CA2219090A1 - Universal targets for species identification - Google Patents

Universal targets for species identification

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Publication number
CA2219090A1
CA2219090A1 CA002219090A CA2219090A CA2219090A1 CA 2219090 A1 CA2219090 A1 CA 2219090A1 CA 002219090 A CA002219090 A CA 002219090A CA 2219090 A CA2219090 A CA 2219090A CA 2219090 A1 CA2219090 A1 CA 2219090A1
Authority
CA
Canada
Prior art keywords
seq
organism
primer
sequence
group
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.)
Granted
Application number
CA002219090A
Other languages
French (fr)
Other versions
CA2219090C (en
Inventor
Anthony W. Chow
Swee Han Goh
Sean Hemmingsen
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of British Columbia
National Research Council of Canada
Original Assignee
Individual
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Individual filed Critical Individual
Publication of CA2219090A1 publication Critical patent/CA2219090A1/en
Application granted granted Critical
Publication of CA2219090C publication Critical patent/CA2219090C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

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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
    • 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
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor

Abstract

The present invention provides oligonucleotide primers and a method of using these primers for identification of the species of an organism, wherein the identification includes amplification of a variable polynucleotide sequence encoding a highly conserved region of a heat shock polypeptide.

Claims (18)

1. Isolated oligonucleotide primer(s) for identification of the species of an organism wherein the primer hybridizes with a target polynucleotide sequence having substantially the sequence selected from the group consisting of:
5'-GTTGTCGTACC(G/A)TCACCAGCAATTTC-3' (SEQ ID NO:1) and 5'-AA(G/A)GCGCCTGGTTT(C/T)GGTGAT(C/A)(G/A)(A/T/C/G) (C/A)(G/A)-3'(SEQ ID NO:2), and sequences substantially complementary thereto.
2. The primer of claim 1, wherein the primer is 5'-GAIIIIGCIGGIGA(T/C)GGIACIACIAC-3' (SEQ ID NO:3) or 5'-(T/C)(T/G)I(T/C)(T/G)ITCICC(A/G)AAICCIGGIGC(T/C)TT3' (SEQID NO:4).
3. The method of claim 1, wherein the organism is a microorganism.
4. The primer of claim 3, wherein the organism is a prokaryote.
5. The primer of claim 4, wherein the prokaryote is a member of a genus selected from the group consisting of Staphylococcus, Pseudomonas, Escherichia, Bacillus, Salmonella, Chlamydia, Helicobacter, and Streptococcus.
6. The primer of claim 5, wherein the species of the genus is selected from the group consisting of S. haemolyticus, S. epidermidis, S. lugdunensis, S. hominis,E. coli, B. subtilis, and P. aeruginosa.
7 A method for identification of the species of an organism comprising:
a) amplifying a region of the genomic nucleic acid of the organism by means of oligonucleotide primers which hybridize to target flanking 5' and 3' polynucleotide sequences of the genomic nucleic acid, the target polynucleotide sequence having substantially the sequence selected from the group consisting of:
5'-GTTGTCGTACC(G/A)TCACCAGCAATTTC-3' (SEQ ID NO: 1 ) and 5'-AA(G/A)GCGCCTGGTT(C/T)GGTGAT(C/A)(G/A) (A/T/C/G)(C/A)(G/A)-3' (SEQ ID NO:2), and sequences substantially complementary thereto; and b) detecting the amplified region.
8. The method of claim 7, wherein the amplifying is by polymerase chain reaction (PCR).
9. The method of claim 7, wherein the primer is 5'-GAIIIlGCIGGIGA(T/C)GGIACIACIAC-3' (SEQ ID NO:3) or 5'-(T/C)(T/G)I(T/C)(T/G)ITCICC(A/G)AAICCIGGIGC(T/C)TT3' (SEQ ID NO:4).
10 The method of claim 9, wherein the organism is a microorganism
11. The method of claim 10, wherein the organism is a prokaryote.
12. The method of claim 11, wherein the prokaryote is a member of a genus is selected from the group consisting of Staphylococcus, Pseudomonas, Escherichia, Bacillus, Salmonella, and Streptococcus.
13. The method of claim 12, wherein the species of the genus is selected from the group consisting of S. aureus, S. haemolyticus, S. epidermidis, S. lugdunensis, S. hominis, E. coli, B. subtilis, and P. aeruginosa.
14. A genomic polynucleotide locus which is defined by being amplified by primers having a sequence:
5'-GAIIIIGCIGGIGA(T/C)GGIACIACIAC-3' (SEQ ID NO:3) or 5'-(T/C)(T/G)I(T/C)(T/G)ITCICC(A/G)AAICCIGGIGC(T/C)TF3' (SEQ ID NO:4) or primer sequences substantially complementary thereto, wherein the polynucleotide locus does not hybridize with a polynucleotide locus from Staphylococcus aureus amplified by primers having a sequence:
5'-GAIIIIGCIGGIGA(T/C)GGIACIACIAC-3' (SEQ ID NO:3) or 5'-(T/C)(T/G)I(T/C)(T/G)ITCICC(A/G)AAICCIGGIGC(T/C)TT3' (SEQ ID NO:4) or primer sequences substantially complementary thereto.
15. The genomic locus of claim 14, wherein the locus encodes a heat shock polypeptide.
16. A kit useful for the isolation of target DNA for identification of the species of an organism, the kit comprising means for amplifying target DNA, said means comprising the necessary enzyme(s) and oligonucleotide primers for amplifying said target DNA from the organism or a cell of the organism.
17. The kit of claim 16, wherein the oligonucleotide primers include primers having a sequence:
5'-GAIIIIGCIGGIGA(T/C)GGIACIACIAC-3'(SEQ ID NO:3) or 5'-(T/C)(T/G)I(T/C)(T/G)ITCICC(A!G)AAICCIGGIGC(T/C)TT3' (SEQ ID NO:4) or primer sequences substantially complementary thereto.
18. The kit of claim 16, wherein the target flanking 5' and 3' polynucleotide sequence has substantially the sequence selected from the group consisting of:
5'-GTTGTCGTACC(G/A)TCACCAGCAATTTC-3' (SEQ ID NO: 1 ) and 5'-AA(G/A)GCGCCTGGTTT(C/T)GGTGAT(C/A)(G/A)(A/T/C/G) (C/A)(G/A)-3'(SEQID NO:2), and sequences substantially complementary thereto.
CA2219090A 1995-04-26 1996-04-26 Universal targets for species identification Expired - Fee Related CA2219090C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US08/429,121 1995-04-26
US08/429,121 US5708160A (en) 1995-04-26 1995-04-26 HSP-60 genomic locus and primers for species identification
PCT/IB1996/000635 WO1996034116A2 (en) 1995-04-26 1996-04-26 Universal targets for species identification

