WO2009017902A3 - Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis - Google Patents

Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis Download PDF

Info

Publication number
WO2009017902A3
WO2009017902A3 PCT/US2008/067911 US2008067911W WO2009017902A3 WO 2009017902 A3 WO2009017902 A3 WO 2009017902A3 US 2008067911 W US2008067911 W US 2008067911W WO 2009017902 A3 WO2009017902 A3 WO 2009017902A3
Authority
WO
WIPO (PCT)
Prior art keywords
mycobacterium tuberculosis
methods
compositions
identification
subspecies
Prior art date
Application number
PCT/US2008/067911
Other languages
French (fr)
Other versions
WO2009017902A2 (en
Inventor
Christian Massire
Rangarajan Sampath
Lawrence B. Blyn
David J. Ecker
Original Assignee
Ibis Biosciences, Inc.
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 Ibis Biosciences, Inc. filed Critical Ibis Biosciences, Inc.
Priority to US12/666,239 priority Critical patent/US20110105531A1/en
Priority to EP08826817A priority patent/EP2179041A4/en
Publication of WO2009017902A2 publication Critical patent/WO2009017902A2/en
Publication of WO2009017902A3 publication Critical patent/WO2009017902A3/en
Priority to ZA2010/00218A priority patent/ZA201000218B/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
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/627—Detection means characterised by use of a special device being a mass spectrometer
    • 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

Abstract

The present invention provides compositions, kits and methods for rapid genotyping of strains of Mycobacterium tuberculosis by molecular mass and base composition analysis. Drug-resistant strains of Mycobacterium tuberculosis may be identified in human clinical samples and as such, provide for methods of treatment of humans infected with drug resistant strains of Mycobacterium tuberculosis.
PCT/US2008/067911 2007-06-22 2008-06-23 Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis WO2009017902A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
US12/666,239 US20110105531A1 (en) 2007-06-22 2008-06-23 Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis
EP08826817A EP2179041A4 (en) 2007-06-22 2008-06-23 Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis
ZA2010/00218A ZA201000218B (en) 2007-06-22 2010-01-12 Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US94585007P 2007-06-22 2007-06-22
US60/945,850 2007-06-22
US3788408P 2008-03-19 2008-03-19
US61/037,884 2008-03-19

Publications (2)

Publication Number Publication Date
WO2009017902A2 WO2009017902A2 (en) 2009-02-05
WO2009017902A3 true WO2009017902A3 (en) 2009-10-15

Family

ID=40305160

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2008/067911 WO2009017902A2 (en) 2007-06-22 2008-06-23 Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis

Country Status (3)

Country Link
EP (1) EP2179041A4 (en)
WO (1) WO2009017902A2 (en)
ZA (1) ZA201000218B (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9598724B2 (en) 2007-06-01 2017-03-21 Ibis Biosciences, Inc. Methods and compositions for multiple displacement amplification of nucleic acids

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2957641B1 (en) 2009-10-15 2017-05-17 Ibis Biosciences, Inc. Multiple displacement amplification
US20130095489A1 (en) * 2010-05-04 2013-04-18 Centers For Disease Control And Prevention Process for detection of multidrug resistant tuberculosis using real-time pcr and high resolution melt analysis
GB201203903D0 (en) * 2012-03-06 2012-04-18 Vela Operations Pte Ltd Real-time PCR detection of mycobacterium tuberculosis complex
EP3572509B1 (en) * 2017-01-19 2023-09-20 Kaneka Corporation Primer set, probe, kit, and method for detecting mycobacterium kansasii
CN108165562B (en) * 2017-12-01 2021-06-08 北京蛋白质组研究中心 Mycobacterium tuberculosis H37Rv encoding gene and application thereof
CN108165561B (en) * 2017-12-01 2021-06-18 北京蛋白质组研究中心 Mycobacterium tuberculosis H37Rv encoding gene and application thereof
CN108165560B (en) * 2017-12-01 2021-06-08 北京蛋白质组研究中心 Mycobacterium tuberculosis H37Rv encoding gene and application thereof
KR20210124360A (en) * 2019-03-04 2021-10-14 미쓰이 가가쿠 가부시키가이샤 A method for determining the existence state of an organism having a cell wall, and a method for identifying an organism having a cell wall
CN112481399B (en) * 2020-12-21 2022-08-30 上海国际旅行卫生保健中心(上海海关口岸门诊部) Primer group for mycobacterium tuberculosis MLST typing based on second-generation sequencing technology and library construction method
CN115029453B (en) * 2021-11-16 2023-06-16 江汉大学 MNP (MNP) marking site of streptococcus pyogenes, primer composition, kit and application of MNP marking site

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1098003A2 (en) * 1999-11-02 2001-05-09 Marine Biotechnology Institute Co., Ltd. Identification method and specific detection method of slow growing mycobacteria utilizing DNA gyrase gene
US6892139B2 (en) * 1999-01-29 2005-05-10 The Regents Of The University Of California Determining the functions and interactions of proteins by comparative analysis

