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WO2005098047A3 - Compositions for use in identification of bacteria - Google Patents

Compositions for use in identification of bacteria Download PDF

Info

Publication number
WO2005098047A3
WO2005098047A3 PCT/US2005/005356 US2005005356W WO2005098047A3 WO 2005098047 A3 WO2005098047 A3 WO 2005098047A3 US 2005005356 W US2005005356 W US 2005005356W WO 2005098047 A3 WO2005098047 A3 WO 2005098047A3
Authority
WO
WIPO (PCT)
Prior art keywords
bacteria
compositions
identification
amplification
segment
Prior art date
Application number
PCT/US2005/005356
Other languages
French (fr)
Other versions
WO2005098047A2 (en
Inventor
Rangarajan Sampath
Thomas A Hall
David J Ecker
Mark W Eschoo
Christian Massire
Brons M Larson
Terrance Leighton
Original Assignee
Isis Pharmaceuticals Inc
Science Applic Int Corp
Rangarajan Sampath
Thomas A Hall
David J Ecker
Mark W Eschoo
Christian Massire
Brons M Larson
Terrance Leighton
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 Isis Pharmaceuticals Inc, Science Applic Int Corp, Rangarajan Sampath, Thomas A Hall, David J Ecker, Mark W Eschoo, Christian Massire, Brons M Larson, Terrance Leighton filed Critical Isis Pharmaceuticals Inc
Publication of WO2005098047A2 publication Critical patent/WO2005098047A2/en
Publication of WO2005098047A3 publication Critical patent/WO2005098047A3/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
    • C12Q1/6876—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

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)

Abstract

The present invention provides oligonucleotide primers and compositions and kits containing the same for rapid identification of bacteria by amplification of a segment of bacterial nucleic acid followed by molecular mass analysis.
PCT/US2005/005356 2004-02-18 2005-02-18 Compositions for use in identification of bacteria WO2005098047A2 (en)

Applications Claiming Priority (10)

Application Number Priority Date Filing Date Title
US54542504P 2004-02-18 2004-02-18
US60/545,425 2004-02-18
US55975404P 2004-04-05 2004-04-05
US60/559,754 2004-04-05
US63286204P 2004-12-03 2004-12-03
US60/632,862 2004-12-03
US63906804P 2004-12-22 2004-12-22
US60/639,068 2004-12-22
US64818805P 2005-01-28 2005-01-28
US60/648,188 2005-01-28

Publications (2)

Publication Number Publication Date
WO2005098047A2 WO2005098047A2 (en) 2005-10-20
WO2005098047A3 true WO2005098047A3 (en) 2007-10-04

Family

ID=35125687

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2005/006133 WO2006071241A2 (en) 2004-02-18 2005-02-18 Compositions for use in identification of bacteria
PCT/US2005/005356 WO2005098047A2 (en) 2004-02-18 2005-02-18 Compositions for use in identification of bacteria

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2005/006133 WO2006071241A2 (en) 2004-02-18 2005-02-18 Compositions for use in identification of bacteria

Country Status (5)

Country Link
EP (1) EP1725686A4 (en)
JP (1) JP2007525978A (en)
AU (2) AU2005322640B2 (en)
CA (1) CA2560521C (en)
WO (2) WO2006071241A2 (en)

