WO2001036683A3 - Method for rapid and accurate identification of microorganisms - Google Patents

Method for rapid and accurate identification of microorganisms Download PDF

Info

Publication number
WO2001036683A3
WO2001036683A3 PCT/US2000/031579 US0031579W WO0136683A3 WO 2001036683 A3 WO2001036683 A3 WO 2001036683A3 US 0031579 W US0031579 W US 0031579W WO 0136683 A3 WO0136683 A3 WO 0136683A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
rapid
microorganisms
accurate identification
identification
Prior art date
Application number
PCT/US2000/031579
Other languages
French (fr)
Other versions
WO2001036683A2 (en
Inventor
Zhiping Liu
Original Assignee
Apollo Biotechnology Inc
Zhiping Liu
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 Apollo Biotechnology Inc, Zhiping Liu filed Critical Apollo Biotechnology Inc
Priority to EP00980462A priority Critical patent/EP1261716A2/en
Priority to CA002391571A priority patent/CA2391571A1/en
Priority to AU17719/01A priority patent/AU1771901A/en
Publication of WO2001036683A2 publication Critical patent/WO2001036683A2/en
Priority to US10/151,484 priority patent/US20030134293A1/en
Publication of WO2001036683A3 publication Critical patent/WO2001036683A3/en

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
    • C12Q1/6844—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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6876—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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • 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

Landscapes

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

Abstract

Methods and compositions useful for rapid identification of microorganisms are provided. Methods and compositions useful for rapid and simultaneous identification in a biological sample of multiple microorganisms, including bacteria, yeast, fungi and viruses are also provided. The methods and compositions utilize amplification techniques and sequence specific hybridization to detect species specific polynucleotide sequence in a sample. Novel methods for coupling oligonucleotide probes to glass surfaces with increased efficiency are also provided.
PCT/US2000/031579 1999-11-16 2000-11-16 Method for rapid and accurate identification of microorganisms WO2001036683A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP00980462A EP1261716A2 (en) 1999-11-16 2000-11-16 Method for rapid and accurate identification of microorganisms
CA002391571A CA2391571A1 (en) 1999-11-16 2000-11-16 Method for rapid and accurate identification of microorganisms
AU17719/01A AU1771901A (en) 1999-11-16 2000-11-16 Method for rapid and accurate identification of microorganisms
US10/151,484 US20030134293A1 (en) 1999-11-16 2002-05-16 Method for rapid and accurate identification of microorganisms

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US16588199P 1999-11-16 1999-11-16
US60/165,881 1999-11-16
US47945700A 2000-01-06 2000-01-06
US09/479,457 2000-01-06

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US10/151,484 Continuation-In-Part US20030134293A1 (en) 1999-11-16 2002-05-16 Method for rapid and accurate identification of microorganisms

Publications (2)

Publication Number Publication Date
WO2001036683A2 WO2001036683A2 (en) 2001-05-25
WO2001036683A3 true WO2001036683A3 (en) 2002-09-26

Family

ID=26861776

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/031579 WO2001036683A2 (en) 1999-11-16 2000-11-16 Method for rapid and accurate identification of microorganisms

Country Status (4)

Country Link
EP (1) EP1261716A2 (en)
AU (1) AU1771901A (en)
CA (1) CA2391571A1 (en)
WO (1) WO2001036683A2 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1421216A4 (en) * 2001-09-01 2006-05-17 Samsung Electronics Co Ltd Method for manufacturing hydrogel biochip by using star-like polyethylene glycol derivative having epoxy group
JP2003144153A (en) * 2001-11-09 2003-05-20 Gifu Univ Method for detecting gene, primer for detecting gene, dna microarray and kit for detecting gene
US20050202414A1 (en) * 2001-11-15 2005-09-15 The Regents Of The University Of California Apparatus and methods for detecting a microbe in a sample
US6881835B2 (en) * 2002-01-04 2005-04-19 Dr. Chip Biotechnology Inc. Detection of respiratory viruses
DE10244456A1 (en) * 2002-09-24 2004-04-15 Hain Lifescience Gmbh Methods for the detection and differentiation of bacteria
FI113549B (en) * 2002-11-19 2004-05-14 Mobidiag Oy Diagnostic method for identifying and identifying bacteria causing respiratory tract infections and primer composition useful in the process
FR2860801B1 (en) * 2003-10-10 2007-09-21 Bertin Technologies Sa METHOD FOR RAPID DETECTION OF MICROORGANISMS ON DNA CHIPS
WO2006050479A2 (en) * 2004-11-01 2006-05-11 George Mason University Compositions and methods for diagnosing colon disorders
RU2348695C2 (en) * 2006-05-23 2009-03-10 Закрытое акционерное общество "Молекулярно-медицинские технологии" Differentiating and specific oligonucleotids for dna sequence identification for infection agents in biological materials, method of species identification of infection agents, biochip and method implementation kit
JP5596894B2 (en) * 2006-11-10 2014-09-24 キヤノン株式会社 Probe set, probe fixing carrier, and genetic testing method
AU2011220736C1 (en) 2010-02-24 2014-12-18 The Broad Institute, Inc Methods of diagnosing infectious disease pathogens and their drug sensitivity
GB201314873D0 (en) * 2013-08-20 2013-10-02 Univ Cape Town Method for diagnosing tuberculosis in a urine sample
WO2018185105A1 (en) * 2017-04-03 2018-10-11 Bio-Me As Microorganism detection methods

