# US 2021/0340634 A1 · Compositions for detecting candida species

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- Number: US 2021/0340634 A1
- Document ID: US20210340634A1
- Status: Published application
- Kind: A1
- Application number: 17/371,274
- Filed: 2021-07-09
- Published: 2021-11-04
- Earliest claimed: 2016-01-04
- Assignees: Gen-Probe Incorporated
- Applicants: Gen-Probe Incorporated
- Inventors: Angela S. Hudson; Damon K. Getman; Alice Jiang; Barbara Eaton
- Web page: https://patentgrep.com/patent/US20210340634A1

## CPC

- C12Q 1/6895: for plants, fungi or algae
- C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence)
- C12Q 1/686: Polymerase chain reaction [PCR]
- C12Q 1/689: for bacteria
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/16: Primer sets for multiplex assays
- C12Q 2600/166: Oligonucleotides used as internal standards, controls or normalisation probes
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

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.

## Claims

### Claim 1

A reaction mixture for determining the presence or absence of Candida species (sp.) in a sample, wherein the Candida sp. is one or more of C. albicans, C. parapsilosis, C. dubliniensis, C. tropicalis, and C. glabrata, the reaction mixture comprising:
a first amplification oligomer combination and a second amplification oligomer combination, wherein
(a) the first amplification oligomer combination comprises first and second Candida-specific amplification oligomers for amplifying a first Candida 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; and
(b) the second amplification oligomer combination comprises first and second C. glabrata-specific amplification oligomers for amplifying a third Candida sp. nucleic acid target 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/or
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;
wherein each of the first Candida-specific amplification oligomer and the first C. glabrata-specific amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the respective target-hybridizing sequence, and
wherein each of the second Candida-specific amplification oligomer and the second C. glabrata-specific amplification oligomer is a non-promoter primer; and
a Candida-specific detection probe that specifically hybridizes to the first or second Candida sp. target region and a C. glabrata-specific detection probe that specifically hybridizes to the third Candida sp. target region, wherein each of the Candida-specific and C. glabrata-specific detection probes is a molecular torch.

### Claim 2 (depends on 1)

The reaction mixture of claim 1, wherein the first C. glabrata-specific target-hybridizing sequence consists of the nucleotide sequence of residues 28-49 of SEQ ID NO:14.

### Claim 3 (depends on 1)

The reaction mixture of claim 1, wherein the second C. glabrata-specific target-hybridizing sequence consists of the nucleotide sequence of SEQ ID NO:12.

### Claim 4 (depends on 1)

The reaction mixture of claim 1, wherein the promoter sequence is a T7 promoter sequence.

### Claim 5 (depends on 4)

The reaction mixture of claim 4, wherein the promoter sequence has the nucleotide sequence of residues 1-27 of SEQ ID NO:9.

### Claim 6 (depends on 1)

The reaction mixture of claim 1, wherein the first Candida-specific amplification oligomer has the nucleotide sequence of SEQ ID NO:9.

### Claim 7 (depends on 1)

The reaction mixture of claim 1, wherein the first C. glabrata-specific amplification oligomer has the nucleotide sequence of SEQ ID NO:14.

### Claim 8 (depends on 1)

The reaction mixture of claim 1, wherein the Candida-specific detection probe target-hybridizing sequence comprises a sequence selected from the group consisting of
the sequence of residues 1-22 of SEQ ID NO:27,
the DNA equivalent or an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing.

### Claim 9 (depends on 1)

The reaction mixture of claim 1, wherein the C. glabrata-specific detection probe target-hybridizing sequence comprises 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 an RNA/DNA chimeric of any of the foregoing, and
the full complement of any of the foregoing.

### Claim 10 (depends on 1)

The reaction mixture of claim 1, wherein the Candida-specific detection probe has a sequence selected from the group consisting of
the sequence of SEQ ID NO:27,
the DNA equivalent or an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing.

### Claim 11 (depends on 1)

The reaction mixture of claim 1, wherein the C. glabrata-specific detection probe target-hybridizing sequence has a sequence selected from the group consisting of
SEQ ID NO:60,
SEQ ID NO:45,
SEQ ID NO:18,
SEQ ID NO:21,
the DNA equivalent or an RNA/DNA chimeric of any of the foregoing, and
the full complement of any of the foregoing.

### Claim 12

A kit for determining the presence or absence of Candida species (sp.) in a sample, wherein the Candida sp. is one or more of C. albicans, C. parapsilosis, C. dubliniensis, C. tropicalis, and C. glabrata, the kit comprising:
a first amplification oligomer combination and a second amplification oligomer combination, wherein
(a) the first amplification oligomer combination comprises first and second Candida-specific amplification oligomers for amplifying a first Candida 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; and
(b) the second amplification oligomer combination comprises first and second C. glabrata-specific amplification oligomers for amplifying a third Candida sp. nucleic acid target 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/or
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;
wherein each of the first Candida-specific amplification oligomer and the first C. glabrata-specific amplification oligomer is a promoter primer or promoter provider further comprising a promoter sequence located 5′ to the respective target-hybridizing sequence, and
wherein each of the second Candida-specific amplification oligomer and the second C. glabrata-specific amplification oligomer is a non-promoter primer; and
a Candida-specific detection probe that specifically hybridizes to the first or second Candida sp. target region and a C. glabrata-specific detection probe that specifically hybridizes to the third Candida sp. target region, wherein each of the Candida-specific and C. glabrata-specific detection probes is a molecular torch.

### Claim 13 (depends on 12)

The kit of claim 12, wherein the first C. glabrata-specific target-hybridizing sequence consists of the nucleotide sequence of residues 28-49 of SEQ ID NO:14.

### Claim 14 (depends on 12)

The kit of claim 12, wherein the second C. glabrata-specific target-hybridizing sequence consists of the nucleotide sequence of SEQ ID NO:12.

### Claim 15 (depends on 12)

The kit of claim 12, wherein the promoter sequence is a T7 promoter sequence.

### Claim 16 (depends on 15)

The kit of claim 15, wherein the promoter sequence has the nucleotide sequence of residues 1-27 of SEQ ID NO:9.

### Claim 17 (depends on 12)

The kit of claim 12, wherein the first Candida-specific amplification oligomer has the nucleotide sequence of SEQ ID NO:9.

### Claim 18 (depends on 12)

The kit of claim 12, wherein the first C. glabrata-specific amplification oligomer has the nucleotide sequence of SEQ ID NO:14.

### Claim 19 (depends on 12)

The kit of claim 12, wherein
the Candida-specific detection probe target-hybridizing sequence comprises a sequence selected from the group consisting of
the sequence of residues 1-22 of SEQ ID NO:27,
the DNA equivalent or an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing; and/or
the C. glabrata-specific detection probe target-hybridizing sequence comprises 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 an RNA/DNA chimeric of any of the foregoing, and
the full complement of any of the foregoing.

### Claim 20 (depends on 12)

The kit of claim 12, wherein
the Candida-specific detection probe has a sequence selected from the group consisting of
the sequence of SEQ ID NO:27,
the DNA equivalent or an RNA/DNA chimeric thereof, and
the full complement of any of the foregoing; and/or
the C. glabrata-specific detection probe target-hybridizing sequence has a sequence selected from the group consisting of
SEQ ID NO:60,
SEQ ID NO:45,
SEQ ID NO:18,
SEQ ID NO:21,
the DNA equivalent or an RNA/DNA chimeric of any of the foregoing, and
the full complement of any of the foregoing.