Compositions and methods for detecting group B
Disclosed are nucleic acid oligomers, including amplification oligomers and detection probes, for detection of Group B Streptococcus (GBS; Streptococcus agalactiae ) nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.
1. A method for determining the presence or absence of Group B Streptococcus (GBS) in a sample, said method comprising:
(1) contacting a sample containing or suspected of containing GBS with an amplification oligomer combination comprising first and second synthetic surface immunogenic protein (SIP)-specific amplification oligomers for amplifying a target region of a GBS SIP target nucleic acid, wherein the first and second synthetic SIP-specific amplification oligomers are each less than 60 nucleotides in length and comprise, respectively, first (A) and second (B) SIP-specific target-hybridizing sequences selected from the group consisting of:
(a) (A) SEQ ID NO:3, or an RNA equivalent or DNA/RNA chimeric thereof, and
(B) SEQ ID NO:4, or an RNA equivalent or DNA/RNA chimeric thereof; and
(b) (A) SEQ ID NO:7, or an RNA equivalent or DNA/RNA chimeric thereof, and
(B) SEQ ID NO:8, or an RNA equivalent or DNA/RNA chimeric thereof;
(2) performing an in vitro nucleic acid amplification reaction, wherein performing the in vitro nucleic acid amplification reaction comprises incubating the sample and the SIP-specific amplification oligomers under conditions suitable for amplification, wherein the target region of the GBS SIP target nucleic, if present in the sample, is amplified to generate an amplicon; and
(3) contacting the in vitro nucleic acid amplification reaction with a SIP-specific detection probe oligomer comprising a detectable label and a SIP-specific detection probe target-hybridizing sequence that is from about 15 to about 35 nucleotides in length and is configured to hybridize to a target sequence contained within a SIP amplicon amplifiable by the first and second synthetic SIP-specific amplification oligomers, wherein SIP-specific detection probe oligomer provides a detectable signal in the presence of the amplicon;
wherein the presence of the detectable signal indicates the presence of GBS in the sample and absence of the detectable signal indicates the absence of the GBS in the sample.
2. The method of claim 1 , wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a).
3. The method of claim 1 , wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b).
4. The method of claim 1 , wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (a) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:9, or an RNA equivalent or DNA/RNA chimeric thereof.
5. The method of claim 1 , wherein the first and second SIP-specific target-hybridizing sequences are the target-hybridizing sequences of (b) and the SIP-specific detection probe target-hybridizing sequence is SEQ ID NO:11, or an RNA equivalent or DNA/RNA chimeric thereof.
6. The method of claim 1 , wherein the detectable label is selected from the group consisting of a fluorescent label and a chemiluminescent label.
7. The method of claim 6 , wherein the detectable label is a fluorescent label and the detection probe oligomer further comprises a non-fluorescent quencher.
8. The method of claim 1 , wherein detectable signal is detected in real time.