1
|
Oyenihi AB, Haines R, Trama J, Faro S, Mordechai E, Adelson ME, Osei Sekyere J. Molecular characterization of vaginal microbiota using a new 22-species qRT-PCR test to achieve a relative-abundance and species-based diagnosis of bacterial vaginosis. Front Cell Infect Microbiol 2024; 14:1409774. [PMID: 39006741 PMCID: PMC11239351 DOI: 10.3389/fcimb.2024.1409774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/07/2024] [Indexed: 07/16/2024] Open
Abstract
Background Numerous bacteria are involved in the etiology of bacterial vaginosis (BV). Yet, current tests only focus on a select few. We therefore designed a new test targeting 22 BV-relevant species. Methods Using 946 stored vaginal samples, a new qPCR test that quantitatively identifies 22 bacterial species was designed. The distribution and relative abundance of each species, α- and β-diversities, correlation, and species co-existence were determined per sample. A diagnostic index was modeled from the data, trained, and tested to classify samples into BV-positive, BV-negative, or transitional BV. Results The qPCR test identified all 22 targeted species with 95 - 100% sensitivity and specificity within 8 hours (from sample reception). Across most samples, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, Prevotella bivia, and Megasphaera sp. type 1 were relatively abundant. BVAB-1 was more abundant and distributed than BVAB-2 and BVAB-3. No Mycoplasma genitalium was found. The inter-sample similarity was very low, and correlations existed between key species, which were used to model, train, and test a diagnostic index: MDL-BV index. The MDL-BV index, using both species and relative abundance markers, classified samples into three vaginal microbiome states. Testing this index on our samples, 491 were BV-positive, 318 were BV-negative, and 137 were transitional BV. Although important differences in BV status were observed between different age groups, races, and pregnancy status, they were statistically insignificant. Conclusion Using a diverse and large number of vaginal samples from different races and age groups, including pregnant women, the new qRT-PCR test and MDL-BV index efficiently diagnosed BV within 8 hours (from sample reception), using 22 BV-associated species.
Collapse
Affiliation(s)
- Ayodeji B Oyenihi
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| | - Ronald Haines
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| | - Jason Trama
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| | - Sebastian Faro
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
- Memorial Women's Care, Houston, TX, United States
| | - Eli Mordechai
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| | - Martin E Adelson
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| | - John Osei Sekyere
- Institute for Biomarker Research, Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton, NJ, United States
| |
Collapse
|
2
|
Muzny CA, Elnaggar JH, Sousa LGV, Lima Â, Aaron KJ, Eastlund IC, Graves KJ, Dong C, Van Gerwen OT, Luo M, Tamhane A, Long D, Cerca N, Taylor CM. Microbial interactions among Gardnerella, Prevotella and Fannyhessea prior to incident bacterial vaginosis: protocol for a prospective, observational study. BMJ Open 2024; 14:e083516. [PMID: 38316599 PMCID: PMC10859992 DOI: 10.1136/bmjopen-2023-083516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
INTRODUCTION The aetiology of bacterial vaginosis (BV), a biofilm-associated vaginal infection, remains unknown. Epidemiologic data suggest that it is sexually transmitted. BV is characterised by loss of lactic acid-producing lactobacilli and an increase in facultative and strict anaerobic bacteria. Gardnerella spp are present in 95%-100% of cases; Gardnerella vaginalis has been found to be more virulent than other BV-associated bacteria (BVAB) in vitro. However, G. vaginalis is found in women with normal vaginal microbiota and colonisation is not sufficient for BV development. We hypothesise that Gardnerella spp initiate BV biofilm formation, but incident BV (iBV) requires incorporation of other key BVAB (ie, Prevotella bivia, Fannyhessea vaginae) into the biofilm that alter the transcriptome of the polymicrobial consortium. This study will investigate the sequence of microbiologic events preceding iBV. METHODS AND ANALYSIS This study will enrol 150 women aged 18-45 years with normal vaginal microbiota and no sexually transmitted infections at a sexual health research clinic in Birmingham, Alabama. Women will self-collect twice daily vaginal specimens up to 60 days. A combination of 16S rRNA gene sequencing, qPCR for Gardnerella spp, P. bivia and F. vaginae, and broad range 16S rRNA gene qPCR will be performed on twice daily vaginal specimens from women with iBV (Nugent score 7-10 on at least 2 consecutive days) and controls (with comparable age, race, contraceptive method and menstrual cycle days) maintaining normal vaginal microbiota to investigate changes in the vaginal microbiota over time for women with iBV. Participants will complete daily diaries on multiple factors including sexual activity. ETHICS AND DISSEMINATION This protocol is approved by the University of Alabama at Birmingham Institutional Review Board (IRB-300004547) and written informed consent will be obtained from all participants. Findings will be presented at scientific conferences and published in peer-reviewed journals as well as disseminated to providers and patients in communities of interest.
