COMPOSITIONS FOR USE IN IDENTIFICATION OF MIXED POPULATIONS OF BIOAGENTS
First Claim
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1. A method for identifying a population genotype comprising the steps of:
- (a) obtaining a sample suspected of comprising a population of bioagents;
(b) amplifying a nucleic acid from each of two or more bioagents from said population of bioagents in said sample using a primer pair that is configured to generate an amplicon from within a region defined by SEQ ID NO;
10, thereby generating amplicons from said nucleic acids;
(c) determining a molecular mass measurement for each of said amplicons using a mass spectrometer;
(d) calculating a base composition from each molecular mass measurement; and
(e) identifying a population genotype for said population of bioagents by comparing each of said base compositions calculated in step (d) to a database of base compositions indexed to the primer pair of step (b) and a known bioagent genotype.
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Abstract
The present invention provides oligonucleotide primers, compositions, and kits containing the same for rapid identification of bacterial bioagents and populations of bioagents which are members of the Staphylococcus bacterial genus by amplification of a segment of bioagent nucleic acid followed by molecular mass analysis.
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Citations
79 Claims
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1. A method for identifying a population genotype comprising the steps of:
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(a) obtaining a sample suspected of comprising a population of bioagents; (b) amplifying a nucleic acid from each of two or more bioagents from said population of bioagents in said sample using a primer pair that is configured to generate an amplicon from within a region defined by SEQ ID NO;
10, thereby generating amplicons from said nucleic acids;(c) determining a molecular mass measurement for each of said amplicons using a mass spectrometer; (d) calculating a base composition from each molecular mass measurement; and (e) identifying a population genotype for said population of bioagents by comparing each of said base compositions calculated in step (d) to a database of base compositions indexed to the primer pair of step (b) and a known bioagent genotype. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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29. A method of reducing a population of bacteria in a person needing such a treatment comprising the steps of:
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(a) obtaining from a person a sample suspected of comprising a population of bacterial bioagents; (b) amplifying a nucleic acid from each of two or more bacterial bioagents in said sample using a primer pair that is configured to generate an amplicon from within a region of defined by SEQ ID NO;
10, thereby generating amplicons from said nucleic acids;(c) determining a molecular mass measurement for each of said amplicons using a mass spectrometer; (d) calculating a base composition from each molecular mass measurement; (e) identifying a population genotype for said population of bioagents by comparing each of said base compositions calculated in step (d) to a database of base compositions indexed to the primer pair of step (b) and a known bioagent genotype; and (f) administering to a person in need thereof an antibiotic regimen tailored to treat the identified genotypes for the population of bacterial bioagents. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57)
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58. A composition of matter comprising a purified oligonucleotide primer pair wherein each primer member of said primer pair is 20 to 35 nucleobases in length and wherein the forward primer comprises at least 80% identity with a first portion of SEQ ID NO:
- 10 and the reverse primer comprises at least 80% reverse complementarity with a second portion of SEQ ID NO;
10. - View Dependent Claims (59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79)
- 10 and the reverse primer comprises at least 80% reverse complementarity with a second portion of SEQ ID NO;
Specification