US20060115819A1 - Detection, identification and differentiation of eubacterial taxa using a hybridization assay - Google Patents
Detection, identification and differentiation of eubacterial taxa using a hybridization assay Download PDFInfo
- Publication number
- US20060115819A1 US20060115819A1 US10/537,787 US53778705A US2006115819A1 US 20060115819 A1 US20060115819 A1 US 20060115819A1 US 53778705 A US53778705 A US 53778705A US 2006115819 A1 US2006115819 A1 US 2006115819A1
- Authority
- US
- United States
- Prior art keywords
- seq
- staphylococcus
- probes
- nucleic acid
- dna
- 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.)
- Abandoned
Links
- 238000009396 hybridization Methods 0.000 title claims description 68
- 238000001514 detection method Methods 0.000 title claims description 48
- 238000003556 assay Methods 0.000 title description 9
- 241001112695 Clostridiales Species 0.000 title description 3
- 230000004069 differentiation Effects 0.000 title 1
- 239000000523 sample Substances 0.000 claims abstract description 165
- 241000191940 Staphylococcus Species 0.000 claims abstract description 135
- 238000000034 method Methods 0.000 claims abstract description 47
- 150000007523 nucleic acids Chemical group 0.000 claims abstract description 46
- 102000039446 nucleic acids Human genes 0.000 claims abstract description 38
- 108020004707 nucleic acids Proteins 0.000 claims abstract description 38
- 125000006850 spacer group Chemical group 0.000 claims abstract description 18
- 108091033319 polynucleotide Proteins 0.000 claims description 72
- 102000040430 polynucleotide Human genes 0.000 claims description 72
- 239000002157 polynucleotide Substances 0.000 claims description 59
- 125000003729 nucleotide group Chemical group 0.000 claims description 41
- 239000002773 nucleotide Substances 0.000 claims description 39
- 230000000295 complement effect Effects 0.000 claims description 30
- 239000012634 fragment Substances 0.000 claims description 16
- 230000002441 reversible effect Effects 0.000 claims description 5
- 239000000203 mixture Substances 0.000 claims description 4
- 238000003199 nucleic acid amplification method Methods 0.000 abstract description 41
- 230000003321 amplification Effects 0.000 abstract description 40
- 108091023242 Internal transcribed spacer Proteins 0.000 abstract description 16
- 241000191967 Staphylococcus aureus Species 0.000 abstract description 12
- 238000011895 specific detection Methods 0.000 abstract description 4
- 239000012472 biological sample Substances 0.000 abstract description 3
- 108700022487 rRNA Genes Proteins 0.000 abstract description 3
- 210000003705 ribosome Anatomy 0.000 abstract description 2
- 229920002477 rna polymer Polymers 0.000 abstract description 2
- 108020004414 DNA Proteins 0.000 description 92
- 238000002844 melting Methods 0.000 description 28
- 230000008018 melting Effects 0.000 description 28
- 241000894007 species Species 0.000 description 22
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 20
- 238000002866 fluorescence resonance energy transfer Methods 0.000 description 19
- 241000191963 Staphylococcus epidermidis Species 0.000 description 17
- 241000191984 Staphylococcus haemolyticus Species 0.000 description 17
- 239000000047 product Substances 0.000 description 9
- 230000008901 benefit Effects 0.000 description 8
- 238000011880 melting curve analysis Methods 0.000 description 8
- 238000003753 real-time PCR Methods 0.000 description 8
- 230000035945 sensitivity Effects 0.000 description 8
- 241000192099 Staphylococcus schleiferi Species 0.000 description 7
- 238000009640 blood culture Methods 0.000 description 7
- 244000052769 pathogen Species 0.000 description 7
- 238000012360 testing method Methods 0.000 description 7
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical compound N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 6
- 241000295644 Staphylococcaceae Species 0.000 description 6
- 238000006243 chemical reaction Methods 0.000 description 6
- 239000012528 membrane Substances 0.000 description 6
- 241000192087 Staphylococcus hominis Species 0.000 description 5
- 108091028043 Nucleic acid sequence Proteins 0.000 description 4
