WO1995013396A3 - A method for identifying microorganisms, and aids useful thereof - Google Patents

A method for identifying microorganisms, and aids useful thereof Download PDF

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Publication number
WO1995013396A3
WO1995013396A3 PCT/NL1994/000283 NL9400283W WO9513396A3 WO 1995013396 A3 WO1995013396 A3 WO 1995013396A3 NL 9400283 W NL9400283 W NL 9400283W WO 9513396 A3 WO9513396 A3 WO 9513396A3
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WO
WIPO (PCT)
Prior art keywords
microorganism
nucleic acid
sample
subjected
conserved
Prior art date
Application number
PCT/NL1994/000283
Other languages
French (fr)
Other versions
WO1995013396A2 (en
Inventor
Adriaan Camille Fluit
Myra Noorely Widjojoatmodjo
Original Assignee
U Gene Research Bv
Adriaan Camille Fluit
Myra Noorely Widjojoatmodjo
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 U Gene Research Bv, Adriaan Camille Fluit, Myra Noorely Widjojoatmodjo filed Critical U Gene Research Bv
Publication of WO1995013396A2 publication Critical patent/WO1995013396A2/en
Publication of WO1995013396A3 publication Critical patent/WO1995013396A3/en

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    • 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
    • C12Q1/6858—Allele-specific amplification
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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]
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Identification of a microorganism, in particular a bacterium, present in a sample. Nucleic acid (DNA or RNA) of the microorganism present in the sample is subjected to PCR or a different nucleic acid amplification method, utilizing one or more sets of universal primers based on a gene of the microorganism to be identified which comprises both conserved and variable regions, in particular the 16S rRNA gene, the primers being chosen in conserved areas which enclose a variable region. The product of the amplification is brought into single-stranded form, if necessary, and subjected to electrophoresis by which single-stranted nucleic acids of equal lengths can be separated from each other on the basis of differences in nucleotide sequence. The electrophoresed nucleic acid is detected and its position compared with those of a set of reference nucleic acids of known microorganisms. Set of suitable aids for practicing the method.
PCT/NL1994/000283 1993-11-11 1994-11-11 A method for identifying microorganisms, and aids useful thereof WO1995013396A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
NL9301957 1993-11-11
NL9301957A NL9301957A (en) 1993-11-11 1993-11-11 Method for identifying microorganisms, and useful tools.

Publications (2)

Publication Number Publication Date
WO1995013396A2 WO1995013396A2 (en) 1995-05-18
WO1995013396A3 true WO1995013396A3 (en) 1995-06-08

Family

ID=19863128

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/NL1994/000283 WO1995013396A2 (en) 1993-11-11 1994-11-11 A method for identifying microorganisms, and aids useful thereof

Country Status (2)

Country Link
NL (1) NL9301957A (en)
WO (1) WO1995013396A2 (en)

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US6593086B2 (en) 1996-05-20 2003-07-15 Mount Sinai School Of Medicine Of New York University Nucleic acid amplification methods
USRE38442E1 (en) * 1994-06-22 2004-02-24 Mount Sinai School Of Medicine Nucleic acid amplification method hybridization signal amplification method (HSAM)
US5942391A (en) 1994-06-22 1999-08-24 Mount Sinai School Of Medicine Nucleic acid amplification method: ramification-extension amplification method (RAM)
GB9420774D0 (en) * 1994-10-14 1994-11-30 Univ Wales Method of detecting and identifying spore forming bacteria
DE19716456C2 (en) * 1997-04-21 2002-05-08 Schmitt Heinz Josef Use of a combination of primers for the detection of infectious agents
GB9719044D0 (en) * 1997-09-08 1997-11-12 Inst Of Ophthalmology Assay
WO1999035285A2 (en) * 1998-01-08 1999-07-15 Merck Sharp & Dohme De Espana, S.A.E. Hybridization probes which differentiate between the actinomadura madurae group of bacteria and maduromycetes
AU5062500A (en) * 1999-04-26 2000-11-10 Amersham Pharmacia Biotech Ab Primers for identifying typing or classifying nucleic acids
DE19945916A1 (en) 1999-09-24 2001-04-05 Biotecon Diagnostics Gmbh Nucleic acid molecules for the detection of bacteria and phylogenetic units of bacteria
WO2001023608A2 (en) * 1999-09-27 2001-04-05 Merck Sharp & Dohme De Espana, S.A.E. Hybridization probes which specifically detect strains of the genera microbispora, microtetraspora, nonomuria and planobispora
DE10027113A1 (en) 1999-12-23 2001-09-27 Andreas Hoeft Method for determining microbial DNA / RNA, kit therefor and use of the method
US20040121311A1 (en) 2002-12-06 2004-06-24 Ecker David J. Methods for rapid detection and identification of bioagents in livestock
US20030027135A1 (en) 2001-03-02 2003-02-06 Ecker David J. Method for rapid detection and identification of bioagents
AU2013231102B2 (en) * 2001-03-02 2016-04-28 Ibis Biosciences, Inc. Methods for rapid identification of pathogens in humans and animals
US7666588B2 (en) 2001-03-02 2010-02-23 Ibis Biosciences, Inc. Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy
US7226739B2 (en) 2001-03-02 2007-06-05 Isis Pharmaceuticals, Inc Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations
US7217510B2 (en) * 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
JP2006516193A (en) 2002-12-06 2006-06-29 アイシス・ファーマシューティカルス・インコーポレーテッド Rapid identification of pathogens in humans and animals
US8057993B2 (en) 2003-04-26 2011-11-15 Ibis Biosciences, Inc. Methods for identification of coronaviruses
US7964343B2 (en) 2003-05-13 2011-06-21 Ibis Biosciences, Inc. Method for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US8158354B2 (en) 2003-05-13 2012-04-17 Ibis Biosciences, Inc. Methods for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
US7205111B2 (en) * 2003-07-24 2007-04-17 Marshfield Clinic Rapid identification of bacteria from positive blood cultures
US8546082B2 (en) 2003-09-11 2013-10-01 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US8097416B2 (en) 2003-09-11 2012-01-17 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US20120122103A1 (en) 2003-09-11 2012-05-17 Rangarajan Sampath Compositions for use in identification of bacteria
US8163895B2 (en) 2003-12-05 2012-04-24 Ibis Biosciences, Inc. Compositions for use in identification of orthopoxviruses
US7666592B2 (en) 2004-02-18 2010-02-23 Ibis Biosciences, Inc. Methods for concurrent identification and quantification of an unknown bioagent
EP1766659A4 (en) 2004-05-24 2009-09-30 Ibis Biosciences Inc Mass spectrometry with selective ion filtration by digital thresholding
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US7811753B2 (en) 2004-07-14 2010-10-12 Ibis Biosciences, Inc. Methods for repairing degraded DNA
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Also Published As

Publication number Publication date
NL9301957A (en) 1995-06-01
WO1995013396A2 (en) 1995-05-18

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