WO2004067702B1 - Methods, oligonucleotides and kits for the identification of mycobacterium in a sample - Google Patents
Methods, oligonucleotides and kits for the identification of mycobacterium in a sampleInfo
- Publication number
- WO2004067702B1 WO2004067702B1 PCT/GB2004/000390 GB2004000390W WO2004067702B1 WO 2004067702 B1 WO2004067702 B1 WO 2004067702B1 GB 2004000390 W GB2004000390 W GB 2004000390W WO 2004067702 B1 WO2004067702 B1 WO 2004067702B1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- sample
- nucleic acid
- oligonucleotide primer
- primer pair
- mycobacterium
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Ceased
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Analytical Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Immunology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Micro-Organisms Or Cultivation Processes Thereof (AREA)
Abstract
The invention relates to a method for the identification of Mycobacterium in samples.
Claims
AMENDED CLAIMS
[received by the International Bureau on 14 September 2004 (14.09.04); original claim 20 amended; remaining claims unchanged 1-19 and 21-29 (5 pages)]
Claims
1. A method for the identification of Mycobacterium in a sample comprising; forming a preparation comprising; a sample to be tested, polymerase chain reaction reagents and at least one oligonucleotide primer pair, characterised in that said oligonucleotide primer pair is selected from the group consisting of nucleic acid primers comprising;
5 tgggaaactgggaaactgggtctaata 3 5 cccgcacgcccaagttaagctgtgag 3 or;
5 cgacgaaggtccgggttctctcggattgac 3 5 gccatgcaccacctgcacacaggcccac 3 or modifications thereof, which modifications are the addition, deletion or substitution of at least one nucleotide base of at least one oligonucleotide primer of said pair, wherein said oligonucleotide or modified oligonucleotides hybridize to 16S ribosomal nucleic acid;
(ii) providing conditions suitable for 16S ribosomal nucleic acid" amplification; and optionally; i) detecting 16S ribosomal nucleic acid amplification products.
2. A method according to claim 1, wherein said oligonucleotide primer pair consists of;
5 tgggaaactgggaaactgggtctaata 3 5 cccgcacgcccaagttaagctgtgag 3 , and wherein said oligonucleotide pair enables the identification of both fast and slow growing Mycobacterium within said sample to be tested.
3. A method according to claim 1, wherein said oligonucleotide primer pair consists of;
5' cgacgaaggtccgggttctctcggattgac
V gccatgcaccacctgcacacaggcccac 3' , and wherein said oligonucleotide primer pair enables the identification of slow growing Mycobacterium within said sample to be tested.
4. A method according to claim 2 and 3, wherein said slow growing Mycobacterium group comprises; M.bovis, M.tuberculosis, M.kansaii, M.paratuberculosis, M.gordonae, M.leprae and M.celatum.
5. A method according to claims 1 to 3, wherein at least one Mycobacterium species- specific oligonucleotide primer pair is incorporated into said preparation.
6. A method according to claim 5, wherein said one Mycobacterium species-specific ' oligonucleotide primer pair is specific for a Mycobacterium species selected from the group comprising; 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.shimodei, M.simiae, M.smegmatis, M.szulgai, M.terrae, M.trivale, M.tuberculosis, M.ulcerans orM.xenopi.
1. A method according to claim 6, wherein said Mycobacterium species is M.bovis.
8. A method according to claim 6 or 1, wherein said species-specific oligonucleotide primer pair hybridises with nucleic acid sequences in MPB64, MPB70 or Esat-6.
. A method according to claim 8, wherein said oligonucleotide primer pairs are selected from; acg gca teg teg tea gcc ag gtg att ggc ttg cga tag gc or; gaa caa tec gga gtt gac aa age acg ctg tea ate atg ta or; aca tga cag age age agt gg tga caa cct etc aga gtg eg
10. A method according to claim 1-9, wherein said sample is an environmental sample.
11. A method according to claim 10, wherein said environmental sample is from within a farm environment.
12. A method according to claim 11, wherein said sample is selected from the group consisting of; soil, vegetation, slurry, water, animal feed, ammal waste.
13. A method according to claim 12, wherein said vegetation is selected from the group consisting of; grass, hay or straw.
14. A method according to claim 1-9, wherem said sample is a cell/tissue/fluid sample.
15. A method according to claim 14, wherein said sample is a sample derived from an animal or human.
16. A method according to claim 14 or 15, wherein said biological sample is selected from the group consisting of; milk, sputum, respiratory tissue, respiratory exudates, blood, plasma, serum, cervical swab samples, biopsy tissue, gastrointestinal tissue, gastrointestinal fluids, urine, feces, semen or other biological samples.
17. A method according to claim 15, wherein said animal is selected from the group consisting of; human, cows, bulls, steers, oxen, goats, sheep, badgers, deer and opossums.
18. A method according to claim 17, wherein said animal is bovine.
19. A method for the identification of Mycobacterium in a sample comprising; forming a preparation to be tested comprising; a sample to be tested, polymerase chain reaction reagents and at least one oligonucleotide primer pair, characterised in that said oligonucleotide primer pair is selected from the group consisting of;
5 tgggaaactgggaaactgggtctaata 3 5 cccgcacgcccaagttaagctgtgag 3 and;
5 cgacgaaggtccgggttctctcggattgac 3 gccatgcaccacctgcacacaggcccac and; ii) providing conditions suitable for 16S nucleic acid amplification; and iii) detecting 16S nucleic acid amplification products.
