Methods of diagnosing, treating, ameliorating, and / or preventing bacterial vaginosis (BV)

Abstract

Described herein is a method of predicting whether a bacterial vaginosis (BV) patient will respond to metronidazole treatment. The method comprises detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the patient. Also described herein is a method of treating, ameliorating, and / or preventing BV in a subject, which comprises administering to the subject an effective amount of metronidazole or an effective amount of clindamycin based on a prediction of whether the subject responds well to metronidazole treatment.

Description

[0001] METHODS OF DIAGNOSING, TREATING, AMELIORATING, AND / OR PREVENTING BACTERIAL VAGINOSIS (BV)

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] The present application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 63 / 652,375, filed May 28, 2024, which is incorporated herein by reference in its entirety.

[0004] STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

[0005] This invention was made with government support under DC01428 and DK082316 awarded by the National Institutes of Health. The government has certain rights in the invention.

[0006] SEQUENCE LISTING

[0007] The XML file named "046528-7141WOl_Seq Listing.xml" created on May 21, 2025, comprising 58.452 bytes, is hereby incorporated by reference in its entirety.

[0008] BACKGROUND

[0009] Bacterial vaginosis (BV) affects 20-50% of reproductive age women annually.

[0010] Affecting over 21.2 million individuals in the United States annually, individuals with BV experience discharge, dysuria, malodor, and itching, and are at an increased risk of postcesarean endometritis, urinary tract infections, and HIV acquisition. One proposed causative species of BV is Gardnerella vaginalis spp. (Gv), a rod-shaped. Gram-indeterminate, facultative anaerobe present in 90-97% of BV cases and in less than half of healthy vaginal microbiomes

[0011] Currently, the antibiotic metronidazole is used as the first-line antibiotic treatment for BV. However, many patients fail to respond to the first-line therapy, due to the presence of metronidazole-resistant Gv species and strains.

[0012] No current diagnostic exists for the discriminating between highly metronidazole- resistant species / clades of Gv and those that are treatable with metronidazole. Prescribers use Nugent scoring and Amsel Criteria to diagnose BV, but these are phenotypic assays that do not provide information as to the appropriate antibiotic for treatment. Thus, current prescribing decisions are based wholly on guesswork or failure of first-line antibiotics.

[0013] Therefore, there is a need for diagnostic methods that can identify antibiotics susceptibility of the causal agents in individual cases of BV, as well as method to treat, ameliorate, and / or prevent BV based on the identified antibiotics susceptibility in an individualized manner. The present invention addresses these needs.

[0014] SUMMARY

[0015] In some aspects, the present invention is directed to the following non-limiting embodiments:

[0016] Method of stratifying BV patient

[0017] In some aspects, the present invention is directed to a method of stratifying a bacterial vaginosis (BV) patient based on metronidazole-susceptibility or metronidazole-resistance.

[0018] In some embodiments, the method comprising detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH. Ami, Cluster 1311, comEA, crcB. group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA. or an mRNA product, a protein product, or a metabolite thereof, in a sample from the patient.

[0019] In some embodiments, the patient is stratified into the metronidazole-susceptible group when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0020] In some embodiments, the patient is stratified into the metronidazole-resistant group when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0021] In some embodiments, the metronidazole-resistant group is a clindamycin-susceptible group.

[0022] In some embodiments, the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0023] In some embodiments, the patient is stratified according to the presence or absence of the Gv aruH gene as detected by a PCR-based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6. In some embodiments, the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA.

[0024] Method of treating, ameliorating, and or preventing BV

[0025] In some aspects, the present invention is directed to a method of treating, ameliorating, and / or preventing bacterial vaginosis (BV) in a subject in need thereof.

[0026] In some embodiments, the method comprises detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the subject.

[0027] In some embodiments, the method further comprises determining a metronidazole- susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv gene, or the mRNA product, protein product, or metabolite thereof.

[0028] In some embodiments, the method further comprises administering to the subject an effective amount of metronidazole when the BV is determined to be metronidazole- susceptible.

[0029] In some embodiments, the method further comprises administering to the subject an effective amount of clindamycin when the BV is determined to be metronidazole-resistant.

[0030] In some embodiments, the BV is determined to be metronidazole-susceptible when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected in the sample.

[0031] In some embodiments, the BV is determined to be metronidazole-resistant when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0032] In some embodiments, the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0033] In some embodiments, metronidazole-susceptibility or metronidazole-resistance of the BV is determined according to the presence or absence of the Gv aruH gene, and wherein the presence or absence of the Gv aruH gene is detected by a PCR-based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0034] In some embodiments, the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA. Method of diagnosing a metronidazole-susceptible BV or a metronidazole-resistant

[0035] BV

[0036] In some aspects, the present invention is directed to a method of diagnosing a metronidazole-susceptible bacterial vaginosis (BV) or a metronidazole-resistant BV in a BV patient.

[0037] In some embodiments, the method comprises detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the BV patient.

[0038] In some embodiments, the method further comprises determining the metronidazole- susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv genes, or the mRNA product, protein product, or metabolite thereof, in the sample from the BV patient.

[0039] In some embodiments, the patient is diagnosed with metronidazole-susceptible BV when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0040] In some embodiments, the patient is diagnosed with metronidazole-resistant BV when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0041] In some embodiments, the metronidazole-resistant BV is a clindamycin-susceptible BV.

[0042] In some embodiments, the method further comprises performing a polymer chain reaction (PCR)-based method to determine the presence or absence of at least one of the Gv genes.

[0043] In some embodiments, the method further comprises performing a PCR-based method to detect the presence or absence of the Gv aruH gene with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4. and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0044] In some embodiments, the method further comprises collecting the sample from the subject.

[0045] In some embodiments, the method further comprises extracting a Gv DNA from the sample. BRIEF DESCRIPTION OF THE DRAWINGS

[0046] The following detailed description of exemplary embodiments will be better understood when read in conjunction with the appended drawings. For the purpose of illustrating, non-limiting embodiments are shown in the drawings. It should be understood, however, that the instant specification is not limited to the precise arrangements and instrumentalities of the embodiments shown in the drawings.

[0047] Figs. 1 A-1C demonstrate that comparative genomic techniques suggest eleven distinct genospecies of Gardnerella vaginalis spp, in accordance with some embodiments. Fig.

[0048] 1 A: ANI approximates genome similarity using BLAST. Each of the 129 total strains of G. vaginalis are represented on each axis in the same order, where the diagonal represents comparison to self, and off-diagonal represents comparison to a different strain. The range of ANI from least to greatest is 79.0% (w hite) to 99.9% (dark blue). Cluster diagrams were built using single-linkage hierarchical clustering. B Violin plot of ANI values for 129 strains of G. vaginalis (median: 86 ± 0.07%) and 25 strains each of four w ell-characterized species: Escherichia coli (99.7 ± 1.0%), Staphylococcus aureus (99.8 ± 0.5%), Pseudomonas aeruginosa (98.8 ± 2.1%), and Bacillus cereus (95.0 ± 2.4%). Density of data points at a given percentage is indicated by the width of the plot. Median value is indicated by a black diamond. C Distance matrix of G. vaginalis strains calculated from 1-ANI values and hierarchically clustered using the average linkage method. A cutoff w as drawn at 95% similarity (horizontal line) and the number of genospecies counted. Eleven genospecies were observed using this cutoff value. Comparison to genospecies seen in phylogeny is displayed in colored boxes and labeled with clade numbers from the phylogenetic tree in Fig. 2. See also Tables 3-6.