- 241000191982 Staphylococcus hyicus Species 0.000 description 4
- 241001134656 Staphylococcus lugdunensis Species 0.000 description 4
- 241001147691 Staphylococcus saprophyticus Species 0.000 description 4
- 241000192097 Staphylococcus sciuri Species 0.000 description 4
- 241000191978 Staphylococcus simulans Species 0.000 description 4
- 241000192086 Staphylococcus warneri Species 0.000 description 4
- 239000000975 dye Substances 0.000 description 4
- 108090000623 proteins and genes Proteins 0.000 description 4
- 238000007399 DNA isolation Methods 0.000 description 3
- 108091034117 Oligonucleotide Proteins 0.000 description 3
- 241001147687 Staphylococcus auricularis Species 0.000 description 3
- 241001147736 Staphylococcus capitis Species 0.000 description 3
- 241001147695 Staphylococcus caprae Species 0.000 description 3
- 241000201854 Staphylococcus chromogenes Species 0.000 description 3
- 241001147698 Staphylococcus cohnii Species 0.000 description 3
- 241000191980 Staphylococcus intermedius Species 0.000 description 3
- 241000193817 Staphylococcus pasteuri Species 0.000 description 3
- 241001464905 Staphylococcus saccharolyticus Species 0.000 description 3
- 241000191973 Staphylococcus xylosus Species 0.000 description 3
- 238000013459 approach Methods 0.000 description 3
- 239000012620 biological material Substances 0.000 description 3
- 230000015572 biosynthetic process Effects 0.000 description 3
- 229960002685 biotin Drugs 0.000 description 3
- 239000011616 biotin Substances 0.000 description 3
- 235000020958 biotin Nutrition 0.000 description 3
- 210000004369 blood Anatomy 0.000 description 3
- 239000008280 blood Substances 0.000 description 3
- 239000003795 chemical substances by application Substances 0.000 description 3
- 150000001875 compounds Chemical class 0.000 description 3
- 230000009260 cross reactivity Effects 0.000 description 3
- 238000004925 denaturation Methods 0.000 description 3
- 230000036425 denaturation Effects 0.000 description 3
- 238000005516 engineering process Methods 0.000 description 3
- 230000000155 isotopic effect Effects 0.000 description 3
- 238000012986 modification Methods 0.000 description 3
- 230000004048 modification Effects 0.000 description 3
- 238000011002 quantification Methods 0.000 description 3
- 239000007787 solid Substances 0.000 description 3
- 238000003786 synthesis reaction Methods 0.000 description 3
- 108010065152 Coagulase Proteins 0.000 description 2
- 102000053602 DNA Human genes 0.000 description 2
- 241000233866 Fungi Species 0.000 description 2
- 108090000988 Lysostaphin Proteins 0.000 description 2
- TWRXJAOTZQYOKJ-UHFFFAOYSA-L Magnesium chloride Chemical compound [Mg+2].[Cl-].[Cl-] TWRXJAOTZQYOKJ-UHFFFAOYSA-L 0.000 description 2
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 2
- 230000001580 bacterial effect Effects 0.000 description 2
- 238000004364 calculation method Methods 0.000 description 2
- 230000008859 change Effects 0.000 description 2
- 230000008878 coupling Effects 0.000 description 2
- 238000010168 coupling process Methods 0.000 description 2
- 238000005859 coupling reaction Methods 0.000 description 2
- 230000003247 decreasing effect Effects 0.000 description 2
- 230000001419 dependent effect Effects 0.000 description 2
- GNBHRKFJIUUOQI-UHFFFAOYSA-N fluorescein Chemical compound O1C(=O)C2=CC=CC=C2C21C1=CC=C(O)C=C1OC1=CC(O)=CC=C21 GNBHRKFJIUUOQI-UHFFFAOYSA-N 0.000 description 2
- 239000007850 fluorescent dye Substances 0.000 description 2
- 230000014509 gene expression Effects 0.000 description 2
- 208000015181 infectious disease Diseases 0.000 description 2
- 244000005700 microbiome Species 0.000 description 2
- 238000012544 monitoring process Methods 0.000 description 2
- 230000035772 mutation Effects 0.000 description 2
- 239000013642 negative control Substances 0.000 description 2
- 239000013612 plasmid Substances 0.000 description 2
- 102000054765 polymorphisms of proteins Human genes 0.000 description 2
- 238000000746 purification Methods 0.000 description 2
- 239000000758 substrate Substances 0.000 description 2
- 238000012546 transfer Methods 0.000 description 2
- 108091093088 Amplicon Proteins 0.000 description 1
