IP Library › Granted Patent US 8,927,703
Granted Patent B2
US 8,927,703 · App. 12/061,438 · Granted Jan 6, 2015

Compositions, kits and related methods for the detection and/or monitoring of

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Quick Facts
Patent No.
US 8,927,703
App. No.
12/061,438
Granted
Jan 6, 2015
Kind
B2
Abstract

The present invention provides compositions, methods and kits for the species-specific detection of Pseudomonas aeruginosa.

Claims (43)

1. A composition for use in a Pseudomonas aeruginosa nucleic acid amplification assay comprising a T7 provider oligo and a non-T7 primer oligo, wherein the T7 provider oligo is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:1, SEQ ID NO:11 and SEQ ID NO:14, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 725-825 of E. coli 23s rRNA, and the non-T7 primer oligo is selected from the group consisting of SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:19 and SEQ ID NO:15, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 845-950 of E. coli 23s rRNA.

2. The composition of claim 1 , where the T7 provider is selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:1, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 725-775 of E. coli 23s rRNA, and the non-T7 primer is selected from the group consisting of SEQ ID NO:22 and SEQ ID NO:24, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 900-950 of E. coli 23s rRNA.

3. The composition of claim 1 , where the T7 provider is SEQ ID NO:2 and the non-T7 primer is SEQ ID NO:22.

4. The composition of claim 1 , further comprising a detection oligo.

5. The composition of claim 4 , where the detection oligo is a torch oligo or molecular beacon.

6. The composition of claim 5 , where the torch oligo is selected from the group consisting of SEQ ID NO:51, SEQ ID NO:54, SEQ ID NO:50 and SEQ ID NO:56.

7. The composition of claim 1 , further comprising an extend oligo.

8. The composition of claim 7 , where the extend oligo is selected from the group consisting of SEQ ID NO:43 and SEQ ID NO:44.

9. The composition of claim 1 , further comprising a blocker oligo.

10. The composition of claim 9 , wherein the blocker oligo is selected from the group consisting of SEQ ID NO:29, SEQ ID NO:26, SEQ ID NO:40 and SEQ ID NO:42.

11. A composition for use in a transcription-based Pseudomonas aeruginosa nucleic acid amplification assay comprising the T7 provider oligo, SEQ ID NO:2 and the non-T7 primer oligo, SEQ ID NO:24.

12. The composition of claim 11 , further comprising any one of the blocker oligo SEQ ID NO:29, the torch oligo SEQ ID NO:54, the extend oligo SEQ ID NO:44, and the target capture oligo SEQ ID NO:69.

13. The composition of claim 12 , further comprising the target capture helper oligo SEQ ID NO:73.

14. A kit for use in a Pseudomonas aeruginosa amplification assay comprising a T7 provider oligo and a non-T7 primer oligo, wherein the T7 provider oligo is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:1, SEQ ID NO:11 and SEQ ID NO:14, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 725-825 of E. coli 23s rRNA, and the non-T7 primer oligo is selected from the group consisting of SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:19 and SEQ ID NO:15, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 845-950 of E. coli 23s rRNA.

15. The kit of claim 14 , where the T7 provider is selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:1, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 725-775 of E. coli 23s rRNA, and the non-T7 primer is selected from the group consisting of SEQ ID NO:22 and SEQ ID NO:24, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 900-950 of E. coli 23s rRNA.

16. The kit of claim 14 , where the T7 provider is SEQ ID NO:2 and the non-T7 primer is SEQ ID NO:22.

17. The kit of claim 14 , further comprising a detection oligo.

18. The kit of claim 17 , where the detection oligo is a torch oligo or molecular beacon.

19. The kit of claim 18 , where the torch oligo is selected from the group consisting of SEQ ID NO:51, SEQ ID NO:54, SEQ ID NO:50 and SEQ ID NO:56.

20. The kit of claim 14 , further comprising an extend oligo.

21. The kit of claim 20 , where the extend oligo is selected from the group consisting of SEQ ID NO:43 and SEQ ID NO:44.

22. The kit of claim 14 , further comprising a blocker oligo.

23. The kit of claim 22 , wherein the blocker oligo is selected from the group consisting of SEQ ID NO:29 SEQ ID NO:26, SEQ ID NO:40 and SEQ ID NO:42.