Collapse
Affiliation(s)
- Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jacob H Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Lúcia G V Sousa
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Ângela Lima
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Kristal J Aaron
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Isaac C Eastlund
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Keonte J Graves
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chaoling Dong
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olivia T Van Gerwen
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Microbial Genomics Resource Group, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Ashutosh Tamhane
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Dustin Long
- Department of Biostatistics, University of Alabama at Birmingham, School of Public Health, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
- LABBELS-Associate Laboratory, Braga, Guimarães, Portugal
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| |
Collapse
|
3
|
Ardizzone CM, Taylor CM, Toh E, Lillis RA, Elnaggar JH, Lammons JW, Mott PD, Duffy EL, Shen L, Quayle AJ. Association of Chlamydia trachomatis burden with the vaginal microbiota, bacterial vaginosis, and metronidazole treatment. Front Cell Infect Microbiol 2023; 13:1289449. [PMID: 38149008 PMCID: PMC10750252 DOI: 10.3389/fcimb.2023.1289449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is a common coinfection with Chlamydia trachomatis (Ct), and BV-associated bacteria (BVAB) and their products have been implicated in aiding Ct evade natural immunity. Here, we determined if a non-optimal vaginal microbiota was associated with a higher genital Ct burden and if metronidazole, a standard treatment for BV, would reduce Ct burden or aid in natural clearance of Ct infection. Cervicovaginal samples were collected from women at enrollment and, if testing positive for Ct infection, at a follow-up visit approximately one week later. Cervical Ct burden was assessed by inclusion forming units (IFU) and Ct genome copy number (GCN), and 16S rRNA gene sequencing was used to determine the composition of the vaginal microbiota. We observed a six-log spectrum of IFU and an eight-log spectrum of GCN in our study participants at their enrollment visit, but BV, as indicated by Amsel's criteria, Nugent scoring, or VALENCIA community state typing, did not predict infectious and total Ct burden, although IFU : GCN increased with Amsel and Nugent scores and in BV-like community state types. Ct burden was, however, associated with the abundance of bacterial species in the vaginal microbiota, negatively with Lactobacillus crispatus and positively with Prevotella bivia. Women diagnosed with BV were treated with metronidazole, and Ct burden was significantly reduced in those who resolved BV with treatment. A subset of women naturally cleared Ct infection in the interim, typified by low Ct burden at enrollment and resolution of BV. Abundance of many BVAB decreased, and Lactobacillus increased, in response to metronidazole treatment, but no changes in abundances of specific vaginal bacteria were unique to women who spontaneously cleared Ct infection.
Collapse
Affiliation(s)
- Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Evelyn Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rebecca A. Lillis
- Department of Medicine, Section of Infectious Diseases, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - John W. Lammons
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Patricia Dehon Mott
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Emily L. Duffy
- Department of Medicine, Section of Infectious Diseases, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Li Shen
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Alison J. Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| |
Collapse
|