- 241000272525 Anas platyrhynchos Species 0.000 description 1
- 208000031729 Bacteremia Diseases 0.000 description 1
- 241000894006 Bacteria Species 0.000 description 1
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 description 1
- 206010011409 Cross infection Diseases 0.000 description 1
- 230000004568 DNA-binding Effects 0.000 description 1
- SHIBSTMRCDJXLN-UHFFFAOYSA-N Digoxigenin Natural products C1CC(C2C(C3(C)CCC(O)CC3CC2)CC2O)(O)C2(C)C1C1=CC(=O)OC1 SHIBSTMRCDJXLN-UHFFFAOYSA-N 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- 108060002716 Exonuclease Proteins 0.000 description 1
- 108091092584 GDNA Proteins 0.000 description 1
- 241000282412 Homo Species 0.000 description 1
- UGQMRVRMYYASKQ-KQYNXXCUSA-N Inosine Chemical compound O[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C2=NC=NC(O)=C2N=C1 UGQMRVRMYYASKQ-KQYNXXCUSA-N 0.000 description 1
- 229930010555 Inosine Natural products 0.000 description 1
- 238000003820 Medium-pressure liquid chromatography Methods 0.000 description 1
- 241001465754 Metazoa Species 0.000 description 1
- 102000016943 Muramidase Human genes 0.000 description 1
- 108010014251 Muramidase Proteins 0.000 description 1
- 108010062010 N-Acetylmuramoyl-L-alanine Amidase Proteins 0.000 description 1
- 239000000020 Nitrocellulose Substances 0.000 description 1
- 101710163270 Nuclease Proteins 0.000 description 1
- 108020004711 Nucleic Acid Probes Proteins 0.000 description 1
- 239000004677 Nylon Substances 0.000 description 1
- 229910019142 PO4 Inorganic materials 0.000 description 1
- 108091093037 Peptide nucleic acid Proteins 0.000 description 1
- 206010036790 Productive cough Diseases 0.000 description 1
- 241000589516 Pseudomonas Species 0.000 description 1
- 108010066717 Q beta Replicase Proteins 0.000 description 1
- CGNLCCVKSWNSDG-UHFFFAOYSA-N SYBR Green I Chemical compound CN(C)CCCN(CCC)C1=CC(C=C2N(C3=CC=CC=C3S2)C)=C2C=CC=CC2=[N+]1C1=CC=CC=C1 CGNLCCVKSWNSDG-UHFFFAOYSA-N 0.000 description 1
- 241000813534 Simplicia felix Species 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 241000201788 Staphylococcus aureus subsp. aureus Species 0.000 description 1
- 241000191965 Staphylococcus carnosus Species 0.000 description 1
- 241000520126 Staphylococcus delphini Species 0.000 description 1
- 241001033898 Staphylococcus equorum Species 0.000 description 1
- 241000192085 Staphylococcus gallinarum Species 0.000 description 1
- 241001147689 Staphylococcus kloosii Species 0.000 description 1
- 241000147121 Staphylococcus lentus Species 0.000 description 1
- 241000010986 Staphylococcus lutrae Species 0.000 description 1
- 241000192101 Staphylococcus muscae Species 0.000 description 1
- 241001220301 Staphylococcus piscifermentans Species 0.000 description 1
- 241001234013 Staphylococcus vitulinus Species 0.000 description 1
- 108010006785 Taq Polymerase Proteins 0.000 description 1
- RYYWUUFWQRZTIU-UHFFFAOYSA-N Thiophosphoric acid Chemical class OP(O)(S)=O RYYWUUFWQRZTIU-UHFFFAOYSA-N 0.000 description 1
- 206010000269 abscess Diseases 0.000 description 1
- 230000006978 adaptation Effects 0.000 description 1
- 125000001931 aliphatic group Chemical group 0.000 description 1
- 230000004075 alteration Effects 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 239000003242 anti bacterial agent Substances 0.000 description 1
- 229940088710 antibiotic agent Drugs 0.000 description 1
- 244000052616 bacterial pathogen Species 0.000 description 1
- 239000011324 bead Substances 0.000 description 1
- 230000027455 binding Effects 0.000 description 1
- 230000005540 biological transmission Effects 0.000 description 1
- 238000001574 biopsy Methods 0.000 description 1
- 229910052799 carbon Inorganic materials 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 238000010367 cloning Methods 0.000 description 1
- 239000002299 complementary DNA Substances 0.000 description 1
- 230000002844 continuous effect Effects 0.000 description 1
- 238000001816 cooling Methods 0.000 description 1
- 238000012258 culturing Methods 0.000 description 1
- 230000009089 cytolysis Effects 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 238000003745 diagnosis Methods 0.000 description 1
