Compositions and Methods for Detecting Bacterial Nucleic Acid and Diagnosing Bacterial Vaginosis

A composition or a kit for determining the presence or absence of each of Lactobacillus sp., A. vaginae, and G. vaginalis in a sample, the composition or kit comprising:

• (a) first, second, third, and fourth Lactobacillus-specific amplification oligomers for amplifying a target region of a Lactobacillus sp. target nucleic acid, wherein (i) the first Lactobacillus-specific amplification oligomer comprises a first Lactobacillus-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 28-45 of SEQ ID NO:10;
• (ii) the second Lactobacillus-specific amplification oligomer comprises a second Lactobacillus-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:7;
• (iii) the third Lactobacillus-specific amplification oligomer comprises a third Lactobacillus-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:8;
• and (iv) the fourth Lactobacillus-specific amplification oligomer comprises a fourth Lactobacillus-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:9;
• (b) first and second A. vaginae-specific amplification oligomers for amplifying a target region of a A. vaginae target nucleic acid, wherein (i) the first A. vaginae-specific amplification oligomer comprises a first A. vaginae-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 28-45 of SEQ ID NO:18 and (ii) the second A. vaginae-specific amplification oligomer comprises a second A. vaginae-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:17;
• and
• (c) first and second G. vaginalis-specific amplification oligomers for amplifying a target region of a G. vaginalis target nucleic acid, wherein (i) the first G. vaginalis-specific amplification oligomer comprises a first G. vaginalis-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 36-52 of SEQ ID NO:15 and (ii) the second G. vaginalis-specific amplification oligomer comprises a second G. vaginalis-specific target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:14.

A method for determining the presence or absence of Bacterial Vaginosis (BV) in a subject, the method comprising:

• (a) providing a sample from a subject suspected of having BV;
• (b) performing an assay for the detection of Lactobacillus sp., A. vaginae, and G. vaginalis in the sample;
• (c) for each of Lactobacillus sp., A. vaginae, and G. vaginalis, assigning a quantitative value based on the detection assay;
• (d) subtracting the Lactobacillus sp. quantitative value from the greater of the A. vaginae quantitative value and the G. vaginalis quantitative value;
• (e) assigning a single BV score based on step (d);
• and
• (f) determining the presence or absence of BV in the subject based on a comparison of the BV score to a cutoff value.

A method for determining the presence or absence of Lactobacillus sp. in a sample, the method comprising:

• (1) contacting a sample, said sample suspected of containing Lactobacillus sp., with first, second, third, and fourth amplification oligomers for amplifying a target region of a Lactobacillus sp. target nucleic acid, wherein (i) the first amplification oligomer comprises a first target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 28-45 of SEQ ID NO:10;
• (ii) the amplification oligomer comprises a second target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:7;
• (iii) the third amplification oligomer comprises a third target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:8;
• and (iv) the fourth amplification oligomer comprises a fourth target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:9;
• (2) performing an in vitro nucleic acid amplification reaction, wherein any Lactobacillus sp. target nucleic acid, if present in the sample, is used as a template for generating one or more amplification products corresponding to the Lactobacillus sp. target region;
• and
• (3) detecting the presence or absence of the one or more amplification products, thereby determining the presence or absence of Lactobacillus sp. in the sample.

A method for determining the presence or absence of A. vaginae in a sample, the method comprising:

• (1) contacting a sample, said sample suspected of containing A. vaginae, with first and second amplification oligomers for amplifying a target region of a A. vaginae target nucleic acid, wherein (i) the first amplification oligomer comprises a first target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 28-45 of SEQ ID NO:18 and (ii) the second amplification oligomer comprises a second target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:17;
• (2) performing an in vitro nucleic acid amplification reaction, wherein any A. vaginae target nucleic acid, if present in the sample, is used as a template for generating one or more amplification products corresponding to the A. vaginae target region;
• and
• (3) detecting the presence or absence of the one or more amplification products, thereby determining the presence or absence of A. vaginae in the sample.

A method for determining the presence or absence of G. vaginalis in a sample, the method comprising:

• (1) contacting a sample, said sample suspected of containing G. vaginalis, with first and second amplification oligomers for amplifying a target region of a G. vaginalis target nucleic acid, wherein (i) the first amplification oligomer comprises a first target-hybridizing sequence substantially corresponding to the nucleotide sequence of residues 36-52 of SEQ ID NO:15 and (ii) the second amplification oligomer comprises a second target-hybridizing sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:14;
• (2) performing an in vitro nucleic acid amplification reaction, wherein any G. vaginalis target nucleic acid, if present in the sample, is used as a template for generating one or more amplification products corresponding to the G. vaginalis target region;
• and
• (3) detecting the presence or absence of the one or more amplification products, thereby determining the presence or absence of G. vaginalis in the sample.