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US7226739B2 (en) 2001-03-02 2007-06-05 Isis Pharmaceuticals, Inc Methods for rapid detection and identification of bioagents in epidemiological and forensic investigations
US20030027135A1 (en) 2001-03-02 2003-02-06 Ecker David J. Method for rapid detection and identification of bioagents
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
US20040121313A1 (en) 2002-12-06 2004-06-24 Ecker David J. Methods for rapid detection and identification of bioagents in organs for transplantation
CA2348042A1 (en) 2001-06-04 2002-12-04 Ann Huletsky Sequences for detection and identification of methicillin-resistant staphylococcus aureus
US7217510B2 (en) 2001-06-26 2007-05-15 Isis Pharmaceuticals, Inc. Methods for providing bacterial bioagent characterizing information
US8073627B2 (en) 2001-06-26 2011-12-06 Ibis Biosciences, Inc. System for indentification of pathogens
EP1578399A4 (en) 2002-12-06 2007-11-28 Isis Pharmaceuticals Inc PROCESS FOR THE RAPID IDENTIFICATION OF PATHOGENS IN ANIMAL AND MAN
US8057993B2 (en) 2003-04-26 2011-11-15 Ibis Biosciences, Inc. Methods for identification of coronaviruses
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
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
US8546082B2 (en) 2003-09-11 2013-10-01 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
US8242254B2 (en) 2003-09-11 2012-08-14 Ibis Biosciences, Inc. Compositions for use in identification of bacteria
US8097416B2 (en) 2003-09-11 2012-01-17 Ibis Biosciences, Inc. Methods for identification of sepsis-causing bacteria
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
US20050266411A1 (en) 2004-05-25 2005-12-01 Hofstadler Steven A Methods for rapid forensic analysis of mitochondrial DNA
US7811753B2 (en) 2004-07-14 2010-10-12 Ibis Biosciences, Inc. Methods for repairing degraded DNA
WO2006135400A2 (en) 2004-08-24 2006-12-21 Isis Pharmaceuticals, Inc. Methods for rapid identification of recombinant organisms
WO2006094238A2 (en) 2005-03-03 2006-09-08 Isis Pharmaceuticals, Inc. Compositions for use in identification of adventitious viruses
US8084207B2 (en) 2005-03-03 2011-12-27 Ibis Bioscience, Inc. Compositions for use in identification of papillomavirus
AU2006272776B2 (en) 2005-07-21 2012-01-19 Ibis Biosciences, Inc. Methods for rapid identification and quantitation of nucleic acid variants
US11834720B2 (en) 2005-10-11 2023-12-05 Geneohm Sciences, Inc. Sequences for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) of MREJ types xi to xx
BRPI0605802A (en) * 2005-11-21 2007-09-04 Biosigma Sa method and arrangement for detecting and identifying microorganisms present in a sample using the genetic regions coding for the different rnat synthetases
CA2663029C (en) * 2006-09-14 2016-07-19 Ibis Biosciences, Inc. Targeted whole genome amplification method for identification of pathogens
JP5680304B2 (en) 2007-02-23 2015-03-04 アイビス バイオサイエンシズ インコーポレイティッド Rapid forensic DNA analysis
EP1997905A1 (en) * 2007-06-01 2008-12-03 Friesland Brands B.V. Nucleic acid amplification
WO2008151023A2 (en) 2007-06-01 2008-12-11 Ibis Biosciences, Inc. Methods and compositions for multiple displacement amplification of nucleic acids
WO2010033627A2 (en) 2008-09-16 2010-03-25 Ibis Biosciences, Inc. Sample processing units, systems, and related methods
EP2344893B1 (en) 2008-09-16 2014-10-15 Ibis Biosciences, Inc. Microplate handling systems and methods
EP2349549B1 (en) 2008-09-16 2012-07-18 Ibis Biosciences, Inc. Mixing cartridges, mixing stations, and related kits, and system
WO2010039848A2 (en) * 2008-10-03 2010-04-08 Ibis Biosciences, Inc. Compositions for use in identification of streptococcus pneumoniae
US8158936B2 (en) 2009-02-12 2012-04-17 Ibis Biosciences, Inc. Ionization probe assemblies
WO2010114842A1 (en) 2009-03-30 2010-10-07 Ibis Biosciences, Inc. Bioagent detection systems, devices, and methods
WO2011008971A1 (en) 2009-07-17 2011-01-20 Ibis Biosciences, Inc. Lift and mount apparatus
EP2454000A4 (en) 2009-07-17 2016-08-10 Ibis Biosciences Inc Systems for bioagent identification
US9416409B2 (en) 2009-07-31 2016-08-16 Ibis Biosciences, Inc. Capture primers and capture sequence linked solid supports for molecular diagnostic tests
EP2488656B1 (en) 2009-10-15 2015-06-03 Ibis Biosciences, Inc. Multiple displacement amplification
EP2545183B1 (en) 2010-03-10 2017-04-19 Ibis Biosciences, Inc. Production of single-stranded circular nucleic acid
US9068017B2 (en) 2010-04-08 2015-06-30 Ibis Biosciences, Inc. Compositions and methods for inhibiting terminal transferase activity
EP2753629B1 (en) 2011-09-06 2016-10-19 Ibis Biosciences, Inc. Methods for detecting lyme disease
WO2013101935A1 (en) 2011-12-27 2013-07-04 Ibis Biosciences, Inc. Bioagent detection oligonucleotides
JP2013171343A (en) 2012-02-17 2013-09-02 Toshiba Corp Storage device
WO2014052590A1 (en) 2012-09-26 2014-04-03 Ibis Biosciences, Inc. Swab interface for a microfluidic device
US20220034900A1 (en) * 2018-09-28 2022-02-03 Keio University Analysis method, analytical method and microorganism identification method
RU2765495C1 (en) * 2021-05-31 2022-01-31 Федеральное казенное учреждение здравоохранения "Ростовский-на-Дону ордена Трудового Красного Знамени научно-исследовательский противочумный институт" Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека Method for the determination of francisella tularensis subspecies by multi-primer pcr

Citations (1)

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US20040121313A1 (en) * 2002-12-06 2004-06-24 Ecker David J. Methods for rapid detection and identification of bioagents in organs for transplantation
JP2003061665A (en) * 2001-08-21 2003-03-04 Yakult Bio-Science Foundation Method for detecting spore forming bacterium

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Publication number Priority date Publication date Assignee Title
US6613509B1 (en) * 1999-03-22 2003-09-02 Regents Of The University Of California Determination of base (nucleotide) composition in DNA oligomers by mass spectrometry

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Title
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BUCK ET AL.: "Design strategies and performance of custom DNA sequencing primers", BIOTECHNIQUES, vol. 27, no. 3, September 1999 (1999-09-01), pages 528 - 536 *
NUBEL ET AL.: "PCR primers to amplify 16S rRNA genes from Cyanobacteria", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 63, no. 8, August 1997 (1997-08-01), pages 3327 - 3332 *

Also Published As

Publication number Publication date
AU2008255266B2 (en) 2011-07-14
EP1725686A4 (en) 2008-12-10
WO2005098047A2 (en) 2005-10-20
WO2006071241A2 (en) 2006-07-06
AU2005322640B2 (en) 2008-09-18
AU2008255266A1 (en) 2009-01-08
JP2007525978A (en) 2007-09-13
CA2560521C (en) 2012-01-03
EP1725686A2 (en) 2006-11-29
CA2560521A1 (en) 2006-07-06
WO2006071241A3 (en) 2007-09-13
AU2005322640A1 (en) 2006-07-06

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