[0049] Fig. 2 illustrates a concatenated core-genome maximum likelihood tree displaying the presence of eleven genetically distinct genospecies. in accordance with some embodiments. The pangenome for 129 strains of CT. vaginalis was calculated and 431 core genes were aligned with PRANK to create a phylogenetic tree with RAxML. Eleven individual genospecies (GS) are highlighted by color and marked with the range of GC content percentages within each. Singleton strains (genospecies 3 and 9) are included with the nearest genospecies with 5 or more strains and marked with a different shaded box. Genospecies designated as individual species by Vaneechoutte et al. Int J Syst Evol Microbiol. 2019;69(3):679-87) and Sousa et al. (Int J Sy st Evol Microbiol. 2023;73) are indicated by colored rings and labeled with their proposed species names. See also Tables 3-4.

[0050] Fig. 3 demonstrates that core genome percentage is more reflective of a single species after GV is separated into individual genospecies. The count of core genes (orange bar) of all 129 GV strains is less than half of the proportion of the independently calculated genospecies' pangenomes. See also Fig. 7.

[0051] Figs. 4A-4C demonstrate that GV genospecies display two major phenotypic responses to metronidazole, in accordance with some embodiments. Fig. 4A: Representative images of MIC assays. Each metronidazole MIC strip contains fifteen twofold dilution concentrations. An ellipse of inhibition forms at the minimum concentration of metronidazole required to stop GV growth. Left: Resistant strain with MIC > 256 pg / mL. Middle: Resistant strain with MIC of 64 pg / mL. Right: Susceptible strain with MIC of 8 pg / mL. Fig.

[0052] 4B: Concatenated core gene tree labeled with MIC data indicate the existence of genospecies correlated with antibiotic resistance. Results of MIC analyses were plotted against the tree. At least one strain from each genospecies reported a result except for genospecies 8. On the right. MIC data are shown for each tested strain. A color legend is available at the top left. Length of MIC bar corresponds with MIC value. Color corresponds to CLSI classification. Fig. 4C: Alignment of syntenic regions identified in the metronidazole- resistant partner of three resistant / susceptible strain pairings within the mixed-response genospecies. Colored arrows represent each of the genes with one of five KEGG-annotated functions (see legend). Arrow direction corresponds with coding strand. See also Table 7.

[0053] Fig. 5 demonstrate that selected metronidazole-resistant strains are susceptible to clindamycin, in accordance with some embodiments. Sixty-three strains from various genospecies were subjected to antibiotic susceptibility testing with clindamycin MIC strips. A bar plot is superimposed above the gradient of measurable MIC values, indicating the number of strains with each measured MIC. The clinical sensitivity breakpoint as determined by CLSI for clindamycin is marked with an arrow" (2.0 pg / mL). A representative image is shown at right, demonstrating the ellipse of inhibition observed for a clindamycin-susceptible strain with an MIC of 0.125 pg / mL. See also Table 7.

[0054] Fig. 6 demonstrates that aruH primers specifically amplify strains in metronidazole- resistant genospecies, in accordance with some embodiments. A set of tw o forward and two reverse primers for aruH. encompassing the range of diversity seen in this gene among the various GV species, successfully discriminated between selected clinical isolates within the metronidazole-mixed response genospecies la, 2, 3, 4a, and 4b and the entirely metronidazole-resistant genospecies (5-11). Successful amplification coincided with membership in the highly metronidazole-resistant genospecies (5-11), with the exception of strain B648 (BS610), a resistant strain and the only member of genospecies 9. See also Table 2, Table 8 and Fig. 8.

[0055] Fig. 7 demonstrates that a plateau from 40% - 60% BlastP identity' indicates the minimal rate of changes in gene cluster membership after core cluster count begins to drop. The gene clustering program Roary attempts to split gene clusters if the genes are identified as paralogous. Core gene cluster counts split according to Roary’s criteria for paralogous genes (where gene clusters are not collapsed with paralogous clusters) are blue, and core gene cluster counts where paralogous gene clusters are combined are in red.

[0056] Fig. 8 demonstrates that gradient PCR with strain BS615 and aruH primers to determine optimal annealing temperature, visualized on 2% agarose gel. Temperatures (°C) (L to R): 54.8, 55.9, 57.4, 58.9, 60.2, 61.7, 63.1, 64.3.

[0057] DETAILED DESCRIPTION

[0058] The following disclosure provides many different embodiments, or examples, for implementing different features of the provided subject matter. Specific examples of components and arrangements are described below to simplify the present disclosure. These are, of course, merely examples and are not intended to be limiting. For example, the formation of a first feature over or on a second feature in the description that follows may include embodiments in which the first and second features are formed in direct contact, and may also include embodiments in which additional features may be formed between the first and second features, such that the first and second features may not be in direct contact. In addition, the present disclosure may repeat reference numerals and / or letters in the various examples. This repetition is for the purpose of simplicity and clarity and does not in itself dictate a relationship between the various embodiments and / or configurations discussed.

[0059] In the study described herein, a molecular diagnostic was created. The molecular diagnostic is based on identification of PCR primers for the gene aruH which discriminates between different species of Gardnerella vaginalis spp- the principal etiologic agents of bacterial vaginosis (BV) which affects 21.2 million women annually in the USA. Nearly 50% of Gv strains are resistant to metronidazole, the first-line antibiotic for BV. The present study uncovered significant metronidazole resistance as a core phenotype of seven species within this genus, and confirmed that each metronidazole-resistant strain is also highly susceptible to clindamycin, a secondary' antibiotic used to treat BV. The diagnostic PCR primers designed and synthesized support amplifications that positively identifies six of the seven highly metronidazole-resistant and clindamycin-susceptible species and does not amplify any of the species that have low-level or no resistance to antibiotic responses to metronidazole. The single undetectable Gv species contains only a single strain that is phylogenetically distant from all other Gv strains. The creation of this PCR assay will lead to personalized therapies for individuals with BV. allowing for rapid diagnosis of the correct species and providing for prescribing the appropriate antibiotic for treatment of the disease.

[0060] In the present study, the diagnostic has further been tested on 27 clinical isolates spanning ten Gv species / clades. It has been optimized for PCR on limited (—10 ng / uL) concentrations of purified Gv DNA. It has a 96% accuracy rate for detection of highly resistant species, and a 100% accuracy rate for discrimination against strains that display limited or no resistance to metronidazole

[0061] Definitions

[0062] As used herein, each of the following terms has the meaning associated with it in this section. Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary' skill in the art to which this disclosure belongs. Generally, the nomenclature used herein and the laboratory procedures in animal pharmacology, pharmaceutical science, peptide chemistry’, and organic chemistry are those well-known and commonly employed in the art. It should be understood that the order of steps or order for performing certain actions is immaterial, so long as the present teachings remain operable. Any use of section headings is intended to aid reading of the document and is not to be interpreted as limiting; information that is relevant to a section heading may occur within or outside of that particular section. All publications, patents, and patent documents referred to in this document are incorporated by reference herein in their entirety, as though individually incorporated by reference.

[0063] In the application, where an element or component is said to be included in and / or selected from a list of recited elements or components, it should be understood that the element or component can be any one of the recited elements or components and can be selected from a group consisting of two or more of the recited elements or components.

[0064] In the methods described herein, the acts can be carried out in any order, except when a temporal or operational sequence is explicitly recited. Furthermore, specified acts can be carried out concurrently unless explicit claim language recites that they be carried out separately. For example, a claimed act of doing X and a claimed act of doing Y can be conducted simultaneously within a single operation, and the resulting process will fall within the literal scope of the claimed process.

[0065] In this document, the terms "a," "an," or "the" are used to include one or more than one unless the context clearly dictates otherwise. The term "or" is used to refer to a nonexclusive "or" unless otherwise indicated. The statement "at least one of A and B" or "at least one of A or B" has the same meaning as "A, B, or A and B."

[0066] "About" as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, in certain embodiments ±5%. in certain embodiments ±1%, in certain embodiments ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

[0067] Methods of Stratifying Bacterial Vaginosis (BV) Patients and / or Methods of Diagnosis

[0068] In some aspects, the present invention is directed to a method of stratifying a bacterial vaginosis (BV) patient.