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5851763A (en) * 1992-09-17 1998-12-22 Institut Pasteur Rapid detection of antibiotic resistance in mycobacterium tuberculosis
US5658733A (en) * 1994-04-18 1997-08-19 Mayo Foundation For Medical Education And Research Detection of isoniazid resistant strains of M. tuberculosis
AU1543000A (en) * 1998-12-11 2000-07-03 Visible Genetics Inc. Method and kit for the characterization of antibiotic-resistance mutations in (mycobacterium) tuberculosis
US20030027135A1 (en) * 2001-03-02 2003-02-06 Ecker David J. Method for rapid detection and identification of bioagents
KR100454585B1 (en) * 2001-10-09 2004-11-02 주식회사 에스제이하이테크 Microarray comprising probes for Mycobacteria genotyping, M. tuberculosis strain differentiation and antibiotic-resistance detection
AU2003299867A1 (en) * 2002-12-27 2004-07-29 University Of Medicine And Dentistry Of New Jersey Method for single nucleotide polymorphism detection
GB0428255D0 (en) * 2004-12-23 2005-01-26 Health Prot Agency Detection of nucleic acid mutations

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6892139B2 (en) * 1999-01-29 2005-05-10 The Regents Of The University Of California Determining the functions and interactions of proteins by comparative analysis
EP1098003A2 (en) * 1999-11-02 2001-05-09 Marine Biotechnology Institute Co., Ltd. Identification method and specific detection method of slow growing mycobacteria utilizing DNA gyrase gene

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
IWAMOTO T. ET AL.: "Comparative study of two typing methods, hsp65 PRA and ITS sequencing, revealed a possible evolutionary link between Mycobacterium kansasii type I and II isolates.", FEMS MICROBIOL LETT., vol. 254, 2006, pages 129 - 133, XP008129601 *
KASAI H. ET AL.: "Differentiation of phylogenetically related slowly growing Mycobacteria by their gyrB sequences.", IN JOURNAL OF CLINICAL MICROBIOLOGY, vol. 38, no. 1, January 2000 (2000-01-01), pages 301 - 308, XP002263236 *
NIEMANN S. ET AL.: "The species Mycobacterium africanum in the light of new molecular markers.", JOURNAL OF CLINICAL MICROBIOLOGY, vol. 42, no. 9, September 2004 (2004-09-01), pages 3958 - 3962, XP008129609 *
See also references of EP2179041A4 *
TAKIFF H.E. ET AL.: "Cloning and nucleotide sequence of Mycobacterium tuberculosis gyrA and gyrB genes and detection of quinolone resistance mutations.", ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 38, no. 4, 1994, pages 773 - 780, XP008129608 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9598724B2 (en) 2007-06-01 2017-03-21 Ibis Biosciences, Inc. Methods and compositions for multiple displacement amplification of nucleic acids

Also Published As

Publication number Publication date
WO2009017902A2 (en) 2009-02-05
ZA201000218B (en) 2012-04-25
EP2179041A2 (en) 2010-04-28
EP2179041A4 (en) 2010-12-22

Similar Documents

Publication Publication Date Title
WO2009017902A3 (en) Compositions and methods for identification of subspecies characteristics of mycobacterium tuberculosis
WO2007118222A3 (en) Compositions for the use in identification of fungi
WO2006094238A3 (en) Compositions for use in identification of adventitious viruses
WO2006116127A3 (en) Compositions for use in identification of bacteria
WO2007086904A3 (en) Compositions for use in identification of adenoviruses
WO2008042231A3 (en) Compositions and methods for evaluating and treating heart failure
WO2008024473A3 (en) Mapping of genomic interactions
WO2008118587A3 (en) Therapeutic applications of activation of human antigen-presenting cells through dectin-1
WO2007100397A3 (en) Compositions for use in identification of adventitious contaminant viruses
WO2006020773A3 (en) Methods for preparing freeze-dried platelets, compositions comprising freeze-dried platelets, and methods of use
WO2009156462A3 (en) Organic compounds
BRPI0717219A2 (en) "immunogenic composition, method for treating or preventing disease, and use of an immunogenic composition."
WO2011045544A3 (en) Method for characterizing at least one microorganism by means of mass spectrometry
WO2007035814A3 (en) Reagents, methods and kits for classification of fungi and direction of anti-fungal therapy
BRPI0510170B8 (en) compound, pharmaceutical composition for the treatment of diseases mediated by the muscarinic acetylcholine receptor and use of the compound
EP2020445A4 (en) Detection of inflammatory disease and composition for prevention or treatment of inflammatory disease
BR112012011485A2 (en) "compositions and methods for treating centrally mediated nausea and vomiting".
WO2008157697A3 (en) Copolymer assay
WO2010039819A3 (en) Compositions for use in identification of fungi
WO2007132120A3 (en) Procedure and methods for detecting alzheimer's disease
WO2008112903A3 (en) Genetic alterations on chromosome 16 and methods of use thereof for the diagnosis and treatment of type 1 diabetes
BRPI0910884A2 (en) immunogenic composition, method for treating or preventing staphylococcal infection or disease, and use of an immunogenic composition.
WO2009120183A3 (en) System for the detection of a biological pathogen and use thereof
WO2012031752A3 (en) Tuberculosis mutants
WO2008127839A3 (en) Compositions for use in identification of bacteria

Legal Events

Date Code Title Description
NENP Non-entry into the national phase

Ref country code: DE

WWE Wipo information: entry into national phase

Ref document number: 2008826817

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: 12666239

Country of ref document: US