24. A kit for use in a transcription-based Pseudomonas aeruginosa nucleic acid amplification assay comprising the T7 provider oligo, SEQ ID NO:2 and the non-T7 primer oligo, SEQ ID NO:24.

25. The kit of claim 24 , further comprising anyone of the blocker oligo SEQ ID NO:29, the torch oligo SEQ ID NO:54, the extend oligo SEQ ID NO:44, and the target capture oligo SEQ ID NO:69.

26. The kit of claim 25 , further comprising the target capture helper oligo SEQ ID NO:73.

27. A method for detecting the presence of Pseudomonas aeruginosa in a sample, said method comprising performing a nucleic acid amplification assay using a T7 provider oligo and a non-T7 primer oligo, wherein the T7 provider oligo is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:1, SEQ ID NO:11 and SEQ ID NO:14, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 725-825 of E. coli 23s rRNA, and the non-T7 primer oligo is selected from the group consisting of SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:19 and SEQ ID NO:15, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases from 845-950 of E. coli 23s rRNA.

28. The method of claim 27 , where the T7 provider is selected from the group consisting of SEQ ID NO:2 and SEQ ID NO:1, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 725-775 of E. coli 23s rRNA, and the non-T7 primer is selected from the group consisting of SEQ ID NO:22 and SEQ ID NO:24, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 900-950 of E. coli 23s rRNA.

29. The method of claim 28 , further comprising detecting amplified nucleic acid with a detection oligo.

30. The method of claim 29 , where the detection oligo is a torch oligo or molecular beacon.

31. The method of claim 30 , where the torch oligo is selected from the group consisting of SEQ ID NO:51, SEQ ID NO:54, SEQ ID NO:50 and SEQ ID NO:56.

32. The method of claim 30 wherein detecting said amplified nucleic acid occurs in real-time.

33. The method of claim 32 wherein P. aeruginosa nucleic acid is specifically detected in the presence of closely related Pseudomonads.

34. The method of claim 32 wherein the detection cut-off is set whereby P. aeruginosa nucleic acid and one or more closely related but not all Pseudomonads are detected.

35. The method of claim 28 , further comprising a blocker oligo.

36. The method of claim 35 , wherein the blocker oligo is selected from the group consisting of SEQ ID NO:29, SEQ ID NO:26, SEQ ID NO:40 and SEQ ID NO:42.

37. The method of claim 27 , where the T7 provider is SEQ ID NO:2, which targets a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 739-766 of E. coli 23s rRNA, and the non-T7 primer is SEQ ID NO:24, which targets the complement of a sequence in a region of Pseudomonas aeruginosa nucleic acid corresponding to bases 918-943 of E. coli 23s rRNA.

38. The method of claim 27 , where the T7 provider is SEQ ID NO:2 and the non-T7 primer is SEQ ID NO:22.

39. The method of claim 27 , further comprising an extend oligo.

40. The method of claim 39 , where the extend oligo is selected from the group consisting of SEQ ID NO:43 and SEQ ID NO:44.

41. The method of claim 27 , where the amplification assay is transcription-based.

42. The method of claim 41 , where the method further includes the use of anyone of the blocker oligo SEQ ID NO:29, the torch oligo SEQ ID NO:54, the extend oligo SEQ ID NO:44, and the target capture oligo SEQ ID NO:69.