[0069] In some embodiments, the BV patient is stratified based on metronidazole- susceptibility or metronidazole-resistance.

[0070] In some embodiments, the method comprises detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH. Ami, Cluster 1311. comEA, crcB, group 2326. group 2343, group 2558. group 2577. ssb. truB, yfeA,ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the patient.

[0071] It has been discovered that what is currently referred to as Gardnerella vaginalis is not a single species, but rather a genus composed of several distinct clades each with its own characteristic genome size, core genome, and GC content. Accordingly, in some embodiments, the terms “Gardnerella vaginalis f “G. vaginalis f or ‘’Gv” as used herein include one or more Gv genospecies. Such genospecies include, for example, G. piotii, G. swidsinskii, G. leopoldii. G. pickettii and G. greenwoodii, among others.

[0072] In some embodiments, the patient is stratified into the metronidazole-susceptible group when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0073] In some embodiments, the patient is stratified into the metronidazole-resistant group when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected. The present study discovered that Gv genospecies that are resistant to metronidazole are also susceptible to clindamycin. Accordingly, in some embodiments, the metronidazole- resistant group is a clindamycin-susceptible group.

[0074] In some embodiments, the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0075] In some embodiments, the Gv gene is aruH. and the PCR-based method uses at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0076] In some embodiments, the sample is a vaginal swab sample, optionally a vaginal swab sample extracted for a Gv DNA.

[0077] In some aspects, the present invention is directed to a method of diagnosing a metronidazole-susceptible bacterial vaginosis (BV) or a metronidazole-resistant BV in a BV patient. In some embodiments, the method comprises detecting a presence or absence the Gv genes, or the mRNA product, a protein product, or a metabolite thereof described herein, in a sample (such as vaginal sample), according to the steps of the stratifying methods herein.

[0078] Methods of Treating, Ameliorating, and / or Preventing Bacterial Vaginosis (BV)

[0079] In some embodiments, the instant specification is directed to a method of treating, ameliorating, and / or preventing BV in a subject in need thereof.

[0080] In some embodiments, the method comprises detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the subject.

[0081] In some embodiments, the method further comprises determining a metronidazole- susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv gene, or the mRNA product, protein product, or metabolite thereof.

[0082] In some embodiments, the method further comprises administering to the subject an effective amount of metronidazole when the BV is determined to be metronidazole- susceptible.

[0083] In some embodiments, the method further comprises administering to the subject an effective amount of clindamycin when the BV is determined to be metronidazole-resistant. In some embodiments, the BV is determined to be metronidazole-susceptible when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected in the sample.

[0084] In some embodiments, the BV is determined to be metronidazole-resistant when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0085] In some embodiments, the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0086] In some embodiments, the Gv gene is aruH. and the PCR-based method uses at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0087] In some embodiments, the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA.

[0088] Examples

[0089] The instant specification further describes in detail by reference to the following experimental examples. These examples are provided for purposes of illustration only, and are not intended to be limiting unless so specified. Thus, the instant specification should in no way be construed as being limited to the following examples, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

[0090] Example 1: Metronidazole response profiles of Gardnerella species are congruent with phylogenetic and comparative genomic analyses

[0091] Bacterial vaginosis (BV) affects 20-50% of reproductive-age female patients annually, arising when opportunistic pathogens outcompete healthy vaginal flora. Many patients fail to resolve symptoms w ith a course of metronidazole, the current first-line treatment for BV. Our study was designed to identify genomic variation associated with metronidazole resistance among strains of Gardnerella vaginalis spp. (GV), a genus of biogenic-amine-producing bacteria closely associated with BV pathogenesis, for the development of a companion molecular diagnostic.

[0092] Whole-genome sequencing and comparative genomic metrics, including average nucleotide identity and GC content, were performed on a diverse set of 129 GV genomes to generate data for detailed taxonomic analyses. Pangenomic analyses were employed to construct a phylogenetic tree and cluster highly related strains within genospecies. G. vaginalis spp. clinical isolates within the collection were subjected to plate-based minimum inhibitory concentration (MIC) testing of metronidazole (n = 60) and clindamycin (n = 63). DECIPHER and MAFFT were used to identify genospecies-specific primers associated with antibiotic-resistance phenotypes. PCR-based analyses with these primers were used to confirm their specificity for the relevant genospecies.

[0093] Eleven distinct genospecies based on standard ANI criteria were identified among the GV strains in the collection. Metronidazole MIC testing revealed six genospecies within a closely related phylogenetic clade contained only highly metronidazole-resistant strains (MIC > 32 pg / mL) and suggested at least two mechanisms of metronidazole resistance within the eleven GV genospecies. All strains within the six highly metronidazole-resistant genospecies displayed susceptibility to clinically relevant clindamycin concentrations (MIC < 2 pg / mL). A PCR-based molecular diagnostic assay was developed to distinguish between members of the metronidazole-resistant and mixed-response genospecies, which should be useful for determining the clade membership of various GV strains and could assist in the selection of appropriate antibiotic therapies for BV cases.

[0094] This study provides comparative genomic and phylogenetic evidence for eleven distinct genospecies within the genus Gardnerella vaginalis spp., and identifies genospecies- specific responses to metronidazole, the first-line treatment for BV. A companion molecular diagnostic assay was developed that is capable of identifying essentially all highly metronidazole-resistant strains that phylogenetically cluster together within the GV genospecies, which is informative for antibiotic treatment options.

[0095] Example 2:

[0096] Bacterial vaginosis (BV) is a commonly occurring microbial dysbiosis of the lower female genital tract arising when opportunistic pathogens outcompete healthy vaginal flora. Affecting over 21.2 million individuals in the USA annually, patients with BV experience discharge, dysuria, malodor, and itching and are at an increased risk of post-cesarean endometritis, urinary tract infections, and HIV acquisition. The Centers for Disease Control recommends topical or oral metronidazole, a nitroimidazole antibiotic, as the most common treatment for BV, followed by topical clindamycin. Tinidazole and secnidazole are recommended as alternative regimens. Antibiotic use resolves approximately 70-80% of BV cases, but yearly recurrences range from 50 to 70%. The composition of human vaginal microbiomes in individuals of reproductive age are predominantly characterized by acid-producing bacteria such as members of the Lactobacillus and Limosilactobacillus genera or mixed anaerobe communities. The major species of healthy vaginal microbiomes produce hydrogen peroxide, lactic acid, and bacteriocins that reduce vaginal pH, promote their own growth, and inhibit the growth of pathogens. Menstruation, pregnancy, and sexual intercourse can reduce the abundance of commensal microbes, which increases the pH and facilitates the growth of pathogens that produce biogenic amines such as putrescine, cadaverine, and trimethylamine. This further increases the vaginal pH and produces the malodorous symptoms of BV. One proposed causative species of BV is Gardnerella vaginalis spp. (GV), a rod-shaped, Gram- indeterminate, facultative anaerobe present in 90-97% of BV cases and in less than half of healthy vaginal microbiomes. The GV genome also encodes several virulence factors for biofilm formation, nutrient scavenging, and biogenic amine production, providing a survival advantage in the acidic vaginal niche.

[0097] G. vaginalis spp. has been a species in taxonomic flux since its discovery in 1953. Initially characterized as Haemophilus vaginalis in 1955. it was recharacterized as Corynebacterium vaginalis then renamed again as Gardnerella vagincdis. Early typing efforts identified a series of biotypes and genotypes that distinguished among subtypes of the “species.” GV is not a single species, but rather a genus composed of at least four distinct clades each with its own characteristic genome size, core genome, and GC content. This was followed by the development of qPCR primers that could differentiate with high confidence between the four clades, and correlation of cpn60 subtypes with each clade. Shortly after, metronidazole resistance (MIC > 32 pg / mL) was determined to vary among clades; strains contained within clades 1 and 2 reported irregular metronidazole response profiles (clade 1 = 35% resistant, clade 2 = 7. 1% resistant), whereas all strains within clades 3 and 4 were fully resistant to this first-line antibiotic.

