US 12,291,753 B2
Compositions and methods for detecting bacterial nucleic acid and diagnosing bacterial vaginosis
Damon Kittredge Getman, Poway, CA (US); Angela Sebring Hudson, San Diego, CA (US); Jimmykim Pham, San Diego, CA (US); Xianqun Wang, San Diego, CA (US); and Caroline Clark, Oceanside, CA (US)
Assigned to Gen-Probe Incorporated, San Diego, CA (US)
Filed by Gen-Probe Incorporated, San Diego, CA (US)
Filed on Feb. 23, 2021, as Appl. No. 17/182,861.
Application 17/182,861 is a continuation of application No. PCT/US2019/047854, filed on Aug. 23, 2019.
Claims priority of provisional application 62/722,627, filed on Aug. 24, 2018.
Prior Publication US 2021/0198720 A1, Jul. 1, 2021
Int. Cl. C12Q 1/689 (2018.01)
CPC C12Q 1/689 (2013.01) [C12Q 2600/16 (2013.01)] 11 Claims
 
1. 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 a nucleic-acid-based detection assay for the detection of Lactobacillus sp., A. vaginae, and G. vaginalis in the sample, wherein the detection assay is an amplification-based assay comprising an in vitro nucleic acid amplification reaction, and wherein performing the detection assay comprises contacting the sample with
(i) first, second, third, and fourth Lactobacillus-specific amplification oligomers for amplifying a target region of a Lactobacillus sp. target nucleic acid, wherein each of the first, second, third, and fourth Lactobacillus-specific amplification oligomers comprises a target-hybridizing sequence for hybridizing to the target region of the Lactobacillus sp. target nucleic acid, wherein
the first Lactobacillus-specific amplification oligomer comprises a first target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO: 10, wherein the first Lactobacillus-specific amplification oligomers is a promoter primer or a promoter provider further comprising a promoter sequence located 5′ to the target-hybridizing sequence;
the second Lactobacillus-specific amplification oligomer comprises a second target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:7;
the third Lactobacillus-specific amplification oligomer comprises a third target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:8; and
the fourth Lactobacillus-specific amplification oligomer comprises a fourth target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:9;
(ii) first and a second A. vaginae-specific amplification oligomers for amplifying a target region of a A. vaginae target nucleic acid, wherein each of the first and second A. vaginae-specific amplification oligomers comprises a target-hybridizing sequence for hybridizing to the target region of the A. vaginae target nucleic acid; and
(iii) first and a second G. vaginalis-specific amplification oligomers for amplifying a target region of a G. vaginalis target nucleic acid, wherein each of the first and second G. vaginalis-specific amplification oligomers comprises a target-hybridizing sequence for hybridizing to the target region of the G. vaginalis target nucleic acid;
(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, wherein step (d) further comprises adding an internal control (IC) adjustment factor that compensates for sample inhibition of the detection assay, wherein the IC adjustment factor is based on a ratio of (i) an observed internal control (IC) value generated from the detection assay to (ii) an expected IC value for the detection assay;
(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.