Nucleic acid amplification and detection of mycobacterium species

• US 6,664,081 B2
• Filed: 12/15/2000
• Issued: 12/16/2003
• Est. Priority Date: 12/17/1999
• Status: Expired due to Term

• Current Assignee: Biomerieux Incorporated (Compagnie Merieux Alliance SAS), Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Biomerieux Incorporated (Compagnie Merieux Alliance SAS), Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Jucker, Markus T., Delgado, Francisco D., Brentano, Steven T., Rodrigue, Marc, Cleuziat, Philippe
• Primary Examiner(s): Benzion, Gary
• Assistant Examiner(s): SWITZER, JULIET CAROLINE
• Application Number:
  US09/738,274
• Publication Number:
  US 20030165824A1
• Time in Patent Office: 1,096 Days
• Field of Search: 435/6, 435/91.2, 536/24.32, 536/24.3, 536/24.33
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Methods of detecting Mycobacterium species using oligonucleotides to amplify in vitro 16S rRNA sequences or DNA encoding 16S rRNA sequences for many species in the genus Mycobacterium are disclosed. Amplification oligonucleotides for in vitro amplification of 16S rRNA sequences or DNA encoding 16S rRNA sequences from many Mycobacterium species are disclosed. Kits containing oligonucleotides useful for in vitro amplification of 16S rRNA sequences or DNA encoding 16S rRNA sequences from many Mycobacterium species are disclosed.

Claims

1. A composition comprising a combination of oligonucleotides for amplifying in an in vitro amplification reaction a Mycobacterium 16S rRNA sequence or DNA encoding the Mycobacterium 16S rRNA, wherein the oligonucleotides are:

an oligonucleotide in a size range of about 21 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

5, and

an oligonucleotide in a size range of about 18 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

34.

2. The composition of claim 1, wherein the composition comprises:

at least one first oligonucleotide containing the base sequence of any one of SEQ ID NO;

1 to SEQ ID NO;

5, and

at least one second oligonucleotide containing the base sequence of any one of SEQ ID NO;

28 to SEQ ID NO;

34, or SEQ ID NO;

27.

3. The composition of claim 2, wherein the first oligonucleotide containing the base sequence of any one of SEQ ID NO:

1 to SEQ ID NO;

5 is modified to include a 5′

promoter sequence.

7. The composition of claim 3, wherein the 5′

promoter sequence is a T7 promoter sequence.

8. The composition of claim 3, wherein the first oligonucleotide containing the base sequence of SEQ ID NO:

5 and modified to include a 5′

promoter sequence is combined with a second oligonucleotide containing the base sequence of SEQ ID NO;

28, SEQ ID NO;

29, SEQ ID NO;

30, SEQ ID NO;

31, SEQ ID NO;

32, SEQ ID NO;

33, SEQ ID NO;

34, or SEQ ID NO;

37.

4. A kit comprising a combination of oligonucleotides wherein the oligonucleotides are:

an oligonucleotide in a size range of about 21 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

5, and

an oligonucleotide in a size range of about 18 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

34.

5. The kit of claim 4, comprising:

at least one first oligonucleotide containing the base sequence of any one of SEQ ID NO;

1 to SEQ ID NO;

5, and

at least one second oligonucleotide containing the base sequence of any one of SEQ ID NO;

28 to SEQ ID NO;

34, or SEQ ID NO;

27.

6. The composition of claim 5, wherein the first oligonucleotide containing the base sequence of any one of SEQ ID NO:

1 to SEQ ID NO;

5 is modified to include a 5′

promoter sequence.

9. The kit of claim 6, wherein the 5′

promoter sequence is a T7 promoter sequence.

10. A method of detecting Mycobacterium species present in a biological sample, comprising the steps of:

providing a biological sample containing nucleic acid from at least one Mycobacterium species comprising a Mycobacterium 16S ribosomal RNA (rRNA) or a DNA encoding the Mycobacterium 16S ribosomal rRNA;

amplifying the Mycobacterium 16S rRNA or DNA in an in vitro nucleic acid amplification mixture comprising at least one polymerase activity, and a combination of at least two primers, to produce amplified Mycobacterium nucleic acid, wherein the primers are an oligonucleotide in a size range of about 21 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

5, and an oligonucleotide in a size range of about 18 to 26 bases containing a base sequence consisting of at least 18 contiguous bases contained in SEQ ID NO;

34; and

detecting the amplified Mycobacterium nucleic acid by detecting a label associated with the amplified Mycobacterium nucleic acid.

11. The method of claim 10, further comprising in the steps of:

adding to the biological sample at least one capture oligonucleotide that specifically hybridizes to the Mycobacterium 16S rRNA and an immobilized nucleic acid the hybridizes to the capture oligonucleotide under hybridizing conditions to produce a hybridization complex; and

separating the hybridization complex from other components of the biological sample before the amplifying step.

12. The method of claim 10, wherein the amplifying step amplifies 16s rRNA or DNA of M. tuberculosis or a Mycobacterium other than tuberculosis (MOTT) species.

13. The method of claim 10, wherein the amplifying step amplifies 16S rRNA or DNA of M. abscessus, M. africanum, M. asiaticum, M. avium, M. bovis, M. celatum, M. chelonae, M. flavescens, M. fortuitum, M. gastri, M. gordonae, M. haemophilum, M. intracellulare, M. interjectum, M. intermedium, M. kansasii, M. malmoense, M. marinum, M. non-chromogenicum, M. paratuberculosis, M. phlei, M. scrofulaceum, M. shimodei, M. simiae, M. smegmatis, M. szulgai, M. terrae, M. triviale, M. tuberculosis, M. ulcerans or M. xenopi.

14. The method of claim 10, wherein the detecting step uses at least one probe that hybridize specifically to the amplified Mycobacterium nucleic acid.

15. The method of claim 14, wherein the detecting step uses a plurality of probes that hybridize specifically to the amplified Mycobacterium nucleic acid.

16. The method of claim 10, wherein the amplifying step uses a combination of at least a first primer and a second primer, wherein the first primer has the sequence of SEQ ID NO:

5 attached to a 5′

promoter sequence, and the second primer has the sequence of SEQ ID NO;

30 or SEQ ID NO;

37.