[0098] Additional comparative genomic analyses such as average nucleotide identity (ANI) and digital DNA-DNA hybridization on larger GV datasets led to the discovery of nine to thirteen component “genomospecies” or “genospecies,” providing an amended species definition and new species names for three of the well-defined species (G. piotii. G. swidsinskii, and G. leopoldii). Since that time, additional studies have confirmed this diversity by analyzing genotypes of virulence factors or through evidence of lateral gene transfer, and a recent study has announced two additional named genospecies, G. pickettii and G. grcenwoodii. highlighting a need for additional genus-level analyses. Comparative bacterial genomic methodologies were originally developed to test the distributed genome hypothesis, in which it was posited that each bacterial strain within a species possesses a unique complement of non-core (distributed / accessory) genes. The results of these studies defined the bacterial species-level supragenome / pan-genome and ushered in a new era in phylogenetically supported taxonomy. The underlying technologies were then extended to study genus and family-level pangenomes. The clinical fruits of these advances enabled gene-based diagnostics and therapeutics for infectious diseases.

[0099] The association of bacterial gene presence or absence with clinical metadata can answer many questions regarding tropism, virulence, and antibiotic resistance. Should analysis of a species reveal that a distributed gene is ‘‘core’' to a clinically distinct group of strains, that gene can serve as a biomarker to inform a patient’s treatment. The present study aimed to improve the clade-level resolution of strains into genospecies within GV using comparative genomics to discriminate between highly metronidazole-resistant and mixed- metronidazole response genospecies.

[0100] Example 3: Methods

[0101] Bacterial strains and growth conditions

[0102] All 129 strains of Gardnerella vaginalis spp. used in this project are listed in Tables 3-4 and 7. Strains were streaked from glycerol stock onto 12-h pre-reduced A80 selective plates (Hardy Diagnostics. Santa Maria. CA, USA) and grown under anaerobic conditions (37 °C, anaerobic mixed gas canister [5.5% H2, 10% CO2, N2] + N2 canister) in an anaerobic chamber (BugBox, Baker Ruskinn, Sanford ME USA) for 3-10 days. Liquid cultures were cultivated in Bacto BHI (BD Biosciences, San Jose, CA, USA) or Casman Broth (HiMedia, Kennett Square, PA, USA) supplemented with 10% horse serum (Boston BioProducts. Ashland, MA, USA) and grown under anaerobic conditions.

[0103] Genome acquisition

[0104] Genomes analyzed in this project were acquired from several different sources. Clinical isolates (n = 57) were acquired from the biorepository of one of us (SLH) at the University of Pittsburgh and Magee-Women’s Research Institute in Pittsburgh, PA, USA. Vaginal, endometrial, and placental samples were collected from symptomatic and asymptomatic females with known pregnancy status, and rectal samples were collected from males (Table 4). The bacterial isolates w ere obtained from individuals enrolled in nine different clinical trials or observational cohort studies. All participants provided written informed consent prior to the collection of their samples and provided future use consent for use of their samples or sample remnants. Samples in this biorepository are deidentified and cannot be linked with patient identifiers.

[0105] High-quality genomes (n = 59) were downloaded from NCBI in addition to 13 strains originally described by Ahmed et al. (J Bacterial. 2012;194:3922-37), for a total of 129 strains included in this study. Accession numbers and additional metadata for each downloaded strain, including non-published direct submissions to NCBI. can be found in Table 3. Taxator-tk (vl.2), performed on all strains, was used to exclude genome sequences that were not considered G. vaginalis from further analysis (Schuyler et al., Genome Announc. 2015;3: e00992-15).

[0106] Isolation of DNA

[0107] Strain DNA was isolated using the “Purification of Total DNA from Animal Tissues Spin-Column Protocol” from the DNeasy Blood and Tissue Kit (Qiagen, Venlo, NED) after pretreatment for Gram-positive bacteria in enzymatic lysis buffer (20 mM Tris-Cl. pH 8.0; 2 mM sodium EDTA; 1.2% Triton X-100; lysozyme at 20 mg / mL directly before use). DNA quality was confirmed by NanoDrop (ThermoFisher, Waltham, MA USA). Genomic DNA w as visualized via gel electrophoresis run at 180 V on a 1% agarose gel stained with ethidium bromide.

[0108] WGS assembly

[0109] Genomes generated using Roche / 454 Life Sciences GS FLX Titanium sequencing technology (n = 20) were prepared, assembled, and annotated. Briefly , individual fragment libraries (optimized to produce between 300 and 400 base pair average read length) were created from each strain. Preparation and pyrosequencing were performed as described in GS FLX Titanium emPCR and Sequencing Protocols (October 2008). The raw sequence reads for each strain were assembled into contigs using a Roche / 454 Life Sciences GS de novo Newbler assembler (version 2.0.00.20 or 2.0.01.14) and the default parameters except for minimum overlap identity, which was adjusted to obtain the fewest contigs. Raw sequence reads were assembled into contigs with the software Newbler (version > = 2.0.00.20). These strains were spread across the tree and did not make up any one genospecies in its entirety, indicating that 454 sequencing artifacts are not responsible for the genomic variation seen between the genospecies. The remaining strains (n = 37) were sequenced as paired end runs at 2 x 150nt on an Illumina NextSeq500. Individual libraries were created with Nextera XT and multiplexed to target 100-300 x coverage per sample (raw nucleotide sequence / predicted genome size). Illumina reads were assembled using a custom pipeline. Briefly, reads were trimmed using Trimmomatic v0.30, overlapped when possible using COPE vl. 1.2, error corrected with ALL-PATHS-LG, and assembled with Ray v2.2.0.

[0110] Pan-genome analysis

[0111] Annotation and pan-genome analyses were carried out as described in Hogg et al. (Genome Biol. 2007;8: R103), Boissy et al. (BMC Genomics. 2011 :12: 187) and Moleres et al. (MBio. 2018;9:e01176-218). In short, all 129 assemblies (both novel and downloaded from NCBI) were annotated with Prokka vl . 11. Homologous genes were clustered with Roary v3.5. 1. The threshold used for gene clustering of homologs was set at 60% BlastP identity. The present study examined a range of identity thresholds (at 5% increments) and 60% was determined to be the lowest threshold at which changing the threshold resulted in only a small change in the clustering (See Fig. 7).

[0112] Phylogenetic analysis

[0113] ANI was calculated for all strain pairs with pyani v0.2 using the ANIb method.

[0114] Twenty-five genomes of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus cereus were downloaded from RefSeq and run with ANIb methods for comparison. All analyses were performed using R Statistical software (v3.6.3). Data visualizations were performed with the ggplot2 package (v3.3.0). Self-comparisons were removed with the harrietr package (vO.2.4), then 1-ANI values were converted to a distance matrix and clustered with single linkage. Core genes were aligned with PRANK (v. 140603) and the resulting alignments were concatenated. The phylogenetic tree was constructed from this core gene alignment with RAxML (v8.2.4) and visualized using the ggtree package (v3.4.4).

[0115] Synteny investigation

[0116] Genes of interest were aligned in Mauve (snapshot v. 20,150.226). Genes were analyzed with BlastKOALA via the online KEGG platform and potential homology was studied via BLAST. Results were visualized in R using the gggenes (v0.5. 1) package.

