CA2560521A1 - Compositions for use in identification of bacteria - Google Patents
Compositions for use in identification of bacteria Download PDFInfo
- Publication number
- CA2560521A1 CA2560521A1 CA002560521A CA2560521A CA2560521A1 CA 2560521 A1 CA2560521 A1 CA 2560521A1 CA 002560521 A CA002560521 A CA 002560521A CA 2560521 A CA2560521 A CA 2560521A CA 2560521 A1 CA2560521 A1 CA 2560521A1
- Authority
- CA
- Canada
- Prior art keywords
- nucleobases
- seq
- length
- sequence identity
- oligonucleotide primer
- Prior art date
- Legal status (The legal status 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 status listed.)
- Granted
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Classifications
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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
- C12Q1/6876—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
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- 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.
Claims (16)
1. An oligonucleotide primer selected from the group consisting of: an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 97, an oligonucleotide primer 20 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 451, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 127, an oligonucleotide primer 14 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 482, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 174, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 530, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 310, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 668, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 313, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 670, an oligonucleotide primer 17 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 277, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 632, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 285, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 640, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 301, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 656, an oligonucleotide primer 18 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 308, and an oligonucleotide primer 18 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 663.
NO: 97, an oligonucleotide primer 20 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 451, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 127, an oligonucleotide primer 14 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 482, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 174, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 530, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 310, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 668, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 313, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 670, an oligonucleotide primer 17 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 277, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 632, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 285, an oligonucleotide primer 19 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 640, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 301, an oligonucleotide primer 21 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID
NO: 656, an oligonucleotide primer 18 to 35 nucleobases in length comprising 70% to 100%
sequence identity with SEQ ID NO: 308, and an oligonucleotide primer 18 to 35 nucleobases in length comprising 70% to 100% sequence identity with SEQ ID NO: 663.
2. A composition comprising one or more of the oligonucleotide primers of claim 1.
3. A composition comprising two or more of the oligonucleotide primers of claim 1.
4. The composition of claim 3 wherein either or both of said oligonucleotide primers comprises at least one modified nucleobase.
5. The composition of claim 3 wherein either or both of said oligonucleotide primers comprises a non-templated T residue on the 5'-end.
6. The composition of claim 3 wherein either or both of said oligonucleotide primers comprises at least one non-template tag.
7. The composition of claim 3 wherein either or both of said oligonucleotide primers comprises at least one molecular mass modifying tag.
8. A kit comprising the composition of claim 3.
9. The kit of claim 8 further comprising at least one calibration polynucleotide.
10. The kit of claim 8 further comprising at least one ion exchange resin linked to magnetic beads.
11. A method for identification of an unknown bacterium comprising:
amplifying nucleic acid from said bacterium using the composition of claim 3 to obtain an amplification product;
determining the molecular mass of said amplification product;
optionally determining the base composition of said amplification product from said molecular mass; and comparing said molecular mass or base composition of said amplification product with a plurality of molecular masses or base compositions of known bacterial bioagent identifying amplicons, wherein a match between said molecular mass or base composition of said amplification product and the molecular mass or base composition of a member of said plurality of molecular masses or base compositions identifies said unknown bacterium.
amplifying nucleic acid from said bacterium using the composition of claim 3 to obtain an amplification product;
determining the molecular mass of said amplification product;
optionally determining the base composition of said amplification product from said molecular mass; and comparing said molecular mass or base composition of said amplification product with a plurality of molecular masses or base compositions of known bacterial bioagent identifying amplicons, wherein a match between said molecular mass or base composition of said amplification product and the molecular mass or base composition of a member of said plurality of molecular masses or base compositions identifies said unknown bacterium.