20. A pair of oligonucleotides or modified oligonucleotides, wherem said modified oligonucleotides are modified by addition, deletion or substitution of at least one nucleotide base, and wherein the pair comprises a nucleic acid sequence selected from;
5 tgggaaactgggaaactgggtctaata 3 5 cccgcacgcccaagttaagctgtgag 3 or
5 cgacgaaggtccgggttctctcggattgac 3 5 gccatgcaccacctgcacacaggcccac 3 and the pair hybridises to 16S nucleic acid.
21. An oligonucleotide consisting of the nucleic acid sequence 5 tgggaaactgggaaactgggtctaata 3 or part thereof.
22. An oligonucleotide consisting of the nucleic acid sequence 5 cccgcacgcccaagttaagctgtgag 3 or part thereof.
23. An oligonucleotide consisting of the nucleic acid sequence 5' cgacgaaggtccgggttctctcggattgac or part thereof
24. An oligonucleotide consisting of the nucleic acid sequence gccatgcaccacctgcacacaggcccac or part thereof.
25. A kit comprising a DNA extraction kit, polymerase chain reaction agents and at least one oligonucleotide primer pair according to the invention
26. A kit according to claim 25, wherein said oligonucleotides are;
^tgggaaactgggaaactgggtctaata 3 5 cccgcacgcccaagttaagctgtgag 3
27. A kit according to claim 25, wherein said oligonucleotides are;
5 cgacgaaggtccgggttctctcggattgac 3 5 gccatgcaccacctgcacacaggcccac 3
28. A kit according to claim 25, wherein at least one of said oligonucleotide primer pairs are species-specific for Mycobacterium.
29. A kit according to claim 28, wherein said species-specific oligonucleotide primer pair is specific for M.bovis.
Applications Claiming Priority (4)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| GB0302122.7 | 2003-01-30 | ||
| GB0302122A GB0302122D0 (en) | 2003-01-30 | 2003-01-30 | Screen |
| GB0308115.5 | 2003-04-09 | ||
| GB0308115A GB0308115D0 (en) | 2003-04-09 | 2003-04-09 | Screen |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| WO2004067702A2 WO2004067702A2 (en) | 2004-08-12 |
| WO2004067702A3 WO2004067702A3 (en) | 2004-10-07 |
| WO2004067702B1 true WO2004067702B1 (en) | 2004-12-02 |
Family
ID=32827035
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/GB2004/000390 Ceased WO2004067702A2 (en) | 2003-01-30 | 2004-01-30 | Methods, oligonucleotides and kits for the identification of mycobacterium in a sample |
Country Status (1)
| Country | Link |
|---|---|
| WO (1) | WO2004067702A2 (en) |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US8188256B2 (en) | 2006-05-02 | 2012-05-29 | Wako Pure Chemical Industries, Ltd. | Primer and probe for detection of Mycobacterium intracellulare |
| CN103224932A (en) | 2008-05-28 | 2013-07-31 | 和光纯药工业株式会社 | Primer and probe for detection of mycobacterium intracellulare, and method for detection of mycobacterium intracellulare using the primer or the probe |
| CN106755536B (en) * | 2017-03-02 | 2020-12-01 | 安徽师范大学 | Specific PCR primers for identifying serows and methods for identifying serows using specific PCR primers |
| WO2019135567A1 (en) * | 2018-01-05 | 2019-07-11 | Seegene, Inc. . | Method for determining the presence or absence of m. tuberculosis, m. bovis and m. bovis bcg in a sample |
Family Cites Families (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6150517A (en) * | 1986-11-24 | 2000-11-21 | Gen-Probe | Methods for making oligonucleotide probes for the detection and/or quantitation of non-viral organisms |
| ES2112824T5 (en) * | 1986-11-24 | 2008-03-01 | Gen-Probe Incorporated | NUCLEIC ACID PROBES FOR DETECTION AND / OR QUANTIFICATION OF NON-VIRAL ORGANISMS. |
| US5521300A (en) * | 1991-08-13 | 1996-05-28 | Norval B. Galloway | Oligonucleotides complementary to mycobacterial nucleic acids |
| US6136529A (en) * | 1993-09-03 | 2000-10-24 | Gen-Probe Incorporated | Nucleic acid probes to Mycobacterium avium complex |
| US5712095A (en) * | 1994-06-16 | 1998-01-27 | Becton Dickinson And Company | Rapid and sensitive detection of antibiotic-resistant mycobacteria using oligonucleotide probes specific for ribosomal RNA precursors |
| WO1999045119A2 (en) * | 1998-03-06 | 1999-09-10 | Statens Serum Institut | Production of mycobacterial polypeptides by lactic acid bacteria |
-
2004
- 2004-01-30 WO PCT/GB2004/000390 patent/WO2004067702A2/en not_active Ceased
Also Published As
| Publication number | Publication date |
|---|---|
| WO2004067702A3 (en) | 2004-10-07 |
| WO2004067702A2 (en) | 2004-08-12 |
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