43. The method of claim 42 , where the method further includes the use of the target capture helper oligo, SEQ ID NO:73.

Assignments (8)
RELEASE OF SECURITY INTEREST Recorded Apr 28, 2026
From: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
To: HOLOGIC, INC., ON ITS OWN BEHALF AND AS SUCCESSOR-BY-MERGER TO DIRECT RADIOGRAPHY CORP.; CYTYC CORPORATION, ON ITS OWN BEHALF AND AS SUCCESSOR-BY-MERGER TO BIOLUCENT, LLC; CYTYC SURGICAL PRODUCTS, LLC, AS SUCCESSOR-BY-CONVERSION TO CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; GEN-PROBE INCORPORATED, ON ITS OWN BEHALF AND AS SUCCESSOR-BY-MERGER TO THIRD WAVE TECHNOLOGIES, INC.; GEN-PROBE PRODESSE, INC.; SUROS SURGICAL SYSTEMS, INC.
Reel/Frame 075566/0039 →
SECURITY INTEREST Recorded Apr 8, 2026
From: BIOTHERANOSTICS, INC.; GEN-PROBE INCORPORATED; GEN-PROBE PRODESSE, INC.; CYTYC CORPORATION; SUROS SURGICAL SYSTEMS, INC.; GYNESONICS, INC.; BOLDER SURGICAL, LLC; FAXITRON BIOPTICS, LLC; HEALTH BEACONS, INC.; HOLOGIC, INC.
To: ROYAL BANK OF CANADA, AS COLLATERAL AGENT
Reel/Frame 075462/0440 →
CORRECTIVE ASSIGNMENT TO CORRECT THE INCORRECT PATENT NO. 8081301 PREVIOUSLY RECORDED AT REEL: 028810 FRAME: 0745. ASSIGNOR(S) HEREBY CONFIRMS THE SECURITY AGREEMENT. Recorded Nov 9, 2017
From: HOLOGIC, INC.; BIOLUCENT, LLC; CYTYC CORPORATION; CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; SUROS SURGICAL SYSTEMS, INC.; THIRD WAVE TECHNOLOGIES, INC.; GEN-PROBE INCORPORATED
To: GOLDMAN SACHS BANK USA
Reel/Frame 044432/0565 →
CORRECTIVE ASSIGNMENT TO CORRECT THE INCORRECT PATENT NO. 8081301 PREVIOUSLY RECORDED AT REEL: 035820 FRAME: 0239. ASSIGNOR(S) HEREBY CONFIRMS THE SECURITY INTEREST RELEASE. Recorded Nov 9, 2017
From: GOLDMAN SACHS BANK USA, AS COLLATERAL AGENT
To: HOLOGIC, INC.; BIOLUCENT, LLC; CYTYC CORPORATION; CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; SUROS SURGICAL SYSTEMS, INC.; THIRD WAVE TECHNOLOGIES, INC.; GEN-PROBE INCORPORATED
Reel/Frame 044727/0529 →
SECURITY AGREEMENT Recorded Aug 7, 2015
From: HOLOGIC, INC.; BIOLUCENT, LLC; CYTYC CORPORATION; CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; DIRECT RADIOGRAPHY CORP.; GEN-PROBE INCORPORATED; GEN-PROBE PRODESSE, INC.; SUROS SURGICAL SYSTEMS, INC.; THIRD WAVE TECHNOLOGIES, INC.
To: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
Reel/Frame 036307/0199 →
SECURITY INTEREST RELEASE REEL/FRAME 028810/0745 Recorded Jun 4, 2015
From: GOLDMAN SACHS BANK USA, AS COLLATERAL AGENT
To: HOLOGIC, INC.; BIOLUCENT, LLC; CYTYC CORPORATION; CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; SUROS SURGICAL SYSTEMS, INC.; THIRD WAVE TECHNOLOGIES, INC.; GEN-PROBE INCORPORATED
Reel/Frame 035820/0239 →
SECURITY AGREEMENT Recorded Aug 1, 2012
From: HOLOGIC, INC.; BIOLUCENT, LLC; CYTYC CORPORATION; CYTYC SURGICAL PRODUCTS, LIMITED PARTNERSHIP; SUROS SURGICAL SYSTEMS, INC.; THIRD WAVE TECHNOLOGIES, INC.; GEN-PROBE INCORPORATED
To: GOLDMAN SACHS BANK USA
Reel/Frame 028810/0745 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jul 17, 2008
From: KAPLAN, SHANNON K.; LIVEZEY, KRISTIN W.; BUNGO, JENNIFER J.; HOGAN, JAMES J.
To: GEN-PROBE INCORPORATED
Reel/Frame 021255/0766 →