Publications (2)

Publication Number Publication Date
CA2219090A1 true CA2219090A1 (en) 1996-10-31
CA2219090C CA2219090C (en) 2010-04-06

Family

ID=23701901

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2219090A Expired - Fee Related CA2219090C (en) 1995-04-26 1996-04-26 Universal targets for species identification

Country Status (11)

Country Link
US (2) US5708160A (en)
EP (1) EP0824599B1 (en)
JP (1) JPH11503921A (en)
KR (1) KR19990008049A (en)
AT (1) ATE315663T1 (en)
AU (1) AU702237B2 (en)
CA (1) CA2219090C (en)
DE (1) DE69635735D1 (en)
DK (1) DK0824599T3 (en)
NO (1) NO974946L (en)
WO (1) WO1996034116A2 (en)

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US20020055101A1 (en) 1995-09-11 2002-05-09 Michel G. Bergeron Specific and universal probes and amplification primers to rapidly detect and identify common bacterial pathogens and antibiotic resistance genes from clinical specimens for routine diagnosis in microbiology laboratories
US20030049636A1 (en) 1999-05-03 2003-03-13 Bergeron Michel G. Species-specific, genus-specific and universal DNA probes and amplification primers to rapidly detect and identify common bacterial and fungal pathogens and associated antibiotic resistance genes from clinical specimens for diagnosis in microbiology laboratories
US20100267012A1 (en) 1997-11-04 2010-10-21 Bergeron Michel G Highly conserved genes and their use to generate probes and primers for detection of microorganisms
US6497880B1 (en) 1998-12-08 2002-12-24 Stressgen Biotechnologies Corporation Heat shock genes and proteins from Neisseria meningitidis, Candida glabrata and Aspergillus fumigatus
US6821770B1 (en) 1999-05-03 2004-11-23 Gen-Probe Incorporated Polynucleotide matrix-based method of identifying microorganisms
ES2265344T3 (en) 1999-05-03 2007-02-16 Gen-Probe Incorporated POLINUCLEOTIDE PROBES FOR THE DETECTION AND QUANTIFICATION OF ACTINOMYCES.
CA2370138C (en) 1999-05-03 2010-09-21 Gen-Probe Incorporated Polynucleotide probes for detection and quantitation of staphylococcus
WO2000066785A2 (en) 1999-05-03 2000-11-09 Gen-Probe Incorporated Polynucleotide probes for detection and quantitation of bacteria in the family enterobacteriaceae
CA2905326C (en) 1999-09-28 2016-09-27 Geneohm Sciences Canada Inc. Nucleic acids and methods for the detection of klebsiella
WO2001036683A2 (en) * 1999-11-16 2001-05-25 Apollo Biotechnology, Inc. Method for rapid and accurate identification of microorganisms
US20030134293A1 (en) * 1999-11-16 2003-07-17 Zhiping Liu Method for rapid and accurate identification of microorganisms
FR2812005B1 (en) * 2000-07-21 2004-10-22 Univ Clermont Auvergne DETECTION METHOD FOR MICROORGANISMS
DE60118392T2 (en) * 2000-07-21 2006-12-07 Compagnie Gervais Danone METHOD FOR DETECTING MICROORGANISMS
US7294490B2 (en) * 2000-07-21 2007-11-13 Compagnie Gervais Danone Method for detecting microorganisms
US20020086313A1 (en) * 2000-09-25 2002-07-04 Kilbane John J. Application of bioinformatics for direct study of unculturable microorganisms
US7241566B2 (en) * 2001-06-22 2007-07-10 Marshfield Clinic Methods and oligonucleotides for the detection of Salmonella sp., E. coli O157:H7, and Listeria monocytogenes
US20040259226A1 (en) * 2003-05-30 2004-12-23 Robey W. Wade Monitoring for and detecting microbes used in bioterrorism
US20040101860A1 (en) * 2002-11-27 2004-05-27 Jones Alison M. Predicting animal performance