[0117] Antibiotic susceptibility tests and MIC determination Strains from the clinical isolate collection and those included from the Ahmed et al. (J Bacterial. 2012;194:3922-37) were revived from - 80 °C glycerol stocks on A80 plates and re-plated once. Colonies were scraped and suspended in Casman broth; 200 pL of suspension was streaked in duplicate or triplicate on pre-reduced A80 plates. Metronidazole or clindamycin MIC strips (0.016-256 ng / pL, Liofdchem, Waltham, MA, USA) were added to plate centers and incubated under anaerobic conditions. MICs were recorded where the nogrowth ellipse intersected the MIC strip on day 3 for clindamycin and day 10 for metronidazole, in accordance with reported clinical treatment practices (Faught et al., J Womens Health (Larchmt). 2019;28: 1218-26; Ahmed- Jushuf et al., B V Investigators Group Genitourin Med. 1995:71 :254-6). The median of triplicate readings was reported as the MIC; in duplicate readings, the higher number was reported. Metronidazole and clindamycin breakpoints were used as recommended by CLSI (Metronidazole: R (resistant) > 32 pg / mL, I (intermediate) = 16 pg / mL, S (sensitive) < 8 pg / mL; Clindamycin: R> 8 pg / rnL, 1 = 4 pg / mL, S <2 pg / mL).

[0118] Scoary analysis

[0119] Scoary v 1.6.16 was provided with a gene presence-absence table from Roary, a discrete trait file with susceptible and resistant phenotypes, and the concatenated core gene tree (see ‘‘Phylogenetic analysis'’). Results were subjected to Bonferroni and Benjamini- Hochberg multiple testing correction procedures, candidates were ranked by worstcase p values for different potential evolutionary histories, and the remaining significant genes were selected for analysis.

[0120] Identification of candidate genes

[0121] A gene presence-absence table was constructed by Roary (see “Phylogenetic analysis”). Genes present in every strain of highly metronidazole-resistant genospecies and absent in every strain of mixed-susceptibility genospecies w ere considered primer set candidates.

[0122] Primer set development

[0123] FASTA files for candidate genes were aligned with MAFFT v7, utilizing G-INS-1 and default parameters. Alignments were then provided to the DECIPHER “Design Primers” tool. Genes requiring fewer than 4 distinct F and R primers were selected for oligo synthesis (IDT. Coralville, Iowa USA). Degenerate bases were incorporated if necessary. In silico PCR using USEARCH compared primers against genomic datasets.

[0124] Clade-specific PCR

[0125] Amplifications were performed as 25 pL reaction mixtures containing 10 pL genomic DNA. Reactions were prepared according to the specifications for GoTaq DNA Polymerase (Promega, Madison, WI. USA). Final concentrations of IX reaction buffer. 10 mM dNTP (Promega, Madison, WI, USA), 1.0 pM forward and reverse primers, and 1.25 u polymerase were used. PCR was performed in a Mastercycler X50 Thermocycler (Eppendorf, Hamburg, DE). Cycling parameters began with a 2-min denaturation at 95 °C. followed by 35 cycles of 15 s denaturation at 95 °C. 15-s annealing at 55 °C, and 30-s elongation at 72 °C. A final extension for 7 min was performed at 72 °C, followed by a hold at 4 °C. Annealing temperatures for primers were identified by gradient PCR (See Fig. 8). PCR products were visualized on 2% agarose gels stained with ethidium bromide.

[0126] Example 4: Phylogenetics and comparative genomics suggest eleven distinct genospecies of Gardnerella vaginalis spp.

[0127] Prior research into the genomic and phylogenetic structure of G. vaginalis spp. isolates revealed a minimum of four clades within the taxa, a discovery supported by: > 0.5% differences in GC content; changes in the estimated core genome size from 27 to 91% when calculated within or among clades; sequence length variations ranging from 1.491 to 1.717 MB, and the observation that horizontal gene transfer (HGT) was frequently seen within, but not among the four clades.

[0128] The present study sequenced 57 additional genetically diverse clinical isolates of G. vaginalis spp, 36 of which were selected after prescreening a set of 50 strains by PCR for unique combinations of distributed genes from the four original clades and combined them with 72 previously characterized genomes to assemble a 129-strain pangenome that likely contains the majority of the clade (genospecies) structure within the GV genus (Tables 4-6).

[0129] To determine nucleotide diversity among the GV genomes and estimate the number of distinct genospecies present in the pangenome, the present study calculated the difference in Average Nucleotide Identity (ANI) among all possible strain pairs (n = 16,641), using the ANIb (BLASTN +) method (Fig. 1A). ANIb calculates pairwise comparisons among all strains in a set using BLAST, and values of 95% or greater are considered indicative of a single genospecies. After removal of self-comparisons, the median ANIb value among all strains was 84.1%. The two most genetically similar strains, GV_75712 and B473, had an ANIb value of 99.9%, while the two least similar strains (GED7760B and BS611) possessed an ANIb value of 79.0%. A comparison of the median ANI value to a 25-strain subset of several well-characterized bacterial species indicates that the median ANIb value for all GV strains is far outside the range for a single species (Fig. IB). The presence of larger blocks of deep blue are indicative of strains pairs with highly similar ANI values, such as those in the top right encompassing strains GV 101, B719, UMB1686, and B512, or the grouping of 53 strains in the bottom left. The present study suggests that these blocks of highly genomically similar strains belong to distinct phylogenetic clades or genospecies (Fig. 1 A). The ANI data were visualized as a dendrogram and compared to a phylogenetic tree composed of concatenated core genes from all 129 GV strains in the analysis set (Fig. 1C). A cutoff of 5% ANI difference was applied to the dendrogram, in line with the Konstantinidis ANI species definition. Strains were considered to belong to different clades if a vertical branch connecting them crossed that threshold. This method identified eleven distinct genospecies.

[0130] A phylogenetic tree was constructed from alignments of 431 genes determined to be core (as defined below) to the GV genus (Fig. 2). The majority of isolates formed three major genospecies with two sub-species each, all six of which would be classified as individual species based on both the differences in their ANI values (< 95%) and the differences in their % GC content values (> 0.5%). Two of the observed “major” genospecies can be split into component subspecies and the present study presented evidence for the renaming of each. Specifically, genospecies 4 is divided into 4a (G. pickettii) and 4b (G. piotii), and genospecies 7 is divided into 7a (G. swidsinskii), and 7b (G. leopoldii) (Vaneechoutte et al., Int J Syst Evol Microbiol. 2019; 69(3): 679-87: Sousa et al., Int J Syst Evol Microbiol. 2023;73). Genospecies la remains the amended definition of G. vaginalis, but further testing will be required to determine if genospecies lb is included within G. vaginalis or if renaming is required. Notably, if ANI is set at 94%, 8 total groupings are seen, and if the ANI threshold is set to 96%, the total number of groups rises to 16. This indicates that defining an exact number of species in the genus is complicated by high sensitivity to the specific ANI threshold. The exact number notwithstanding, this analysis demonstrates a minimum of eight separate genospecies within GV.

[0131] Example 5: The core genome percentage is more representative of a species when GV is subset into individual genospecies Further support for splitting GV into multiple genospecies was provided by examining how core genome membership changed when pangenomes of individual genospecies were calculated. The pangenome of GV in its entirety contained 3324 genes but only 615 genes were identified as core, comprising - 18% of the total gene content. A review of 295 bacterial species pangenome analyses revealed that the median core gene percentage for a pangenome calculated on at least 25 strains is 39 ± 21%. of which the core genome of GV is a full standard deviation below. However, when individual genospecies pangenomes were recalculated for the three largest GV genospecies (1 a / b, 4a / b, and 7a / b), the core genome of each genospecies increased, ranging in size from 44-51% (Fig. 3). These data further support the claim that GV is comprised of distinct groups of organisms that should be assigned to different species.

