WO2014138119A3 - Method and kit for characterizing microorganisms - Google Patents

Method and kit for characterizing microorganisms Download PDF

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Publication number
WO2014138119A3
WO2014138119A3 PCT/US2014/020408 US2014020408W WO2014138119A3 WO 2014138119 A3 WO2014138119 A3 WO 2014138119A3 US 2014020408 W US2014020408 W US 2014020408W WO 2014138119 A3 WO2014138119 A3 WO 2014138119A3
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WO
WIPO (PCT)
Prior art keywords
characterizing
sequence
gene sequence
microorganisms
kit
Prior art date
Application number
PCT/US2014/020408
Other languages
French (fr)
Other versions
WO2014138119A2 (en
Inventor
Stephen E. FRY
Jeremy Ellis
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Fry Laboratories, LLC
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 Fry Laboratories, LLC filed Critical Fry Laboratories, LLC
Priority to EP14717240.7A priority Critical patent/EP2964785B8/en
Publication of WO2014138119A2 publication Critical patent/WO2014138119A2/en
Publication of WO2014138119A3 publication Critical patent/WO2014138119A3/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804Nucleic acid analysis using immunogens
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1093General methods of preparing gene libraries, not provided for in other subgroups
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/16Primer sets for multiplex assays
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Botany (AREA)
  • Mycology (AREA)

Abstract

The present disclosure provides methods of characterizing one or more microorganisms and kits for characterizing at least one microorganism. Exemplary methods include preparing an amplicon library, sequencing a characteristic gene sequence to obtain a gene sequence, and characterizing the one or more microorganisms based on the gene sequence using a computer-based genomic analysis of the gene sequence. Exemplary kits include at least one forward primer including an adapter sequence and a priming sequence, for a target sequence, and at least one reverse primer.
PCT/US2014/020408 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms WO2014138119A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP14717240.7A EP2964785B8 (en) 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361772425P 2013-03-04 2013-03-04
US61/772,425 2013-03-04

Publications (2)

Publication Number Publication Date
WO2014138119A2 WO2014138119A2 (en) 2014-09-12
WO2014138119A3 true WO2014138119A3 (en) 2014-10-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/020408 WO2014138119A2 (en) 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms

Country Status (3)

Country Link
US (4) US9914979B2 (en)
EP (1) EP2964785B8 (en)
WO (1) WO2014138119A2 (en)

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US9580758B2 (en) 2013-11-12 2017-02-28 Luc Montagnier System and method for the detection and treatment of infection by a microbial agent associated with HIV infection
EP3034618A1 (en) * 2014-12-16 2016-06-22 Marcos Isamat Riviere A nucleic acid CMOS based chip for diagnosing periodontal infectious disease
JP7023711B2 (en) * 2015-04-09 2022-02-22 コーニンクレッカ フィリップス エヌ ヴェ Methods and equipment for estimating the amount of microorganisms in a classification unit in a sample
DE102015206444B3 (en) * 2015-04-10 2016-05-19 Siemens Aktiengesellschaft Method for detecting microorganisms
US11386977B2 (en) 2015-05-22 2022-07-12 The Translational Genomics Research Institute Enhanced amplicon sequencing analysis
WO2016191249A1 (en) * 2015-05-22 2016-12-01 University Of Maryland, Baltimore Next-generation sequencing-based genotyping assay for human papilloma virus (hpv)
CN105567681B (en) * 2015-12-31 2018-08-31 广州赛哲生物科技股份有限公司 A kind of method and label connector based on the noninvasive biopsy virus of high-throughput gene sequencing
CN106775998A (en) * 2016-11-09 2017-05-31 上海派森诺生物科技股份有限公司 High flux 16S sequencing data automatic processing methods
CA3054487A1 (en) * 2017-03-01 2018-09-07 Bluedot Llc Systems and methods for metagenomic analysis
US11053532B2 (en) 2017-04-19 2021-07-06 CAP Diagnostics, LLC Methods for treating polymicrobial infections
US10774377B1 (en) 2017-10-05 2020-09-15 Verily Life Sciences Llc Use of unique molecular identifiers for improved sequencing of taxonomically relevant genes
CN107904297B (en) * 2017-12-28 2020-09-04 苏州协云基因科技有限公司 Primer group, joint group and sequencing method for microbial diversity research
KR20210003120A (en) * 2018-04-20 2021-01-11 롱혼 백신즈 앤드 다이어그나스틱스, 엘엘씨 Rapid microbial resistance detection method
CN109652512A (en) * 2019-01-28 2019-04-19 南京师范大学 The quantitative detecting method of drug resistant gene in Taihu Lake water body and deposit
CA3176586A1 (en) * 2020-04-14 2021-10-21 CAP Diagnostics, LLC, dba Pathnostics Methods for treating polymicrobial infections
CN112710523B (en) * 2020-12-28 2023-09-19 山西省农业科学院农作物品种资源研究所 Collecting device suitable for molecular marker detects
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Also Published As

Publication number Publication date
EP2964785B1 (en) 2020-08-26
WO2014138119A2 (en) 2014-09-12
EP2964785A2 (en) 2016-01-13
EP2964785B8 (en) 2020-10-21
US9914979B2 (en) 2018-03-13
US20180237829A1 (en) 2018-08-23
US20140249037A1 (en) 2014-09-04
US20210388419A1 (en) 2021-12-16
US20140249036A1 (en) 2014-09-04

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