COMPOSITIONS FOR USE IN IDENTIFICATION OF STREPTOCOCCUS PNEUMONIAE
First Claim
1. A composition, comprising at least one purified oligonucleotide primer pair that comprises forward and reverse primers, wherein said primer pair comprises nucleic acid sequences that are substantially complementary to nucleic acid sequences of two or more different Streptococcus pneumoniae bioagents, wherein said primer pair is configured to produce amplicons comprising different base compositions that correspond to said two or more different bioagents.
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Abstract
The present invention relates generally to the identification of Streptococcus pneumoniae, such as antibiotic resistant Streptococcus pneumoniae, and provides methods, compositions, kits and systems useful for this purpose when combined, for example, with molecular mass or base composition analysis.
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Citations
56 Claims
- 1. A composition, comprising at least one purified oligonucleotide primer pair that comprises forward and reverse primers, wherein said primer pair comprises nucleic acid sequences that are substantially complementary to nucleic acid sequences of two or more different Streptococcus pneumoniae bioagents, wherein said primer pair is configured to produce amplicons comprising different base compositions that correspond to said two or more different bioagents.
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20. A composition comprising an isolated primer 15-35 bases in length selected from the group consisting of SEQ ID NOS:
- 1-104.
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21. A kit, comprising at least one purified oligonucleotide primer pair that comprises forward and reverse primers that are about 20 to 35 nucleobases in length, and wherein said forward primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS:
- 1-40 and 81-92, and said reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;
41-80 and 93-104.
- 1-40 and 81-92, and said reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;
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22. A method of determining the presence of Streptococcus pneumoniae in at least one sample, the method comprising:
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(a) amplifying one or more segments of at least one nucleic acid from said sample using at least one purified oligonucleotide primer pair that comprises forward and reverse primers that are about 20 to 35 nucleobases in length, and wherein said forward primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;
1-40 and 81-92, and said reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;
41-80 and 93-104 to produce at least one amplification product; and(b) detecting said amplification product, thereby determining said presence of said Streptococcus pneumoniae in said sample. - View Dependent Claims (23, 24, 25, 26, 27, 28)
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29. A method of identifying one or more antibiotic resistant Streptococcus pneumoniae bioagents in a sample, the method comprising:
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(a) amplifying two or more segments of a nucleic acid from said one or more antibiotic resistant Streptococcus pneumoniae bioagents in said sample with two or more oligonucleotide primer pairs to obtain two or more amplification products; (b) determining two or more molecular masses and/or base compositions of said two or more amplification products; and (c) comparing said two or more molecular masses and/or said base compositions of said two or more amplification products with known molecular masses and/or known base compositions of amplification products of known antibiotic resistant Streptococcus pneumoniae bioagents produced with said two or more primer pairs to identify said one or more antibiotic resistant Streptococcus pneumoniae bioagents in said sample. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48)
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49. A system, comprising:
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(a) a mass spectrometer configured to detect one or more molecular masses of amplicons produced using at least one purified oligonucleotide primer pair that comprises forward and reverse primers, wherein said primer pair comprises nucleic acid sequences that are substantially complementary to nucleic acid sequences of two or more different Streptococcus pneumoniae bioagents; and (b) a controller operably connected to said mass spectrometer, said controller configured to correlate said molecular masses of said amplicons with one or more Streptococcus pneumoniae bioagent identities. - View Dependent Claims (50, 51, 52, 53, 54, 55)
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56. A purified oligonucleotide primer pair, comprising a forward primer and a reverse primer that each independently comprises 14 to 40 consecutive nucleobases selected from the primer pair sequences shown in Table 1 and/or Table 2, which primer pair is configured to generate an amplicon between about 50 and 150 consecutive nucleobases in length.
Specification