[0132] Example 6: Metronidazole resistance is predominantly associated with distinct genospecies

[0133] Antibiotic susceptibility tests (AST) were performed on clinical isolates from ten of the eleven identified genospecies to determine quantitative levels of metronidazole susceptibility in GV clinical isolates (Table 7). Strains from genospecies 8 could not be acquired for this experiment. The minimum inhibitory concentration (MIC) of these strains to metronidazole was measured with test strips containing a gradient of 15 two-fold dilutions (0.016-256 pg / mL). Resistance to metronidazole was determined by breakpoints set by the Clinical & Laboratory Standards Institute (CLSI)- Resistance: MIC > 32 pg / mL; Intermediate (antibiotic response depends on the dose given and the site of infection): MIC between 8 and 32 pg / mL; Sensitivity (or susceptibility): MIC < 8 pg / mL (Fig. 4A). 49 / 60 (82%) of tested strains were classified as metronidazole resistant, and the remaining 11 / 60 strains (18%) were determined to be metronidazole intermediate or sensitive.

[0134] The present study superimposed the metronidazole MIC data onto the core-gene phylogenetic tree (Fig. 4B). Several genospecies are highly enriched for metronidazole resistance. All strains tested in genospecies 7a / 7b. 9, 10, and 11 were highly resistant to metronidazole (22 of 22 strains (100%). MIC range 128-256 pg / mL. median MIC > 256 pg / mL), with 95% of strains reporting an MIC > 256 pg / mL (See Fig. 5). Conversely, genospecies l(a / b) reported mixed MIC responses (range 8-256 pg / mL). Forty7percent of strains in genospecies 1 were classified as sensitive or intermediate responses (8- 24 pg / mL). Full resistance was generally observed to split into two “classes”, which are label low (32-64 pg / mL, 36% of strains) or high (96-256 pg / mL, 24% of strains) resistance responses. Genospecies 1 reported a median MIC of 32 pg / mL. which is strikingly different from the median MIC observed in genospecies 7. Genospecies 4(a / b) also displayed varied metronidazole responses, reporting a median MIC (48 pg / mL) dramatically lower than genospecies 7(a / b) but higher than genospecies 1 (Table 1). The marked differences in resistance response in different genospecies could suggest differences in the mechanisms through which metronidazole resistance is conferred.

[0135] Examination of the phylogenetic tree (Fig. 4B) reveals genospecies 1-4 are primarily composed of metronidazole-intermediate or low-resistance strains. Using Scoary, one gene / operon was found to be significantly (negatively / positively) associated with resistance by Fisher’s exact test but this may have been a spurious association due to population structure (data not shown). However, the present study examined the existence of three intermediate response strains in these genospecies with a metronidazole high-resistance closest neighbor. The gene cluster presence of these three strain pairs: B659 / B482MASH (G. pickettii), BS620 / BS657 (G. vaginalis), and B477 / BS494 (GV genospecies lb) were examined to identify any genes that were exclusive only to the metronidazole intermediate strains or the high-resistant ones. Across all three strain pairs, no gene clusters were found to be exclusive to the intermediate strains that were also not present in the high-resistant genomes. However, eleven genes were identified in all three high-resistant strains that were not present in their intermediate-response neighbors. Alignment of the genes present in these strains (Fig. 4C) revealed that the eleven genes were in a syntenic region. A high degree of similarity’ in the flanking regions was found in the corresponding intermediate-response strain pairs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these genes identified a putative DNA primase / helicase, putative transcriptional regulator, macrolide transport system ATP-binding / permease protein, and an MFS transporter — DHA3 family macrolide efflux protein. Five genes reported no assigned function. Interestingly, the MFS transporter is further defined as a drug transporter and an important antimicrobial resistance gene (KEGG identifier KO8217). The presence of this individual gene is not sufficient to convey metronidazole resistance as three additional strains in genospecies 1 (B661, BS613, and BS668) with intermediate metronidazole response were found to also contain members of this gene cluster, nor is it necessary for metronidazole resistance as it was missing in at least some resistant strains (e.g. BS641). This data also suggests that there may be multiple pathways to metronidazole resistance, and acquisition of this individual gene is not enough to become resistant to metronidazole. Example 7: Metronidazole-resistant strains are susceptible to clindamycin

[0136] The present study next asked whether GV isolates were susceptible to alternative antibiotics used for BV treatment. The present study plated 25 strains from genospecies 5-11, and 38 strains from genospecies 1-4. All 63 strains (100%) showed high sensitivity to clindamycin (CLSI MIC sensitivity7breakpoint < 2 pg / mL) with MICs ranging from 0.016- 0.5 pg / mL and a median MIC of 0.125 pg / mL. Clindamycin treatment was equally effective on strains from genospecies 1-4 and genospecies 5-11 (Fig. 5).

[0137] Example 8: Presence of the aruH gene is diagnostic to genospecies displaying high metronidazole resistance

[0138] The presence of two strikingly different metronidazole response phenotypes, delineated by genospecies, provided the impetus to develop a molecular diagnostic to identify strains within the metronidazole high resistance genospecies. Fourteen genes identified as “core” (present and confirmed via BLAST and Roary in every7strain) to the entirety7of genospecies 5-11 that were absent from the mixed-resistance genospecies (genospecies 1-4) were selected for the creation of diagnostic primers using DECIPHER, an online toolkit which designs primers based on multiple sequence alignments (Table 8). Primers were designed for five genes (yfeA, LysM, aruH, bioY, and comEA), and three hypothetical proteins (group_2343, group_2326. and group_1951) (See Table 2). Names or functions of each named gene were confirmed by blastx. Successful universal PCR amplification among the highly resistant isolates was accomplished with primers for the aruH gens, which catalyzes the transamination of L-arginine and pyruvate into ketoarginine and L- alanine. AruH amplification was observed in all strains tested in genospecies 5. 6, 7a (G. swidsinskii) , 7b (G. leopoldii), 10, and 11 (Fig. 6). Two bands were observed in most amplified strains, likely due to the presence of a gene paralog identified in the genomes of these strains. Genospecies 9, composed of a single strain (BS610 / B648), did not support amplification with these primers. In silico amplification with USEARCH was positive for the gene in all three genospecies 8 genomes (JCP8481B, JCP8481A, PSS_7772B). PCR amplification of aruH was not observed for any strain found in genospecies la (G. vaginalis), 2. 3, 4a (G. pickettii), or 4b (G. piotii), which are associated with a mixed-sensitivity and low- resistance response to metronidazole (median MIC = 32-48 pg / mL) (Fig. 6). Additionally, in silico PCR of the aruH primers herein against NCBI reference strains for three of the most common species colonizing the vaginal microbiome (L. crispatus, L. iners, L. gasseri) did not result in amplification, supporting the specificity of the primer set (data not shown). Example 9:

[0139] GV is best described as a genus composed of at least four distinct clades based on GC content, genome size, number of core genes, and rates of homologous recombination among the clades. Correlations between clade and metronidazole resistance were observed in two of the four original clades, and additional analyses have proposed amending the species definition of Gardnerella vaginalis leading to the newly described genospecies G. leopoldir G. piotip G. swidsinskip G. greenwoodii, and G. pickettii.

[0140] The present study characterized the G. vaginalis spp. phylogenetic clade structure and identified gene content and phenotypic differences among the multiple genospecies within what is now recognized as the GV genus using a large collection of diverse clinical isolates. Phenotypic assays of antibiotic susceptibility revealed that five distinct genospecies displayed complete resistance to metronidazole. Utilizing gene possession differences between high- resistance and sensitive / intermediate / low-resistance genospecies, the present study developed a simple PCR-based molecular diagnostic that can positively identify strains belonging to highly metronidazole-resistant genospecies to help guide clinical management, since all tested members of these resistant genospecies are clindamycin-sensitive.

[0141] Prior to the advent of whole genome sequencing (WGS), microbial species classification was fraught with many taxonomic errors and little consensus as to whether a phenotypic or cladistic taxonomy best captured the true relationships among bacterial strains. Genomic approaches such as pangenomic analyses, core gene content, and ANI follow guidelines stemming from the pre-sequencing era “gold standard” of 70% DNA-DNA hybridization, which was a somewhat arbitrarily set percentage calibrated from an even earlier phenotype-driven species definition, which may or may not accurately reflect more than a half century of research on bacterial speciation and which varies among different bacterial groups. While species classifications for non-sexually reproducing organisms can therefore be challenging, they prove helpful in a clinical setting. Therefore, bacteria need to be classified using a combination of methods that collectively provide sufficient resolution among related strains that require different clinical responses after infection. In practice this means utilizing a number of genomic parameters including comparative genomics, phylogeny, and measurement of HGT.