12. The method of claim 11 wherein said molecular mass is determined by mass spectrometry.
13. A method of determining the presence or absence of a bacterium of a particular clade, genus, species, or sub-species in a sample comprising:
amplifying nucleic acid from said sample using the composition of claim 3 to obtain an amplification product;
determining the molecular mass of said amplification product;
optionally determining the base composition of said amplification product from said molecular mass; and comparing said molecular mass or base composition of said amplification product with the known molecular masses or base compositions of one or more known clade, genus, species, or sub-species bioagent identifying amplicons, wherein a match between said molecular mass or base composition of said amplification product and the molecular mass or base composition of one or more known clade, genus, species, or sub-species bioagent identifying amplicons indicates the presence of said clade, genus, species, or sub-species in said sample.
amplifying nucleic acid from said sample using the composition of claim 3 to obtain an amplification product;
determining the molecular mass of said amplification product;
optionally determining the base composition of said amplification product from said molecular mass; and comparing said molecular mass or base composition of said amplification product with the known molecular masses or base compositions of one or more known clade, genus, species, or sub-species bioagent identifying amplicons, wherein a match between said molecular mass or base composition of said amplification product and the molecular mass or base composition of one or more known clade, genus, species, or sub-species bioagent identifying amplicons indicates the presence of said clade, genus, species, or sub-species in said sample.
14. The method of claim 13 wherein said molecular mass is determined by mass spectrometry.
15. A method for determination of the quantity of an unknown bacterium in a sample comprising:
contacting said sample with the composition of claim 3 and a known quantity of a calibration polynucleotide comprising a calibration sequence;
concurrently amplifying nucleic acid from said bacterium in said sample with the composition of claim 3 and amplifying nucleic acid from said calibration polynucleotide in said sample with the composition of claim 3 to obtain a first amplification product comprising a bacterial bioagent identifying amplicon and a second amplification product comprising a calibration amplicon;
determining the molecular mass and abundance for said bacterial bioagent identifying amplicon and said calibration amplicon; and distinguishing said bacterial bioagent identifying amplicon from said calibration amplicon based on molecular mass, wherein comparison of bacterial bioagent identifying amplicon abundance and calibration amplicon abundance indicates the quantity of bacterium in said sample.
contacting said sample with the composition of claim 3 and a known quantity of a calibration polynucleotide comprising a calibration sequence;
concurrently amplifying nucleic acid from said bacterium in said sample with the composition of claim 3 and amplifying nucleic acid from said calibration polynucleotide in said sample with the composition of claim 3 to obtain a first amplification product comprising a bacterial bioagent identifying amplicon and a second amplification product comprising a calibration amplicon;
determining the molecular mass and abundance for said bacterial bioagent identifying amplicon and said calibration amplicon; and distinguishing said bacterial bioagent identifying amplicon from said calibration amplicon based on molecular mass, wherein comparison of bacterial bioagent identifying amplicon abundance and calibration amplicon abundance indicates the quantity of bacterium in said sample.
16. The method of claim 15 further comprising determining the base composition of said bacterial bioagent identifying amplicon.
Applications Claiming Priority (11)
| 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 | ||
| PCT/US2005/006133 WO2006071241A2 (en) | 2004-02-18 | 2005-02-18 | Compositions for use in identification of bacteria |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2560521A1 true CA2560521A1 (en) | 2006-07-06 |
| CA2560521C CA2560521C (en) | 2012-01-03 |
Family
ID=35125687
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2560521A Expired - Fee Related CA2560521C (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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| WO2009155061A2 (en) * | 2008-05-30 | 2009-12-23 | Ibis Biosciences, Inc. | Compositions for use in identification of strains of e. coli o157:h7 |
