Methods for identification of sepsis-causing bacteria
First Claim
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1. A method for identifying a sepsis-causing bacterium in a sample, comprising:
- a) amplifying a nucleic acid from said sample using an oligonucleotide primer pair comprising a forward primer and a reverse primer, said forward primer and reverse primer respectively comprising sequences selected from the group consisting of SEQ ID NOs;
(forward;
reverse) 1448;
1461, 430;
1321, and 1454;
1468;
wherein said amplifying step generates an amplification product; and
b) determining the molecular mass of said amplification product by mass spectrometry without fragmentation of said amplification product prior to mass spectrometry analysis.
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Abstract
The present invention provides compositions, kits and methods for rapid identification and quantification of sepsis-causing bacteria by molecular mass and base composition analysis.
420 Citations
38 Claims
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1. A method for identifying a sepsis-causing bacterium in a sample, comprising:
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a) amplifying a nucleic acid from said sample using an oligonucleotide primer pair comprising a forward primer and a reverse primer, said forward primer and reverse primer respectively comprising sequences selected from the group consisting of SEQ ID NOs;
(forward;
reverse) 1448;
1461, 430;
1321, and 1454;
1468;
wherein said amplifying step generates an amplification product; andb) determining the molecular mass of said amplification product by mass spectrometry without fragmentation of said amplification product prior to mass spectrometry analysis. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method for identification of a sepsis-causing bacterium in a sample comprising:
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providing one or more primer pairs that hybridize to ribosomal RNA and one or more primer pairs that hybridize to one or more housekeeping genes, wherein said primer pairs that hybridize to one or more housekeeping genes are selected from the group consisting of SEQ ID NOs;
1448;
1461, 430;
1321, and 1454;
1468;obtaining an amplification product from each of said one or more primer pairs that hybridize to ribosomal RNA and an amplification product from each of said one or more primer pairs that hybridize to one or more housekeeping genes; measuring molecular masses of said amplification products without fragmentation of said amplification products prior to molecular mass analysis; calculating base compositions of said amplification products from said molecular masses; and comparing said base compositions to known base compositions of amplification products of known sepsis-causing bacteria produced with said one or more primer pairs, thereby identifying said sepsis-causing bacterium in said sample. - View Dependent Claims (12, 13, 14, 15, 16, 17)
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18. An oligonucleotide primer pair comprising a forward primer having SEQ ID NO:
- 1448 and a reverse primer having SEQ ID NO;
1461. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
- 1448 and a reverse primer having SEQ ID NO;
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35. A kit for identifying a sepsis-causing bacterium, comprising:
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i) a first oligonucleotide primer pair comprising a forward primer having SEQ ID NO;
1448 and a reverse primer having SEQ ID NO;
1461; andii) at least one additional primer pair, wherein the primers of each of said at least one additional primer pair are configured to hybridize to conserved sequence regions within a bacterial gene selected from the group consisting of;
16S rRNA, 23S rRNA, tufB, rpoB, valS, rplB, and gyrB. - View Dependent Claims (36, 37, 38)
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Specification