- QONQRTHLHBTMGP-UHFFFAOYSA-N digitoxigenin Natural products CC12CCC(C3(CCC(O)CC3CC3)C)C3C11OC1CC2C1=CC(=O)OC1 QONQRTHLHBTMGP-UHFFFAOYSA-N 0.000 description 1
- SHIBSTMRCDJXLN-KCZCNTNESA-N digoxigenin Chemical compound C1([C@@H]2[C@@]3([C@@](CC2)(O)[C@H]2[C@@H]([C@@]4(C)CC[C@H](O)C[C@H]4CC2)C[C@H]3O)C)=CC(=O)OC1 SHIBSTMRCDJXLN-KCZCNTNESA-N 0.000 description 1
- 201000010099 disease Diseases 0.000 description 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 1
- 238000006073 displacement reaction Methods 0.000 description 1
- 239000003814 drug Substances 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000001962 electrophoresis Methods 0.000 description 1
- 230000002255 enzymatic effect Effects 0.000 description 1
- 229940088598 enzyme Drugs 0.000 description 1
- 230000005284 excitation Effects 0.000 description 1
- 102000013165 exonuclease Human genes 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 238000005194 fractionation Methods 0.000 description 1
- 229920001519 homopolymer Polymers 0.000 description 1
- 230000007062 hydrolysis Effects 0.000 description 1
- 238000006460 hydrolysis reaction Methods 0.000 description 1
- 239000003112 inhibitor Substances 0.000 description 1
- 230000000977 initiatory effect Effects 0.000 description 1
- 229960003786 inosine Drugs 0.000 description 1
- 239000000138 intercalating agent Substances 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 238000007834 ligase chain reaction Methods 0.000 description 1
- 210000004698 lymphocyte Anatomy 0.000 description 1
- 229960000274 lysozyme Drugs 0.000 description 1
- 235000010335 lysozyme Nutrition 0.000 description 1
- 239000004325 lysozyme Substances 0.000 description 1
- 229910001629 magnesium chloride Inorganic materials 0.000 description 1
- 238000004519 manufacturing process Methods 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 238000005259 measurement Methods 0.000 description 1
- 239000000155 melt Substances 0.000 description 1
- 239000004005 microsphere Substances 0.000 description 1
- 229920001220 nitrocellulos Polymers 0.000 description 1
- 238000007899 nucleic acid hybridization Methods 0.000 description 1
- 239000002853 nucleic acid probe Substances 0.000 description 1
- 229920001778 nylon Polymers 0.000 description 1
- 239000002245 particle Substances 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 239000013610 patient sample Substances 0.000 description 1
- NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 description 1
- 239000010452 phosphate Substances 0.000 description 1
- 238000003752 polymerase chain reaction Methods 0.000 description 1
- 238000006116 polymerization reaction Methods 0.000 description 1
- 239000013641 positive control Substances 0.000 description 1
- 239000002244 precipitate Substances 0.000 description 1
- 239000002243 precursor Substances 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 230000002035 prolonged effect Effects 0.000 description 1
- 102000004169 proteins and genes Human genes 0.000 description 1
- 230000009467 reduction Effects 0.000 description 1
- 238000009877 rendering Methods 0.000 description 1
- 108020004418 ribosomal RNA Proteins 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 238000010187 selection method Methods 0.000 description 1
- 238000012163 sequencing technique Methods 0.000 description 1
- 238000003860 storage Methods 0.000 description 1
- 238000005382 thermal cycling Methods 0.000 description 1
- 210000001519 tissue Anatomy 0.000 description 1
- 238000013518 transcription Methods 0.000 description 1
- 230000035897 transcription Effects 0.000 description 1
- 230000000007 visual effect Effects 0.000 description 1
- 238000005406 washing Methods 0.000 description 1
- 238000012070 whole genome sequencing analysis Methods 0.000 description 1
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
Definitions
- the present invention relates also to said new nucleic acid sequences derived from the ITS region, between the 16S and 23S ribosomal ribonucleic acid (rRNA) or rRNA genes, to be used for the specific detection and/or identification of Staphylococcus species, in particular of S. aureus , in a biological sample.