[0142] The present study endeavored to characterize the component GV genospecies and found ANI and phylogenetic support for eleven GV genospecies using a concatenated core genome. Minor shifts from the canonical species definition of 95% ANI result in a range of eight to sixteen species using ANIs of 94% and 96%, respectively. Pan-genomic analyses also indicate that separation into multiple genospecies is appropriate. The median core gene percentage in single-species pangenome projects containing 25 or more strains is 39%, whereas the core of all 129 GV strains in this study is 18%. Core genomes for individual GV genospecies are nearly triple that of GV in its entirety and are within one standard deviation of the median core gene percentage seen in single-species projects. It is likely that multiple genes confer metronidazole resistance, which may differ between genospecies. This hypothesis is supported by two observations. First, the present study identified the existence of strain pairs in genospecies 1 (la: G. vaginalis and genospecies lb) (B477 / BS494; BS657 / BS620) and genospecies 4 (4a: G. pickettii, 4b: G. piotii) (B659 / B482MASH) in which one strain displays an intermediate response to metronidazole and the other presents significant metronidazole resistance. Analysis of genes found only in the highly resistant strains of each pair uncovered a syntenic region composed of eleven genes with varying functions that could be related to antibiotic resistance, including an MFS transporter — DHA3 family macrolide efflux protein, which is classified as an important antimicrobial resistance gene. This protein was originally identified in Streptococcus pyogenes (PubMed ID 8971709). A BLAST analysis of this gene identifies its presence in multiple Streptococcus genomes at < 99% identity7. The MFS transporter has been identified to function in quorum sensing during biofilm formation in S. pyogenes, and HGT occurrences have been reported between different clades of GV. suggesting a potential mechanism through which this transporter could have been acquired.Expression levels of this gene could play a mechanistic role or help explain one component of how resistance to metronidazole occurs.

[0143] Second, two significantly different metronidazole resistance phenotypes were seen. Resistance broadly fell into one of two categories: low-moderate resistance with an MIC of 32-96 pg / rnL, or total (high) resistance, with an MIC of 128-256 pg / mL or higher. Both low- moderate and total resistance phenotypes were observed in the species that also reported metronidazole susceptible and intermediate strains (genospecies 1-4), but all except for one strain in the genospecies reported as fully metronidazole resistant (genospecies 5-11) displayed resistance greater than 256 pg / mL. These two strikingly different phenotypic patterns likely suggest multiple mechanisms through which metronidazole resistance is conferred in these species, one which leads to the strains eventually succumbing to a moderately high dose of the antibiotic, and another that does not. The observation of strikingly varied resistance response profiles, coupled with the confirmation that strains in genospecies 5-11 were highly susceptible to clindamycin, motivated us to design a simple PCR-based assay for detection of strains in the highly resistant genospecies. Primers have been designed to identify the GV genus through amplification of 16S or 23S rRNA, cpn60, or sialidase A, and a multiplex PCR has been designed that successfully distinguishes between the four original clades. The present study designed a sixteen-primer distributed-gene PCR that can identify members of each of the original clades. However, only seventeen strains were available during the design of the original PCR, which did not provide a sample size necessary to capture the full diversify of G. vaginalis spp. While it is informative, it does not differentiate between the higher- resolution clades, nor does it provide information about specifically metronidazole-resistant genospecies. The present study added primers that are specific for antibiotic-resistant strains or species, in addition to those that distinguish the genus or specific genospecies.

[0144] In this study, 82% of all clinical isolates tested were metronidazole resistant, with highly resistant strains comprising 40% of the total. Development of a molecular diagnostic to identify which genospecies a patient’s GV strain belongs to could change the current treatment modality for BV from guesswork to a more targeted approach, providing rapid relief for millions of patients who presently receive an antibiotic that may or may not treat their symptoms. Thirteen candidate genes were present in all seven highly resistant genospecies and absent in the remaining four mixed response / low resistance genospecies. Seven candidates were suitable for primer design, but only the aruH gene was consistently amplified across most of the resistant genospecies. aruH is involved in arginine catabolism and is associated with production of biogenic poly amines such as putrescine (KEGG: map00330).

[0145] To pave the way for personalized diagnoses and treatments of BV, species differences must be rapidly and accurately identified. A PCR assay allows for the inexpensive classification of GV into two superclades / genera and can be used to rapidly rule out the prescription of metronidazole, one of the most common antibiotics used in BV treatment. This research led to a simple molecular diagnostic to identify highly metronidazole-resistant strains in a clinical setting and present an opportunity for strain-specific antibiotic treatment for patients with BV.

[0146] These results highlight the need for reclassification of Gardnerella vaginalis spp. into a genus composed of multiple species. Pangenomic analyses suggest a minimum of eleven genospecies are contained within the GV genus. Analysis of metronidazole susceptibility on GV clinical isolates identified the existence of a set of closely related genospecies with significantly higher resistance profiles (> 256 pg / mL) to metronidazole than other genospecies within the genus. Notably, all tested isolates were susceptible to clindamycin at clinically relevant levels (< 2 pg / mL), which may be cause for a shift in the current BV treatment paradigm. Lastly , a molecular diagnostic was designed which successfully amplifies a portion of the ctruH gene in the highly metronidazole-resistant strains, allowing for easier identification of strains within those genospecies and opening the door to personalized medicine approaches for treating Bacterial Vaginosis. Example 10: Tables

[0147] Table 1: Range and median metronidazole MIC for tested GV clinical isolates for each genospecies and sub clade / genospecies, with associated species names where appropriate

[0148] Table 2: Sequences of primers tested for genes present in genospecies 5-11 that were not present in genospecies la, 2. 3, or 4

[0149] Table 3: Strain collection metadata for downloaded strains. Collection of strains downloaded from NCBI and associated information.

[0150]

[0151] Table 4: Strain collection metadata for clinical isolates collected by this study. Sequencing information and relevant associated clinical metadata are reported. Biosamples are contained within BioProject PRJNA1071662 (https: / / www.ncbi.nlm.nih.gov / bioproject / 1071662) and were donated by Sharon Hillier at the University of Pittsburgh in Pittsburgh, PA, USA.

[0152] Table 5: Primers used for identification of diversity among different clades of GV. Names and sequences of primers (F / R) are indicated with oligo length, melting temperature (C), and product size. Clade designation refers to the four original clades reported by Ahmed et al (J Bacterial. 2012;194:3922-37). Genospecies refers to clades and subclades proposed in this study.

[0153]

[0154] Table 6: Results of initial PCR amplification for each tested strain with each primer. A Y indicates successful amplification, N indicates no amplification. Bolded names indicate inclusion in the dataset herein.

[0155] Table 7: List of G. vaginalis spp. strains tested for metronidazole (Met) or clindamycin (Clin) antibiotic resistance MIC plate assays. MIC value (pg / mL), classification of Resistant (R) / Intermediate © / Susceptible (S), and clade are listed, following breakpoints determined by CLSI (R 32 pg / mL, 8 pg / mL < I < 32 pg / mL, S < 8 pg / mL). Strains indicated with an asterisk at the MIC value (*) were collected in duplicate.

[0156] Table 8: Gene annotations for candidate genes found exclusively in all strains of genospecies 1-4 (metronidazole susceptible group) or genospecies 5-11 (metronidazole resistant group) with annotations provided by Prokka or BLAST. Genes annotated only as “hypothetical protein” have been excluded from this list.

