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MSphere Mar 2024Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital...
Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital microbiota is unclear as prior studies largely investigated specific pathogens. We used epidemiologic data and whole metagenome sequencing to characterize urogenital microbiota strain concordance between participants of a sexual network study. Individuals who screened positive for genital were enrolled and referred their sexual contacts from the prior 60-180 days. Snowball recruitment of sexual contacts continued for up to four waves. Vaginal swabs and penile urethral swabs were collected for whole metagenome sequencing. We evaluated bacterial strain concordance using inStrain and network analysis. We defined concordance as ≥99.99% average nucleotide identity over ≥50% shared coverage; we defined putative sexual transmission as concordance between sexual contacts with <5 single-nucleotide polymorphisms per megabase. Of 138 participants, 74 (54%) were female; 120 (87%) had genital chlamydia; and 43 (31%) were recruited contacts. We identified 115 strain-concordance events among 54 participants representing 25 bacterial species. Seven events (6%) were between sexual contacts including putative heterosexual transmission of , , , , and (one strain each), and putative sexual transmission of between female contacts. Most concordance events (108, 94%) were between non-contacts, including eight female participants connected through 18 and 3 concordant strains, and 14 female and 2 male participants densely interconnected through 52 concordance events.IMPORTANCEEpidemiologic evidence consistently indicates bacterial vaginosis (BV) is sexually associated and may be sexually transmitted, though sexual transmission remains subject to debate. This study is not capable of demonstrating BV sexual transmission; however, we do provide strain-level metagenomic evidence that strongly supports heterosexual transmission of BV-associated species. These findings strengthen the evidence base that supports ongoing investigations of concurrent male partner treatment for reducing BV recurrence. Our data suggest that measuring the impact of male partner treatment on , , , , and may provide insight into why a regimen does or does not perform well. We also observed a high degree of strain concordance between non-sexual-contact female participants. We posit that this may reflect limited dispersal capacity of vaginal bacteria coupled with individuals' comembership in regional transmission networks where transmission may occur between parent and child at birth, cohabiting individuals, or sexual contacts.
Topics: Infant, Newborn; Child; Humans; Male; Female; Metagenome; Gardnerella vaginalis; Vaginosis, Bacterial; Vagina; Microbiota
PubMed: 38358269
DOI: 10.1128/msphere.00030-24 -
PloS One 2013The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify...
BACKGROUND
The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening.
METHODOLOGY/PRINCIPAL FINDINGS
The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P<0.001, OR 23.3 (95%CI:2.9-190.7)) among the 90 women.
CONCLUSIONS/SIGNIFICANCE
This study highlighted the potential of metatranscriptomics as a tool for characterising metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex.
Topics: Adult; Female; Gene Expression Profiling; Gene Library; Humans; RNA, Bacterial; Sexual Behavior; Vaginosis, Bacterial
PubMed: 24086764
DOI: 10.1371/journal.pone.0076892 -
Sexually Transmitted Diseases Dec 2020Up to 50% of women with nonoptimal vaginal microbial community state type (CST) have bacterial vaginosis (BV). Little is known about what distinguishes women with and...
BACKGROUND
Up to 50% of women with nonoptimal vaginal microbial community state type (CST) have bacterial vaginosis (BV). Little is known about what distinguishes women with and without BV diagnosis within nonoptimal CST. We identified features of women and their male sex partners associated with BV among women with nonoptimal vaginal CST.
METHODS
In this prospective study, 252 heterosexual couples were observed at 1, 6, and 12 months after baseline. Microbiomes were characterized in cervicovaginal lavage and penile meatal swabs through high-throughput 16s ribosomal RNA gene amplicon sequencing. Nonoptimal CST was defined as CST-IV. Bacterial vaginosis was defined as a Nugent score of 7 to 10. Generalized estimating equation analysis estimated adjusted odds ratios (aORs) for BV among women with nonoptimal CST.
RESULTS
At baseline, women with nonoptimal CST were a median age of 22 years, 44% had BV, 16% had HIV, and 66% had herpes simplex virus (HSV) type 2. Male partners were a median age of 27 years, 12% had HIV, 48% had HSV-2, and 55% were circumcised. Within nonoptimal CST, Sneathia sanguinegens, Prevotella species, Prevotella amnii, and Clostridiales, BV-associated bacteria-2 were statistically significantly enriched in observations with BV. In multivariable generalized estimating equation controlling for CST, HIV, and HSV-2, BV was increased among women with CST-IVA (aOR, 1.91; P = 0.087), HIV (aOR, 2.30; P = 0.051), HSV-2 (aOR, 1.75; P = 0.065), and enrichment of male partner penile taxa: Dialister (aOR, 1.16; P = 0.034), Megasphaera (aOR, 1.22; P = 0.001), and Brevibacterium (aOR, 1.13; P = 0.019).These results provide insights into factors differentiating women with BV among those with nonoptimal vaginal CST. Interrupting the sexual exchange of penile and vaginal taxa may be beneficial for preventing pathologic state of vaginal microbiome.