- rRNA ribosomal ribonucleic acid
- An aspect of the present invention relates to new polynucleotides for use as probes and/or primers, which have as target a particular region of the 16S-23S rRNA spacer region of Staphylococcus aureus , and which allow the detection and/or identification of Staphylococcus species, in particular of Staphylococcus aureus.
- Another object of the present invention is a kit, in which said probes and/or primers are used, for the detection and/or identification Staphylococcus species, in particular of Staphylococcus aureus.
- Preferred primers of the invention are single stranded DNA polynucleotides capable of acting as a point of initiation for synthesis of the target sequence of the invention.
- the length and the sequence of a primer of the invention must be such that they allow to prime the synthesis of the extension products.
- Another object of the invention relates to sets of 2 polynucleotide probes, also referred to as HybProbes, both HybProbes hybridizing to the same target sequence, adjacent to each other, with no more than 25 nucleotides between said 2 HybProbes, preferably with no more than 10 nucleotides, in particular with no more than 5 nucleotides.
- the fluorescence may be measured during the amplification step, generating then amplification curves, or after the amplification step, for a melting curve analysis generating melting curves.
- the ability to simultaneously generate hybridization results with a large number of probes is another benefit of the LiPA technology.
- the amount of information which can be obtained by a particular combination of probes greatly outnumbers the data obtained by using single probe assays. Therefore the selection of probes on the membrane strip is of utmost importance since an optimized set of probes will generate the maximum of information possible.
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)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US12/105,380 US8945850B2 (en) | 2002-12-06 | 2008-04-18 | Detection, identification and differentiation of Staphylococcus using a hybridization assay |
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| EP02447247 | 2002-12-06 | ||
| EP02447247.4 | 2002-12-06 | ||
| PCT/EP2003/013907 WO2004052606A2 (en) | 2002-12-06 | 2003-12-08 | Detection, identification and differentiation of eubacterial taxa using a hybridization assay |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| US12/105,380 Continuation US8945850B2 (en) | 2002-12-06 | 2008-04-18 | Detection, identification and differentiation of Staphylococcus using a hybridization assay |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| US20060115819A1 true US20060115819A1 (en) | 2006-06-01 |
Family
ID=32479868
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| US10/537,787 Abandoned US20060115819A1 (en) | 2002-12-06 | 2003-12-08 | Detection, identification and differentiation of eubacterial taxa using a hybridization assay |
| US12/105,380 Expired - Fee Related US8945850B2 (en) | 2002-12-06 | 2008-04-18 | Detection, identification and differentiation of Staphylococcus using a hybridization assay |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| US12/105,380 Expired - Fee Related US8945850B2 (en) | 2002-12-06 | 2008-04-18 | Detection, identification and differentiation of Staphylococcus using a hybridization assay |
Country Status (10)
| Country | Link |
|---|---|
| US (2) | US20060115819A1 (enExample) |
| EP (1) | EP1567668B1 (enExample) |
| JP (2) | JP2006508671A (enExample) |
| AT (1) | ATE430209T1 (enExample) |
| AU (1) | AU2003289984A1 (enExample) |
| CA (1) | CA2504911C (enExample) |
| DE (1) | DE60327462D1 (enExample) |
| DK (1) | DK1567668T3 (enExample) |
| ES (1) | ES2326316T3 (enExample) |
