Compositions and methods to detect atopobium vaginae nucleic acid

1. A method for detecting in a sample a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae , comprising the steps of:

a. providing a sample, wherein said sample is suspected of containing an Atopobium vaginae bacterium;

b. contacting said sample with at least two amplification oligomers, each being from 15 to 25 nucleotides in length and configured to generate from a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae , an amplicon comprising a nucleotide sequence that is SEQ ID NO:43, wherein said at least two amplification oligomers specifically hybridize to A. vaginae target nucleic acid in the presence of one or more of G. vaginalis, Prevotella sp, anaerobic gram positive cocci, Mobiluncus sp, Mycoplasma hominis, Eggerthella hongkongensis, Megasphaera sp, and/or Leptotrichia sanguinegens;

c. performing an in vitro nucleic acid amplification reaction wherein any target nucleic acid present in said sample is used as a template for generating an amplification product; and

d. performing a detection reaction to determine the presence or absence of the amplification product.

2. The method of claim 1 , wherein a first amplification oligomer of said at least two amplification oligomers is about 90% or more identical to SEQ ID NO:2.

3. The method of claim 2 , wherein said first amplification oligomer sequence is about 90% or more identical to SEQ ID NO:2 and is 18 contiguous nucleotides in length.

4. The method of claim 2 , wherein the first amplification oligomer sequence is SEQ ID NO:2 and a second amplification oligomer comprises a target hybridizing sequence that is from about 21 to about 25 contiguous nucleotides in length and is about 90% or more identical to SEQ ID NO:27, and wherein said second amplification oligomer further comprises at its 5′ end a promoter sequence.

5. The method of claim 4 , wherein said second amplification oligomer sequence is SEQ ID NO:3.

6. The method of claim 2 , wherein a second amplification oligomer sequence of said at least two amplification oligomers comprises a target hybridizing sequence that is from about 21 to about 25 contiguous nucleotides in length and is about 90% or more identical to SEQ ID NO:27, and wherein said second amplification oligomer sequence further comprises at its 5′ end a promoter sequence.

7. The method of claim 6 , wherein said second amplification oligomer sequence is SEQ ID NO:3.

8. The method of claim 1 , wherein said at least two amplification oligomers are configured to specifically hybridize to a 16S rRNA of A. vaginae or a gene encoding a 16S rRNA of A. vaginae in the presence of one or more of anaerobic gram-positive cocci; Megasphaera sp.; Lactobacillus sp.; Lactobacillus iners; Lactobacillus crispatus group; Lactobacillus gasseri group; Gardnerella sp; Gardnerella vaginalis; Trichamonas sp; Trichamonas vaginalis; Candida sp; Eggerthella sp.; Bacterium from the order Clostridiales; Clostridium -like sp.; Prevotella sp.; Prevotella bivia group; Prevotella buccalis group; Atopobium sp.; Atopobium vaginae; Enterobacteria; Peptostreptococcus micros; Aerococcus christensenii; Leptotrichia amnionii; Peptoniphilus sp.; Dialister sp.; Mycoplasma hominis; Sneathia sanguinegens; Anaerococcus tetradius; Mobiluncus sp.; Mobiluncus hominis; Eggerthella hongkongensis; Megasphaera sp; Leptotrichia sanguinegens and/or Finegoldia magna.

9. The method of claim 1 , wherein said detection reaction step is performed using a detection probe oligomer, mass spectrometry-based detection, electrophoresis, sequencing reaction or probe array detection.

10. The method of claim 9 , wherein said detection reaction step is performed with a detection probe oligomer for real-time detection, a fluorescently labeled detection probe oligomer, or an acridinium ester labeled detection probe oligomer.

11. The method of claim 9 , wherein said detection probe oligomer sequence is selected from the group consisting of SEQ ID NOS:4, 15, 16 and 17.