Topics: Adult; Bacteria; Female; Humans; Kenya; Male; Microbiota; Prospective Studies; RNA, Ribosomal, 16S; RNA, Viral; Sequence Analysis, DNA; Sexual Partners; Vagina; Vaginosis, Bacterial; Young Adult
PubMed: 32773610
DOI: 10.1097/OLQ.0000000000001259 -
Infection and Immunity Jan 2018Young African females are at an increased risk of HIV acquisition, and genital inflammation or the vaginal microbiome may contribute to this risk. We studied these...
Young African females are at an increased risk of HIV acquisition, and genital inflammation or the vaginal microbiome may contribute to this risk. We studied these factors in 168 HIV-negative South African adolescent females aged 16 to 22 years. Unsupervised clustering of 16S rRNA gene sequences revealed three clusters (subtypes), one of which was strongly associated with genital inflammation. In a multivariate model, the microbiome compositional subtype and hormonal contraception were significantly associated with genital inflammation. We identified 40 taxa significantly associated with inflammation, including those reported previously (, , , , and ) as well as several novel taxa (including increased frequencies of bacterial vaginosis-associated bacterium 1 [BVAB1], BVAB2, BVAB3, , , , , , and and decreased frequencies of , , , and ). Women with inflammation-associated microbiomes had significantly higher body mass indices and lower levels of endogenous estradiol and luteinizing hormone. Community functional profiling revealed three distinct vaginal microbiome subtypes, one of which was characterized by extreme genital inflammation and persistent bacterial vaginosis (BV); this subtype could be predicted with high specificity and sensitivity based on the Nugent score (≥9) or BVAB1 abundance. We propose that women with this BVAB1-dominated subtype may have chronic genital inflammation due to persistent BV, which may place them at a particularly high risk for HIV infection.
Topics: Adolescent; Female; Genitalia; HIV Infections; Humans; Inflammation; Microbiota; RNA, Ribosomal, 16S; Reproductive Tract Infections; Vaginosis, Bacterial; Young Adult
PubMed: 29038128
DOI: 10.1128/IAI.00410-17 -
The Journal of Infectious Diseases Sep 2019While bacterial vaginosis has been associated with an increased risk of Trichomonas vaginalis (TV) acquisition, it is unknown whether other characteristics of the...
BACKGROUND
While bacterial vaginosis has been associated with an increased risk of Trichomonas vaginalis (TV) acquisition, it is unknown whether other characteristics of the vaginal microbiota, including the presence of key bacterial species, influence a woman's risk of TV acquisition.
METHODS
The vaginal microbiota before 25 unique episodes of TV infection involving 18 women was compared to that of 50 controls who remained uninfected. TV was detected by transcription-mediated amplification. Vaginal microbiota were quantified using broad-range polymerase chain reaction analysis and taxon-specific quantitative PCR of the 16S ribosomal RNA gene.
RESULTS
TV acquisition was significantly associated with the presence of Prevotella amnii (risk ratio [RR], 2.21; 95% confidence interval [CI], 1.12-4.38; P = .02) and Sneathia sanguinegens (RR, 2.58; 95% CI, 1.00-6.62; P = .049). When adjusted for menstrual phase, the association between P. amnii and TV acquisition remained similar (adjusted RR, 2.11; 95% CI, 1.03-4.33; P = .04), but the association between S. sanguinegens and TV acquisition was attenuated (adjusted RR, 2.31; 95% CI, .86-6.23; P = .10).
CONCLUSIONS
Key vaginal bacterial species may contribute to the susceptibility to TV acquisition. Understanding how these bacterial species increase a woman's risk of TV acquisition could help to guide the development of novel strategies to reduce women's risk of TV infection.
Topics: Adult; Bacteria; Biota; DNA, Bacterial; DNA, Protozoan; Disease Susceptibility; Female; Humans; Middle Aged; Nucleic Acid Amplification Techniques; Prospective Studies; Risk Assessment; Trichomonas Vaginitis; Trichomonas vaginalis; Vagina
PubMed: 31287879
DOI: 10.1093/infdis/jiz354 -
MSystems Nov 2019Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to...
Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe early childhood caries (ECC), and 19 age-matched, caries-free children as controls were recruited. Saliva samples were collected from the participants and were subjected to metagenomic analyses, whereby the oral microbial communities were investigated. The metagenomic analyses revealed substantial microbiota differences between the two groups, indicating apparent shifts of the oral microbiome present in the ECC group. At the species level, the ECC-enriched microbes included , , and Interestingly, and exhibited apparent differences at the strain level but not the species level between the ECC and control groups. Functional examination showed that the ECC group displayed extensive alterations in metabolic genes/pathways/modules, including enriched functions in sugar metabolism. Finally, an SVM (support vector machine) classifier comprising seven species was developed and generated a moderately good performance in predicting caries onset (area under the receiver operating characteristic curve [AUC] = 78.33%). Together, these findings indicate that caries is associated with considerable changes in the oral microbiome, some of which can potentially be exploited as therapeutic targets or diagnostic markers. (This study has been registered at ClinicalTrials.gov under registration no. NCT02341352.) Dental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level composition and functional profile. Here, we performed metagenomic analyses for a cohort of preschool children with or without caries. Our results showed that caries was associated with extensive microbiota differences at various taxonomic and functional levels. Some caries-associated species had not been previously reported, some of which may have significant clinical implications. A microbiome gene catalogue from children with caries was constructed for the first time. The results demonstrated that caries is associated with alterations of the oral microbiome, including changes in microbial composition and metabolic functional profile.
PubMed: 31690590
DOI: 10.1128/mSystems.00450-19 -
Sexually Transmitted Diseases May 2020In a vaginal 16S ribosomal RNA gene quantitative PCR study of 17 pelvic inflammatory disease (PID) cases and 17 controls who tested positive for Chlamydia trachomatis,...
In a vaginal 16S ribosomal RNA gene quantitative PCR study of 17 pelvic inflammatory disease (PID) cases and 17 controls who tested positive for Chlamydia trachomatis, women who additionally tested positive for Atopobium vaginae, Sneathia spp., Megasphaera spp., Eggerthella-like bacterium or Prevotella amnii were more likely to develop PID.
Topics: Actinobacteria; Adult; Anti-Bacterial Agents; Bacteria; Case-Control Studies; DNA, Bacterial; DNA, Ribosomal; Female; Humans; Pelvic Inflammatory Disease; Polymerase Chain Reaction; Prevotella; RNA, Ribosomal, 16S; Vagina; Vaginosis, Bacterial
PubMed: 32149953
DOI: 10.1097/OLQ.0000000000001164 -
Microbiome Sep 2017Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually... (Clinical Trial)
Clinical Trial Randomized Controlled Trial
BACKGROUND
Bacterial vaginosis (BV) is the most common vaginal syndrome among women in their reproductive years. It is associated with an increased risk of acquiring sexually transmitted infections and complications like preterm labor. BV is characterized by a high recurrence rate for which biofilms frequently found on vaginal epithelial cells may be a reason.
RESULTS
Here, we report a controlled randomized clinical trial that tested the safety and effectiveness of a newly developed pessary containing an amphoteric tenside (WO3191) to disrupt biofilms after metronidazole treatment of BV. Pessaries containing lactic acid were provided to the control group, and microbial community composition was determined via Illumina sequencing of the V1-V2 region of the 16S rRNA gene. The most common community state type (CST) in healthy women was characterized by Lactobacillus crispatus. In BV, diversity was high with communities dominated by either Lactobacillus iners, Prevotella bivia, Sneathia amnii, or Prevotella amnii. Women with BV and proven biofilms had an increased abundance of Sneathia sanguinegens and a decreased abundance of Gardnerella vaginalis. Following metronidazole treatment, clinical symptoms cleared, Nugent score shifted to Lactobacillus dominance, biofilms disappeared, and diversity (Shannon index) was reduced in most women. Most of the patients responding to therapy exhibited a L. iners CST. Treatment with WO 3191 reduced biofilms but did not prevent recurrence. Women with high diversity after antibiotic treatment were more likely to develop recurrence.
CONCLUSIONS
Stabilizing the low diversity healthy flora by promoting growth of health-associated Lactobacillus sp. such as L. crispatus may be beneficial for long-term female health.
TRIAL REGISTRATION
ClinicalTrials.gov NCT02687789.
Topics: Adult; Anti-Bacterial Agents; Biofilms; Female; Gardnerella vaginalis; High-Throughput Nucleotide Sequencing; Humans; Lactobacillus; Lactobacillus crispatus; Metronidazole; Microbiota; Middle Aged; Pessaries; Prevotella; RNA, Ribosomal, 16S; Surface-Active Agents; Vagina; Vaginosis, Bacterial; Young Adult
PubMed: 28903767
DOI: 10.1186/s40168-017-0326-y