[0157] Enumerated Embodiments

[0158] In some aspects, the present invention is directed to the following non-limiting embodiments:

[0159] Embodiment 1 : A method of stratifying a bacterial vaginosis (BV) patient based on metronidazole-susceptibility or metronidazole-resistance. the method comprising: detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, iruli. yfeA, ykol). and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the patient.

[0160] Embodiment 2: The method of Embodiment 1, wherein the patient is stratified into the metronidazole-susceptible group when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected, and / or the patient is stratified into the metronidazole-resistant group when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0161] Embodiment 3: The method of Embodiment 2, wherein the metronidazole-resistant group is a clindamycin-susceptible group.

[0162] Embodiment 4: The method of any one of Embodiments 1-3, wherein the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0163] Embodiment 5: The method of any one of Embodiments 1-4, wherein the patient is stratified according to the presence or absence of the Gv aruH gene as detected by a PCR- based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0164] Embodiment 6: The method of any one of Embodiments 1-5, wherein the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA.

[0165] Embodiment 7 : A method of treating, ameliorating, and / or preventing bacterial vaginosis (BV) in a subject in need thereof, the method comprising detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv genes selected from the group consisting of aruH. Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the subject; determining a melronidazole-susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv gene, or the mRNA product, protein product, or metabolite thereof; and

[0166] (a) administering to the subject an effective amount of metronidazole when the BV is determined to be metronidazole-susceptible, and / or

[0167] (b) administering to the subject an effective amount of clindamycin when the BV is determined to be metronidazole-resistant.

[0168] Embodiment 8: The method of Embodiment 7, wherein the BV is determined to be metronidazole-susceptible when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected in the sample, and / or the BV is determined to be metronidazole-resistant when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0169] Embodiment 9: The method of any one of Embodiments 7-8, wherein the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

[0170] Embodiment 10: The method of any one of Embodiments 7-9, wherein metronidazole-susceptibility or metronidazole-resistance of the BV is determined according to the presence or absence of the Gv aruH gene, and wherein the presence or absence of the Gv aruH gene is detected by a PCR-based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0171] Embodiment 11: The method of any one of Embodiments 7-10. wherein the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA. Embodiment 12: A method of diagnosing a metronidazole-susceptible bacterial vaginosis (BV) or a metronidazole-resistant BV in a BV patient, the method comprising detecting a presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH, Ami, Cluster 1311, comEA, crcB, group_2326, group_2343, group_2558, group_2577, ssb, truB, yfeA, ykol). and YneA. or an mRNA product, a protein product, or a metabolite thereof, in a sample from the BV patient, and determining the metronidazole-susceptibility or metronidazole-resi stance of the BV based on the presence or absence of the Gv genes, or the mRNA product, protein product, or metabolite thereof, in the sample from the BV patient.

[0172] Embodiment 13: The method of Embodiment 12, wherein the patient is diagnosed with metronidazole-susceptible BV when an absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected, and / or the patient is diagnosed with metronidazole-resistant BV when a presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

[0173] Embodiment 14: The method of Embodiment 13, wherein the metronidazole-resistant BV is a clindamycin-susceptible BV.

[0174] Embodiment 15: The method of any one of Embodiments 12-14, wherein the method further comprises performing a polymer chain reaction (PCR)-based method to determine the presence or absence of at least one of the Gv genes.

[0175] Embodiment 16: The method of any one of Embodiments 12-15, wherein the method further comprises performing a PCR-based method to detect the presence or absence of the Gv aruH gene with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

[0176] Embodiment 17: The method of any one of Embodiments 12-16, wherein at least one of the following applies:

[0177] (a) the method further comprises collecting the sample from the patientt;

[0178] (b) the method further comprises extracting a Gv DNA from the sample.

[0179] The foregoing outlines features of several embodiments so that those skilled in the art may better understand the aspects of the present disclosure. Those skilled in the art should appreciate that they may readily use the present disclosure as a basis for designing or modifying other processes and structures for carrying out the same purposes and / or achieving the same advantages of the embodiments introduced herein. Those skilled in the art should also realize that such equivalent constructions do not depart from the spirit and scope of the present disclosure, and that they may make various changes, substitutions, and alterations herein without departing from the spirit and scope of the present disclosure.

Claims

CLAIMSWhat is claimed is:

1. A method of stratifying a bacterial vaginosis (BV) patient based on metronidazole- susceptibilify or metronidazole-resistance, the method comprising: detecting presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH. Ami, Cluster 1311, comEA, crcB, group_2326. group_2343, group_2558, group_2577, ssb, truB,yfeA,ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the patient.

2. The method of claim 1 , wherein the patient is stratified into the metronidazole-susceptible group when absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected, and / or the patient is stratified into the metronidazole-resistant group when presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

3. The method of claim 2, wherein the metronidazole-resistant group is a clindamycin- susceptible group.

4. The method of any one of claims 1-3, wherein the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

5. The method of any one of claims 1-4, wherein the patient is stratified according to the presence or absence of the Gv aruH gene as detected by a PCR-based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

6. The method of any one of claims 1-5, wherein the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA.

7. A method of treating, ameliorating, and / or preventing bacterial vaginosis (BV) in a subject in need thereof, the method comprisingdetecting presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH. Ami, Cluster 1311, comEA, crcB, group_2326. group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the subject; determining metronidazole-susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv gene, or the mRNA product, protein product, or metabolite thereof; and(a) administering to the subject an effective amount of metronidazole when the BV is determined to be metronidazole-susceptible, and / or(b) administering to the subject an effective amount of clindamycin when the BV is determined to be metronidazole-resistant.

8. The method of claim 7, wherein the BV is determined to be metronidazole-susceptible when absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected in the sample, and / or the BV is determined to be metronidazole-resistant when presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

9. The method of any one of claims 7-8, wherein the presence or absence of at least one of the Gv genes is detected by a polymer chain reaction (PCR)-based method.

10. The method of any one of claims 7-9, wherein metronidazole-susceptibility or metronidazole-resistance of the BV is determined according to the presence or absence of the Gv aruH gene, and wherein the presence or absence of the Gv aruH gene is detected by a PCR-based method with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

11. The method of any one of claims 7-10, wherein the sample is a vaginal sample, optionally a vaginal sample extracted for a Gv DNA.

12. A method of diagnosing metronidazole-susceptible bacterial vaginosis (BV) or a metronidazole-resistant BV in a BV patient, the method comprisingdetecting presence or absence of at least one of the Gardnerella vaginalis (Gv) genes selected from the group consisting of aruH. Ami, Cluster 1311, comEA, crcB, group_2326. group_2343, group_2558, group_2577, ssb, truB, yfeA, ykoD, and YneA, or an mRNA product, a protein product, or a metabolite thereof, in a sample from the BV patient, and determining the metronidazole-susceptibility or metronidazole-resistance of the BV based on the presence or absence of the Gv genes, or the mRNA product, protein product, or metabolite thereof, in the sample from the BV patient.

13. The method of claim 12, wherein the patient is diagnosed with metronidazole-susceptible BV when absence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected, and / or the patient is diagnosed with metronidazole-resistant BV when presence of the Gv aruH gene, or the mRNA product, protein product, or metabolite thereof, is detected.

14. The method of claim 13, wherein the metronidazole-resistant BV is a clindamycin- susceptible BV.

15. The method of any one of claims 12-14, wherein the method further comprises performing a polymer chain reaction (PCR)-based method to determine the presence or absence of at least one of the Gv genes.

16. The method of any one of claims 12-15, wherein the method further comprises performing a PCR-based method to detect the presence or absence of the Gv aruH gene with at least one forward primer selected from the group consisting of SEQ ID NOs:3-4, and at least one reverse primer selected from the group consisting of SEQ ID NOs:5-6.

17. The method of any one of claims 12-16, wherein at least one of the following applies:(a) the method further comprises collecting the sample from the patient;(b) the method further comprises extracting a Gv DNA from the sample.

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