US20040185446A1 (en) * 2003-03-18 2004-09-23 Jones Alison M. Cpn60 targets for quantification of microbial species
US20040185559A1 (en) 2003-03-21 2004-09-23 Isis Pharmaceuticals Inc. Modulation of diacylglycerol acyltransferase 1 expression
US20040185454A1 (en) * 2003-03-21 2004-09-23 Jones Alison M. Identification and quantification of microbial species in a sample
US20040185434A1 (en) * 2003-03-21 2004-09-23 Robey W. Wade Detecting microbial contamination in animal by-products
US20050026188A1 (en) * 2003-05-30 2005-02-03 Van Kessel Andrew G. Methods of identifying, characterizing and comparing organism communities
US20040241662A1 (en) * 2003-05-30 2004-12-02 Robey W. Wade Detecting microbial contamination in grain and related products
US7387883B2 (en) * 2003-12-09 2008-06-17 Biomerieux, Inc Methods for detecting bacterial pathogens
US7429464B2 (en) * 2003-12-09 2008-09-30 Biomerieux, Inc. Methods for detecting bacterial pathogens
EP1692511B1 (en) * 2003-12-09 2012-09-19 bioMerieux, Inc. Method for recovering microorganisms from a sample
US20060240442A1 (en) * 2005-04-20 2006-10-26 Vevea Dirk N Methods and oligonucleotides for the detection of Salmonella SP., E coli 0157:H7, and Listeria monocytogenes
US20060246463A1 (en) * 2005-04-20 2006-11-02 Vevea Dirk N Methods and oligonucleotides for the detection of Salmonella SP., E coli 0157:H7, and Listeria monocytogenes
US7507535B2 (en) * 2005-06-07 2009-03-24 National Research Council Of Canada Strong PCR primers and primer cocktails
US7759064B2 (en) * 2005-08-01 2010-07-20 Janet Elizabeth Hill Development of PCR primers and primer mixtures for amplification of cnp60 target sequences
WO2008019351A2 (en) 2006-08-04 2008-02-14 Isis Pharmaceuticals, Inc. Compositions and their uses directed to diacylglycerol acyltransferase 1
US9328388B2 (en) * 2008-02-19 2016-05-03 Opgen, Inc. Methods of identifying an organism
CA2793906A1 (en) 2010-03-26 2011-09-29 University Of Saskatchewan Methods and compositions for the detection and identification of archaea based on the type ii chaperonin (thermosome) gene
CN112961930B (en) * 2021-05-18 2021-08-10 至善时代智能科技(北京)有限公司 Primer group, kit and method for identifying environmental bacteria at genus level

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US5232833A (en) * 1988-09-14 1993-08-03 Stressgen Biotechnologies Corporation Accumulation of heat shock proteins for evaluating biological damage due to chronic exposure of an organism to sublethal levels of pollutants
EP0468520A3 (en) * 1990-07-27 1992-07-01 Mitsui Toatsu Chemicals, Inc. Immunostimulatory remedies containing palindromic dna sequences
GB9023149D0 (en) * 1990-10-24 1990-12-05 British Bio Technology Proteins and nucleic acids
CA2119188A1 (en) * 1993-04-05 1994-10-06 Patricia A. Spears Detection and identification of mycobacteria

Also Published As

Publication number Publication date
NO974946L (en) 1997-12-16
KR19990008049A (en) 1999-01-25
EP0824599A2 (en) 1998-02-25
US5708160A (en) 1998-01-13
JPH11503921A (en) 1999-04-06
DK0824599T3 (en) 2006-05-22
CA2219090C (en) 2010-04-06
AU702237B2 (en) 1999-02-18
NO974946D0 (en) 1997-10-24
AU6134496A (en) 1996-11-18
WO1996034116A3 (en) 1997-01-16
EP0824599B1 (en) 2006-01-11
WO1996034116A2 (en) 1996-10-31
ATE315663T1 (en) 2006-02-15
US5989821A (en) 1999-11-23
DE69635735D1 (en) 2006-04-06

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