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| 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 |
| US20040121309A1 (en) | 2002-12-06 | 2004-06-24 | Ecker David J. | Methods for rapid detection and identification of bioagents in blood, bodily fluids, and bodily tissues |
| CA2348042A1 (en) | 2001-06-04 | 2002-12-04 | Ann Huletsky | Sequences for detection and identification of methicillin-resistant staphylococcus aureus |
| US8073627B2 (en) | 2001-06-26 | 2011-12-06 | Ibis Biosciences, Inc. | System for indentification of pathogens |
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| 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 |
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| US8242254B2 (en) | 2003-09-11 | 2012-08-14 | Ibis Biosciences, Inc. | Compositions for use in identification of bacteria |
| US8546082B2 (en) | 2003-09-11 | 2013-10-01 | Ibis Biosciences, Inc. | Methods for identification of sepsis-causing 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 |
| JP4810533B2 (en) | 2004-05-24 | 2011-11-09 | アイビス バイオサイエンシズ インコーポレイティッド | Mass spectrometry using 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 |
| CA2600184A1 (en) | 2005-03-03 | 2006-09-08 | Isis Pharmaceuticals, Inc. | Compositions for use in identification of adventitious viruses |
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| WO2011008972A1 (en) | 2009-07-17 | 2011-01-20 | 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 |
| US9890408B2 (en) | 2009-10-15 | 2018-02-13 | Ibis Biosciences, Inc. | Multiple displacement amplification |
| US20110224106A1 (en) | 2010-03-10 | 2011-09-15 | 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 |
| EP3170831A1 (en) | 2011-09-06 | 2017-05-24 | Ibis Biosciences, Inc. | Sample preparation methods |
| US9970061B2 (en) | 2011-12-27 | 2018-05-15 | Ibis Biosciences, Inc. | Bioagent detection oligonucleotides |
| JP2013171343A (en) | 2012-02-17 | 2013-09-02 | Toshiba Corp | Storage device |
| EP2901129A4 (en) | 2012-09-26 | 2016-11-02 | Ibis Biosciences Inc | Swab interface for a microfluidic device |
| JP7105454B2 (en) * | 2018-09-28 | 2022-07-25 | 慶應義塾 | Analysis method, analysis 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 |
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| US5849492A (en) * | 1994-02-28 | 1998-12-15 | Phylogenetix Laboratories, Inc. | Method for rapid identification of prokaryotic and eukaryotic organisms |
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| US6514335B1 (en) * | 1997-08-26 | 2003-02-04 | Sumitomo Metal Industries, Ltd. | High-quality silicon single crystal and method of producing the same |
| 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 |
| AU2001288393A1 (en) * | 2000-08-25 | 2002-03-04 | Illumina, Inc. | Probes and decoder oligonucleotides |
| US20030027135A1 (en) * | 2001-03-02 | 2003-02-06 | Ecker David J. | Method for rapid detection and identification of bioagents |
| US20040121309A1 (en) * | 2002-12-06 | 2004-06-24 | Ecker David J. | Methods for rapid detection and identification of bioagents in blood, bodily fluids, and bodily tissues |
| JP2003061665A (en) * | 2001-08-21 | 2003-03-04 | Yakult Bio-Science Foundation | Method for detecting spore forming bacterium |
-
2005
- 2005-02-18 CA CA2560521A patent/CA2560521C/en not_active Expired - Fee Related
- 2005-02-18 JP JP2006554339A patent/JP2007525978A/en active Pending
- 2005-02-18 EP EP05856582A patent/EP1725686A4/en not_active Withdrawn
- 2005-02-18 AU AU2005322640A patent/AU2005322640B2/en not_active Ceased
- 2005-02-18 WO PCT/US2005/006133 patent/WO2006071241A2/en active Application Filing
- 2005-02-18 WO PCT/US2005/005356 patent/WO2005098047A2/en active Application Filing
-
2008
- 2008-12-12 AU AU2008255266A patent/AU2008255266B2/en not_active Ceased
Also Published As
| Publication number | Publication date |
|---|---|
| AU2008255266A1 (en) | 2009-01-08 |
| AU2008255266B2 (en) | 2011-07-14 |
| CA2560521C (en) | 2012-01-03 |
| WO2005098047A3 (en) | 2007-10-04 |
| EP1725686A4 (en) | 2008-12-10 |
| JP2007525978A (en) | 2007-09-13 |
| AU2005322640B2 (en) | 2008-09-18 |
| WO2005098047A2 (en) | 2005-10-20 |
| WO2006071241A2 (en) | 2006-07-06 |
| EP1725686A2 (en) | 2006-11-29 |
| WO2006071241A3 (en) | 2007-09-13 |
| AU2005322640A1 (en) | 2006-07-06 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request | ||
| MKLA | Lapsed |
Effective date: 20150218 |