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US 2015/0031557 A1Published application
Detection of shiga toxin genes in bacteria
AssigneeGen-Probe Prodesse, Inc.
InventorEjan Tyler
Life of this patent
Estimating the term…
Abstract
The disclosed invention is related to methods, compositions and kits for targeting nucleic acid derived from Shiga toxin-producing bacteria such as E. coli. Compositions include amplification oligomers and/or detection probe oligomers. Kits and methods comprise at least one pair of amplification oligomers.
Claims72
A method for identifying a stx1 gene in a sample, said method comprising:
- a) contacting said sample with a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (v) a first oligomer having at least 90% sequence identity to SEQ ID NO:19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 20;
- b) amplifying nucleic acid in said sample with said pair of amplification oligomers to obtain an amplification product;
- and
- c) determining the sequence of said amplification product or detecting said amplification product using a detection probe.
10 more elements
A primer pair for identification of a stx1 gene, said primer pair comprising a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (v) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:20.
6 more elements
A primer-probe set for identification of a stx1 gene, said primer-probe set comprising:
- a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (v) a first oligomer having at least 90% sequence identity to SEQ ID NO:19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:20;
- and
- an oligomer probe hybridizable to a stx1 gene region located between the regions of hybridization of said pair of amplification oligomers.
8 more elements
A method for identifying a stx2 gene in a sample, said method comprising:
- a) contacting said sample with a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48;
- b) amplifying nucleic acid in said sample with said pair of amplification oligomers to obtain an amplification product;
- and
- c) determining the sequence of said amplification product or detecting said amplification product using a detection probe.
8 more elements
A primer pair for identification of a stx2 gene, said primer pair comprising a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48.
4 more elements
A primer probe set for identification of a stx2 gene, said primer-probe set comprising:
- a pair of amplification oligomers, each member of said pair of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of amplification oligomers comprising an oligomer pair selected from the group consisting of
- (i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48;
- and
- an oligomer probe hybridizable to a stx2 gene region located between the regions of hybridization of said pair of amplification oligomers.
7 more elements
An amplicon generated using two primers that are specific for stx1 or stx2 wherein at least one of the primers is from Table 2, and wherein the amplicon is generated in an amplification reaction wherein stx1 or stx2 is the target nucleic acid.
A method for identifying at least one of a stx1 gene and a stx2 gene in a sample, said method comprising:
- a) contacting said sample with a pair or stx1-specific amplification oligomers and a pair of stx2-specific amplification oligomers, each member of said stx1-specific and stx2-specific pairs of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of stx1-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (1-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (1-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (1-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (1-iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (1-v) a first oligomer having at least 90% sequence identity to SEQ ID NO:19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:20;
- and
- said pair of stx2-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (2-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (2-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (2-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (2-iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48;
- b) amplifying nucleic acid in said sample with said stx1-specific and/or stx2-specific pairs of amplification oligomers to obtain at least one amplification product;
- and
- c) determining the sequence of said at least one amplification product or detecting said at least one amplification product using a stx1-specific detection probe and a stx2-specific detection probe.
18 more elements
A primer set for amplification of at least one of a stx1 gene and a stx2 gene in a sample, said primer set comprising:
- a pair of stx1-specific amplification oligomers and a pair of stx2-specific amplification oligomers, each member of said stx1-specific and stx2-specific pairs of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of stx1-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (1-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (1-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (1-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (1-iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (1-v) a first oligomer having at least 90% sequence identity to SEQ ID NO:19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:20;
- and
- said pair of stx2-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (2-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (2-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (2-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (2-iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48.
15 more elements
A primer-probe set for identification of at least one of a stx1 gene and a stx2 gene in a sample, said primer-probe set comprising:
- a pair of stx1-specific amplification oligomers and a pair of stx2-specific amplification oligomers, each member of said stx1-specific and stx2-specific pairs of amplification oligomers having a length of from about 15 to about 25 contiguous nucleotides, said pair of stx1-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (1-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:30 and a second oligomer having at least 90% sequence identity to SEQ ID NO:31;
- (1-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:1 and a second oligomer having at least 90% sequence identity to SEQ ID NO:2;
- (1-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 8 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 9;
- (1-iv) a first oligomer having at least 90% sequence identify to SEQ ID NO:12 and a second oligomer having at least 90% sequence identity to SEQ ID NO:13;
- and
- (1-v) a first oligomer having at least 90% sequence identity to SEQ ID NO:19 and a second oligomer having at least 90% sequence identity to SEQ ID NO:20;
- and
- said pair of stx2-specific amplification oligomers comprising an oligomer pair selected from the group consisting of
- (2-i) a first oligomer having at least 90% sequence identity to SEQ ID NO:33 and a second oligomer having at least 90% sequence identity to SEQ ID NO:34;
- (2-ii) a first oligomer having at least 90% sequence identity to SEQ ID NO:40 and a second oligomer having at least 90% sequence identity to SEQ ID NO:41;
- (2-iii) a first oligomer having at least 90% sequence identity to SEQ ID NO:
- 36 and a second oligomer having at least 90% sequence identity to SEQ ID NO:
- 37;
- and
- (2-iv) a first oligomer having at least 90% sequence identity to SEQ ID NO:47 and a second oligomer having at least 90% sequence identity to SEQ ID NO:48;
- a stx1-specific detection probe hybridizable to a stx1 gene region located between the regions of by hybridization of said pair of stx1-specific amplification oligomers;
- and
- a stx2-specific detection probe hybridizable to a stx2 gene region located between the regions of hybridization of said pair of stx2-specific amplification oligomers.
18 more elements
Dependencies are inferred from the claim text.