| WO (1) | WO2004052606A2 (enExample) |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20080199878A1 (en) * | 2002-12-06 | 2008-08-21 | Innogenetics N.V. | Detection, identification and differentiation of eubacterial taxa using a hybridization assay |
| US20090081663A1 (en) * | 2007-04-19 | 2009-03-26 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| KR101065904B1 (ko) * | 2003-09-02 | 2011-09-19 | 소니 에릭슨 모빌 커뮤니케이션즈 에이비 | 두 메모리 사이의 보안성 데이터 전송 |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| ES2393302T3 (es) * | 2004-09-30 | 2012-12-20 | Innogenetics N.V. | Detección, identificación y diferenciación de la especie serratia utilizando la región intergénica |
| JP4967095B2 (ja) * | 2005-08-12 | 2012-07-04 | 財団法人ヒューマンサイエンス振興財団 | 黄色ブドウ球菌濃度測定方法及び食中毒可能性判定方法 |
| WO2007083852A1 (en) * | 2006-01-20 | 2007-07-26 | Genein Co., Ltd. | Oligonucleotide for detection of bacteria associated with sepsis and microarrays and a methods for detection of the bacteria using the oligonucleotide |
| CN101627133A (zh) * | 2007-01-08 | 2010-01-13 | 株式会社美迪基尼斯 | 用于金黄色葡萄球菌检测的dna芯片 |
Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5849488A (en) * | 1996-02-27 | 1998-12-15 | Oulutech Ltd. | DNA-sequence-based diagnosis of mastitis from a milk sample |
| US6312903B1 (en) * | 1994-06-24 | 2001-11-06 | Innogenetics N.V. | Simulataneous detection, identification and differentiation of eubacterial taxa using a hybridization assay |
Family Cites Families (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5541308A (en) * | 1986-11-24 | 1996-07-30 | Gen-Probe Incorporated | Nucleic acid probes for detection and/or quantitation of non-viral organisms |
| US5210015A (en) * | 1990-08-06 | 1993-05-11 | Hoffman-La Roche Inc. | Homogeneous assay system using the nuclease activity of a nucleic acid polymerase |
| US6737248B2 (en) * | 1996-01-05 | 2004-05-18 | Human Genome Sciences, Inc. | Staphylococcus aureus polynucleotides and sequences |
| JP3844996B2 (ja) * | 2000-11-15 | 2006-11-15 | エフ．ホフマン−ラ ロシュ アーゲー | 反復性ｐｃｒ産物の融解曲線解析方法 |
| US20060115819A1 (en) * | 2002-12-06 | 2006-06-01 | Sofie Claeys | Detection, identification and differentiation of eubacterial taxa using a hybridization assay |
-
2003
- 2003-12-08 US US10/537,787 patent/US20060115819A1/en not_active Abandoned
- 2003-12-08 AT AT03782334T patent/ATE430209T1/de active
- 2003-12-08 DE DE60327462T patent/DE60327462D1/de not_active Expired - Lifetime
- 2003-12-08 DK DK03782334T patent/DK1567668T3/da active
- 2003-12-08 WO PCT/EP2003/013907 patent/WO2004052606A2/en not_active Ceased
- 2003-12-08 AU AU2003289984A patent/AU2003289984A1/en not_active Abandoned
- 2003-12-08 JP JP2004558030A patent/JP2006508671A/ja active Pending
- 2003-12-08 EP EP03782334A patent/EP1567668B1/en not_active Expired - Lifetime
- 2003-12-08 ES ES03782334T patent/ES2326316T3/es not_active Expired - Lifetime
- 2003-12-08 CA CA2504911A patent/CA2504911C/en not_active Expired - Fee Related
-
2008
- 2008-04-18 US US12/105,380 patent/US8945850B2/en not_active Expired - Fee Related
-
2009
- 2009-12-09 JP JP2009279519A patent/JP5156726B2/ja not_active Expired - Fee Related
Patent Citations (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6312903B1 (en) * | 1994-06-24 | 2001-11-06 | Innogenetics N.V. | Simulataneous detection, identification and differentiation of eubacterial taxa using a hybridization assay |
| US5849488A (en) * | 1996-02-27 | 1998-12-15 | Oulutech Ltd. | DNA-sequence-based diagnosis of mastitis from a milk sample |
Cited By (12)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20080199878A1 (en) * | 2002-12-06 | 2008-08-21 | Innogenetics N.V. | Detection, identification and differentiation of eubacterial taxa using a hybridization assay |
