STEC strain.

10. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein the bacteriophage or packaged phagemid for DNA delivery into Escherichia coli strain is derived from a bacteriophage selected from the group consisting of BW73, B278, D6, D108, E, El, E24, E41, FI-2, FI-4, FI-5, HI8A, Ffl8B, i, MM, Mu, (syn=mu), (syn=MuI), (syn=Mu-I), (syn=MU-I), (syn=MuI), (syn=μ), 025, PhI-5, Pk, PSP3, Pl, PlD, P2, P4 (defective), Sl, Wφ, φK13, φR73 (defective), φ1, φ2, φ7, φ92, ψ (defective), 7 A, 8φ, 9φ, 15 (defective), 18, 28-1, 186, 299, HH- Escherichia (2), AB48, CM, C4, C16, DD-VI, (syn=Dd-Vi), (syn=DDVI), (syn=DDVi), E4, E7, E28, FE, FI3, H, Hl, H3, H8, K3, M, N, ND-2, ND-3, ND4, ND-5, ND6, ND-7, Ox-I (syn=OX1), (syn=HF), Ox-2 (syn=0x2), (syn=0X2), Ox-3, Ox-4, Ox-5, (syn=0X5), Ox-6, (syn=66F), (syn=φ66t), (syn=φ66t−)5 0111, PhI-I, RB42, RB43, RB49, RB69, S, SaI-I, Sal-2, Sal-3, Sal-4, Sal-5, Sal-6, TC23, TC45, TuII*-6, (syn=TuII*), TuIP-24, TuII*46, TuIP-60, T2, (syn=ganuTia), (syn=γ), (syn=PC), (syn=P.C.), (syn=T-2), (syn=T2), (syn=P4), T4, (syn=T-4), (syn=T4), T6, T35, αl, 1, IA, 3, (syn=Ac3), 3A, 3T+, (syn=3), (syn=Ml), 5φ, (syn=φ5), 9266Q, CFO103, HK620, J, K, K1F, m59, no. A, no. E, no. 3, no. 9, N4, sd, (syn=Sd), (syn=SD), (syn=Sa)3 (syn=sd), (syn=SD), (syn=CD), T3, (syn=T-3), (syn=T3), T7, (syn=T-7), (syn=T7), WPK, W31, AH, φC3888, φK3, φK7, φK12, φV-1, Φ04-CF, Φ05, Φ06, Φ07, φ1, φ1.2, φ20, φ95, φ263, φ1092, (syn=φW), Ω8, 1, 3, 7, 8, 26, 27, 28-2, 29, 30, 31, 32, 38, 39, 42, 933W, NN- Escherichia (1), Esc-7-11, AC30, CVX-5, Cl, DDUP, EC1, EC2, E21, E29, Fl, F26S, F27S, Hi, HK022, HK97, (syn=(ΦHK97), HK139, HK253, HK256, K7, ND-I, no.D, PA-2, q, S2, T1, (syn=α), (syn=P28), (syn=T-I), (syn=Tx), T3C, T5, (syn=T-5), (syn=T5), UC-I, w, β4, γ2, λ (syn=lambda), (syn=Φλ), ΦD326, φγ, Φ06, Φ7, Φ10, φ80, χ, (syn=χi), (syn=φχ), (syn=φχi), 2, 4, 4A, 6, 8A, 102, 150, 168, 174, 3000, AC6, AC7, AC28, AC43, AC50, AC57, AC81, AC95, HK243, K10, ZG/3A, 5, 5A, 21EL, H19-J and 933H.