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1991002577A1 (en) * 1989-08-15 1991-03-07 Gelman Sciences, Inc. Blotting methods using polyaldehyde activated membranes
US5708160A (en) * 1995-04-26 1998-01-13 The National Research Council HSP-60 genomic locus and primers for species identification
WO1998020157A2 (en) * 1996-11-04 1998-05-14 Infectio Diagnostic (I.D.I.) Inc. 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
WO1998028444A2 (en) * 1996-12-23 1998-07-02 The University Of Chicago Customized oligonucleotide microchips as multiple biosensors
DE19716456A1 (en) * 1997-04-21 1998-10-22 Schmitt Heinz Josef Prof Dr Identification of microorganisms, especially respiratory tract pathogens
EP0899337A2 (en) * 1997-08-29 1999-03-03 Smithkline Beecham FtsY polynucleotides and polypeptides of Stapyloccoccus aureus belonging to the signal recognition protein family

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1991002577A1 (en) * 1989-08-15 1991-03-07 Gelman Sciences, Inc. Blotting methods using polyaldehyde activated membranes
US5708160A (en) * 1995-04-26 1998-01-13 The National Research Council HSP-60 genomic locus and primers for species identification
WO1998020157A2 (en) * 1996-11-04 1998-05-14 Infectio Diagnostic (I.D.I.) Inc. 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
WO1998028444A2 (en) * 1996-12-23 1998-07-02 The University Of Chicago Customized oligonucleotide microchips as multiple biosensors
DE19716456A1 (en) * 1997-04-21 1998-10-22 Schmitt Heinz Josef Prof Dr Identification of microorganisms, especially respiratory tract pathogens
EP0899337A2 (en) * 1997-08-29 1999-03-03 Smithkline Beecham FtsY polynucleotides and polypeptides of Stapyloccoccus aureus belonging to the signal recognition protein family

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BRENDEL V ET AL: "EVOLUTIONARY COMPARISONS OF RECA-LIKE PROTEINS ACROSS ALL MAJOR KINGDOMS OF LIVING ORGANISMS", JOURNAL OF MOLECULAR EVOLUTION, SPRINGER VERLAG, NEW YORK, NY, US, vol. 44, no. 5, May 1997 (1997-05-01), pages 528 - 541, XP001001339, ISSN: 0022-2844 *
KARLIN S ET AL: "BACTERIAL CLASSIFICATIONS DERIVED FROM RECA PROTEIN SEQUENCE COMPARISONS", JOURNAL OF BACTERIOLOGY, WASHINGTON, DC, US, vol. 177, no. 23, December 1995 (1995-12-01), pages 6881 - 6893, XP000857476, ISSN: 0021-9193 *
NOWAK A ET AL: "Genomic species typing of acinetobacters by polymerase chain reaction amplification of the recA gene.", FEMS MICROBIOLOGY LETTERS, vol. 130, no. 2-3, 1995, pages 327 - 332, XP002192745, ISSN: 0378-1097 *
See also references of EP1261716A2 *

Also Published As

Publication number Publication date
CA2391571A1 (en) 2001-05-25
EP1261716A2 (en) 2002-12-04
WO2001036683A2 (en) 2001-05-25
AU1771901A (en) 2001-05-30

Similar Documents

Publication Publication Date Title
WO2000066789A3 (en) Polynucleotide matrix-based method of identifying microorganisms
WO1998028444A3 (en) Customized oligonucleotide microchips as multiple biosensors
WO2001036683A3 (en) Method for rapid and accurate identification of microorganisms
WO1999014377A3 (en) Detection and identification of human papillomavirus by pcr and type-specific reverse hybridization
WO2001096612A3 (en) Method of identifying and quantifying specific fungi and bacteria
ATE358733T1 (en) RAPID METHOD FOR DETECTING MICROORGANISMS IN FOOD SAMPLES
AU3481297A (en) Monitoring hybridization during pcr
AU2003291893A1 (en) Biological reagents and methods to verify the efficiency of sample preparation and nucleic acid amplification and/or detection
EP1055734A3 (en) Method for assaying nucleic acid
CA2321185A1 (en) Method for detection of target nucleic acids using pcr
WO2002072773A3 (en) Methods and compositions for amplification of rna sequences
WO2002044416A3 (en) Sulfonated diarylrhodamine dyes as fluorescent labels
DE60210485D1 (en) METHOD FOR DETERMINING THE PRESENCE OF BACTERIA RESISTANT TO CELL-LYSING ANTIBIOTICS
WO2000050564A3 (en) Method for extracting dna from dried specimens
WO2002036815A3 (en) Genetic analysis of microorganisms
WO1999054510A3 (en) Quantitative analysis of gene expression
WO2003076566A3 (en) Enzymatic ligation-based identification of nucleotide sequences
WO1999022023A3 (en) Method for identifying micro-organisms
WO2005028680A3 (en) Methods, compositions, and kits for the concentration and detection of microorganisms
CA2249635A1 (en) Detection of neisseria gonorrhoeae by amplification and detection of its nucleic acid
AU4397101A (en) Method and kit for the detection of schistosomiasis through the polymerase chainreaction
WO2001023605A3 (en) Method and nucleic acids for determining the presence of micro-organisms specific to the brewing process
AU2003257177A1 (en) Improved compositions for in vitro amplification of nucleic acids
WO2000065093A3 (en) In situ hybridization methods for reducing the occurrence of false positives and for targeting multiple microorganisms
DE50106653D1 (en) IN SITU HYBRIDIZATION ARRANGEMENT FOR THE SPECIFIC DETECTION OF MICRO-ORGANISMS

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
WWE Wipo information: entry into national phase

Ref document number: 2391571

Country of ref document: CA

WWE Wipo information: entry into national phase

Ref document number: 2000980462

Country of ref document: EP

AK Designated states

Kind code of ref document: A3

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CR CU CZ DE DK DM DZ EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 2000980462

Country of ref document: EP

WWW Wipo information: withdrawn in national office

Ref document number: 2000980462

Country of ref document: EP