| US8945850B2 (en) | 2002-12-06 | 2015-02-03 | Fujirebio Europe N.V. | Detection, identification and differentiation of Staphylococcus using a hybridization assay |
| KR101065904B1 (ko) * | 2003-09-02 | 2011-09-19 | 소니 에릭슨 모빌 커뮤니케이션즈 에이비 | 두 메모리 사이의 보안성 데이터 전송 |
| US20090081663A1 (en) * | 2007-04-19 | 2009-03-26 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US20100255490A1 (en) * | 2007-04-19 | 2010-10-07 | Molecular Detection, Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US20110151466A1 (en) * | 2007-04-19 | 2011-06-23 | Molecular Detection, Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US8017337B2 (en) | 2007-04-19 | 2011-09-13 | Molecular Detection, Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US8362228B2 (en) | 2007-04-19 | 2013-01-29 | Molecular Detection, Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US8512954B2 (en) | 2007-04-19 | 2013-08-20 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US8557974B2 (en) | 2007-04-19 | 2013-10-15 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US8557524B2 (en) | 2007-04-19 | 2013-10-15 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
| US9074260B2 (en) | 2007-04-19 | 2015-07-07 | Molecular Detection Inc. | Methods, compositions and kits for detection and analysis of antibiotic-resistant bacteria |
Also Published As
| Publication number | Publication date |
|---|---|
| ATE430209T1 (de) | 2009-05-15 |
| AU2003289984A1 (en) | 2004-06-30 |
| EP1567668A2 (en) | 2005-08-31 |
| US8945850B2 (en) | 2015-02-03 |
| CA2504911A1 (en) | 2004-06-24 |
| US20080199878A1 (en) | 2008-08-21 |
| HK1085159A1 (en) | 2006-08-18 |
| AU2003289984A8 (en) | 2004-06-30 |
| JP5156726B2 (ja) | 2013-03-06 |
| JP2006508671A (ja) | 2006-03-16 |
| WO2004052606A2 (en) | 2004-06-24 |
| CA2504911C (en) | 2015-08-11 |
| ES2326316T3 (es) | 2009-10-07 |
| JP2010088447A (ja) | 2010-04-22 |
| DK1567668T3 (da) | 2009-08-17 |
| EP1567668B1 (en) | 2009-04-29 |
| DE60327462D1 (de) | 2009-06-10 |
| WO2004052606A3 (en) | 2004-07-29 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| EP2834375B1 (en) | Sequences for detection and identification of methicillin-resistant staphylococcus aureus (mrsa) of mrej type xxi | |
| US20090098558A1 (en) | Detection, identification and differentiation of proteus species using the spacer region | |
| US8945850B2 (en) | Detection, identification and differentiation of Staphylococcus using a hybridization assay | |
| CN105793436A (zh) | 对生物样品中耐甲氧西林金黄色葡萄球菌的检测 | |
| WO2012009813A1 (en) | Methods of detecting genetic polymorphisms using melting temperature of probe-amplicon complexes | |
| US20130177910A1 (en) | Detection, identification and differentiation of serratia species using the spacer region | |
| US9273361B2 (en) | Detection, identification and differentiation of eubacterial taxa using a hybridization assay | |
| CN111094595A (zh) | 用于检测金黄色葡萄球菌的组合物和方法 | |
| JP2010536343A (ja) | 薬剤耐性菌検出方法 | |
| HK1085159B (en) | Detection, identification and differentiation of eubacterial taxa using a hybridization assay | |
| HK1085243B (en) | Detection, identification and differentiation of eubacterial taxa using a hybridization assay | |
| US20100092949A1 (en) | Methods for detecting staphylococcus aureus |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| AS | Assignment |
Owner name: INNOGENETICS N.V., BELGIUM Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:CLAEYS, SOFIE;JANNES, GEERT;HABERHAUSEN, GERD;AND OTHERS;REEL/FRAME:017396/0252;SIGNING DATES FROM 20050426 TO 20050511 Owner name: ROCHE DIAGNOSTICS GMBH, GERMANY Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:CLAEYS, SOFIE;JANNES, GEERT;HABERHAUSEN, GERD;AND OTHERS;REEL/FRAME:017396/0252;SIGNING DATES FROM 20050426 TO 20050511 |
|
| STCB | Information on status: application discontinuation |
Free format text: ABANDONED -- FAILURE TO RESPOND TO AN OFFICE ACTION |