11. The engineered bacteriophage or packaged phagemid according to claim 4 , wherein the bacteriophage or packaged phagemid for DNA delivery into Escherichia coli strain is derived from a bacteriophage selected from the group consisting of BW73, B278, D6, D108, E, El, E24, E41, FI-2, FI-4, FI-5, HI8A, Ffl8B, i, MM, Mu, (syn=mu), (syn=MuI), (syn=Mu-I), (syn=MU-I), (syn=MuI), (syn=μ), 025, PhI-5, Pk, PSP3, Pl, P1D, P2, P4 (defective), Sl, Wφ, φK13, φR73 (defective), φ1, φ2, φ7, φ92, ψ (defective), 7 A, 8φ, 9φ, 15 (defective), 18, 28-1, 186, 299, HH- Escherichia (2), AB48, CM, C4, C16, DD-VI, (syn=Dd-Vi), (syn=DDVI), (syn=DDVi), E4, E7, E28, FE, FI3, H, H1, H3, H8, K3, M, N, ND-2, ND-3, ND4, ND-5, ND6, ND-7, Ox-I (syn=OXl), (syn=HF), Ox-2 (syn=0x2), (syn=0X2), Ox-3, Ox-4, Ox-5, (syn=0X5), Ox-6, (syn=66F), (syn=φ66t), (syn=φ66t−)5 0111, PhI-I, RB42, RB43, RB49, RB69, S, SaI-I, Sal-2, Sal-3, Sal-4, Sal-5, Sal-6, TC23, TC45, TuII*-6, (syn=TuII*), TuIP-24, TuII*46, TuIP-60, T2, (syn=ganuTia), (syn=γ), (syn=PC), (syn=P.C.), (syn=T-2), (syn=T2), (syn=P4), T4, (syn=T-4), (syn=T4), T6, T35, αl, 1, IA, 3, (syn=Ac3), 3A, 3T+, (syn=3), (syn=Ml), (syn=φ5), 9266Q, CFO103, HK620, J, K, K1F, m59, no. A, no. E, no. 3, no. 9, N4, sd, (syn=Sd), (syn=SD), (syn=Sa)3 (syn=sd), (syn=SD), (syn=CD), T3, (syn=T-3), (syn=T3), T7, (syn=T-7), (syn=T7), WPK, W31, AH, φC3888, φK3, φK7, φK12, φ-1, Φ04-CF, Φ05, Φ06, Φ07, φ1, φ1.2, φ20, φ95, φ263, φ1O92, (syn=φW), Ω8, 1, 3, 7, 8, 26, 27, 28-2, 29, 30, 31, 32, 38, 39, 42, 933W, NN- Escherichia (1), Esc-7-11, AC30, CVX-5, Cl, DDUP, EC1, EC2, E21, E29, Fl, F26S, F27S, Hi, HK022, HK97, (syn=ΦHK97), HK139, HK253, HK256, K7, ND-I, no.D, PA-2, q, S2, T1, (syn=α), (syn=P28), (syn=T-I), (syn=Tx), T3C, T5, (syn=T-5), (syn=T5), UC-I, w, β4, γ2, λ (syn=lambda), (syn=Φλ), ΦD326, φγ, Φ06, Φ7, Φ10, φ80, χ, (syn=χi), (syn=φχ), (syn=φχi), 2, 4, 4A, 6, 8A, 102, 150, 168, 174, 3000, AC6, AC7, AC28, AC43, AC50, AC57, AC81, AC95, HK243, K1O, ZG/3A, 5, 5A, 21EL, H19-J and 933H.

12. The engineered bacteriophage or packaged phagemid according to claim 1 , wherein the phagemid for DNA delivery into Escherichia coli strain is selected from the group consisting of a lambda derived phagemid or a P4 derived phagemid.

13. The engineered bacteriophage or packaged phagemid according to claim 4 , wherein the phagemid for DNA delivery into the Escherichia coli strain is selected from the group consisting of a lambda derived phagemid; or a P4 derived phagemid.

14. A pharmaceutical or veterinary composition, compris

Assignees

• Eligo Bioscience
• Pasteur Institut

Inventors

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

Classifications

• C12N2795/10332

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

• C12N15/74 Primary

  Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora · CPC title

• C12N15/70 Primary

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

• C12N7/00

  Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00) · CPC title

• Y02A50/30

  Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change · CPC title