Compositions for detecting
Disclosed are methods utilizing specific amplification of Candida sp. target nucleic acid for detecting the presence or absence of Candida sp. in a sample. Also disclosed are corresponding oligomers, including amplification oligomers, capture probes and detection probes, and combinations thereof, as well as corresponding reaction mixtures and kits.
1. An oligomer combination for determining the presence or absence of one or more of Candida ( C .) albicans, C. parapsilosis, C. dubliniensis , and C. tropicalis in a sample, the oligomer combination comprising:
first and second Candida -specific amplification oligomers for amplifying a first Candida species (sp.) nucleic acid target region or a second Candida sp. nucleic acid target region, wherein said first target region corresponds to a region of SEQ ID NO:129 from about nucleotide position 133 or 161 to about nucleotide position 259 and said second region corresponds to a region of SEQ ID NO:130 from about nucleotide position 202 to about nucleotide position 308, and wherein the first and second Candida -specific amplification oligomers respectively comprise first and second Candida -specific target-hybridizing sequences, wherein
the first Candida -specific target-hybridizing sequence consists of the nucleotide sequence of residues 28-46 of SEQ ID NO:9; and
the second Candida -specific target-hybridizing sequence consists of the nucleotide sequence of SEQ ID NO:26;
wherein the first Candida -specific amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the first Candida -specific target-hybridizing sequence, and wherein the second Candida -specific amplification oligomer is a non-promoter primer, and
wherein the oligomer combination further comprises a Candida -specific detection probe that specifically hybridizes to the first or second Candida sp. target region, wherein said detection probe comprises a fluorescent label and a quencher, and wherein said detection probe is a molecular torch.
2. The oligomer combination of claim 1 , wherein the promoter sequence is a T7 promoter sequence.
3. The oligomer combination of claim 2 , wherein the promoter sequence has the nucleotide sequence of residues 1-27 of SEQ ID NO:9.
4. The oligomer combination of claim 1 , wherein the oligomer combination is for further determining the presence or absence of C. glabrata in the sample and further comprises a second oligomer combination comprising first and second C. glabrata -specific amplification oligomers for amplifying a third Candida sp. target nucleic acid region, wherein said third target region corresponds to a region of SEQ ID NO:131 from about nucleotide position 355 to about nucleotide position 554, and wherein the first and second C. glabrata -specific amplification oligomers respectively comprise first and second C. glabrata -specific target-hybridizing sequences, wherein
the first C. glabrata -specific target-hybridizing sequence is a sequence of from 15 to 24 contiguous nucleotides contained in the sequence of SEQ ID NO:134 and that includes at least the sequence of SEQ ID NO:135; and
the second C. glabrata -specific target-hybridizing sequence is a sequence of from 16 to 21 contiguous nucleotides contained in the sequence of SEQ ID NO:136 and that includes at least the sequence of SEQ ID NO:137.
5. The oligomer combination of claim 4 , wherein
the first C. glabrata -specific target-hybridizing sequence consists of the nucleotide sequence of residues 28-49 of SEQ ID NO:14; and/or
the second C. glabrata -specific target-hybridizing sequence consists of the nucleotide sequence of SEQ ID NO:12.
6. The oligomer combination of claim 4 , wherein the first C. glabrata -specific amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the first C. glabrata -specific target-hybridizing sequence.
7. The oligomer combination of claim 1 , wherein the Candida -specific detection probe comprises a Candida -specific detection probe target-hybridizing sequence selected from the group consisting of
(A) a sequence of from 18 to 22 contiguous nucleotides contained in the sequence of SEQ ID NO:145 and that includes at least the sequence of SEQ ID NO:146,
(B) the DNA equivalent or an RNA/DNA chimeric of (A), and
(C) the full complement of (A) or (B).
8. The oligomer combination of claim 7 , wherein the Candida -specific detection probe target-hybridizing sequence consists of a sequence selected from the group consisting of
the sequence of residues 1-22 of SEQ ID NO:27,
the DNA equivalent of an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing.
9. The oligomer combination of claim 4 , further comprising a C. glabrata -specific detection probe that specifically hybridizes to the third Candida -sp. target region.
10. The oligomer combination of claim 1 , wherein
the Candida -specific detection probe comprises a Candida -specific detection probe target-hybridizing sequence selected from the group consisting of
(A1) a sequence of from 18 to 22 contiguous nucleotides contained in the sequence of SEQ ID NO:145 and that includes at least the sequence of SEQ ID NO:146,
(B1) the DNA equivalent or an RNA/DNA chimeric of (A1), and
(C1) the full complement of (A1) or (B1).
11. The oligomer combination of claim 10 , wherein
the Candida -specific detection probe target-hybridizing sequence consists of a sequence selected from the group consisting of
the sequence of residues 1-22 of SEQ ID NO:27,
the DNA equivalent of an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing.
12. The oligomer combination of claim 9 , wherein the C. glabrata -specific detection probe comprises a fluorescent label and a quencher.
13. The oligomer combination of claim 12 , wherein the C. glabrata -specific detection probe is a molecular torch or a molecular beacon.
14. The oligomer combination of claim 1 , wherein
the C. glabrata -specific detection probe comprises a C. glabrata -specific detection probe target-hybridizing sequence selected from the group consisting of
(A2) a sequence of from 17 to 23 contiguous nucleotides contained in the sequence of SEQ ID NO:147 and that includes at least the sequence of SEQ ID NO:148,
(B2) a sequence that substantially corresponds to the sequence of residues 1-17 of SEQ ID NO:18,
(C2) a sequence that substantially corresponds to the sequence of residues 1-20 of SEQ ID NO:21,
(D2) the DNA equivalent or an RNA/DNA chimeric of any of (A2)-(C2), and
(E2) the full complement of any one of (A2)-(D2).
15. The oligomer combination of claim 14 , wherein
the C. glabrata -specific detection probe target-hybridizing sequence consists of a sequence selected from the group consisting of
the sequence of residues 1-17 of SEQ ID NO:60,
the sequence of residues 1-23 of SEQ ID NO:45,
the sequence of residues 1-17 of SEQ ID NO:18,
the sequence of residues 1-20 of SEQ ID NO:21,
the DNA equivalent or RNA/DNA chimeric of any of the foregoing, and
the full complement of any of the foregoing.