Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis

Probiotics reduce the recurrence of asymptomatic bacterial vaginosis in Chinese women

Asymptomatic Bacterial Vaginosis(aBV)increases the risk of acquiring multiple sexually transmitted diseases, HPV, gynecologic complications and adverse reproductive outcomes, and is speculated to affect 10 ~ 35% of women. Without intervention, a significant proportion of aBV would progress. Metronidazole is the most widely used treatment for aBV, yet the main challenge has always been the high rate of recurrence. Probiotics may increase the cure rate and reduce the recurrence rate of symptomatic bacterial vaginosis (sBV), while no study has compared the efficacy of probiotics and metronidazole on treating aBV. This study aims to fill the gap in understanding the difference in efficacy of probiotics and metronidazole in treating aBV by a multicenter, randomized, controlled trial. Participants received either a 10-day intravaginal probiotic capsules or a 7-day oral metronidazole. Follow-up were performed at the end of the 1st, 2nd, and 4th week after completing therapy. Women cured by either method were followed up with three additional visits. The primary outcome was the difference of cure rates between the two groups. The secondary outcome was to evaluate the recurrence rates among patients who were successfully cured using either method. 358 participants received probiotics and another 358 participants received metronidazole. The cumulative cure rates at the end of the 1st, 2nd, and 4th week were higher in probiotics group compared to metronidazole group (OR 1.063, P = 0.715; OR 1.324, P = 0.083; OR 1.338, P = 0.071), while the differences were not statistically significant. Women cured (144 in probiotics and 123 in metronidazole) were followed up. The difference of cumulative recurrence rates between the two groups were statistically significant at the end of the 2nd, 3rd, and 4th month (OR 0.212, P = 0.000; OR 0.160, P = 0.000; OR 0.119, P = 0.000). Adverse events were similar in the two groups (8.3%, 9.6% OR 0.858; P = 0.584). No life-threatening or severe adverse events were reported. Probiotics emerge as a superior therapeutic option for aBV due to their comparable cure rates, lower recurrence rates, and minimal side effects. Chinese Clinical Trial Registry (ChiCTR1800019436, 11/11/2018 ).

Effects of the sampling time on the vaginal microbiota in healthy pregnant women: a prospective observational study

Background

Studies using 16S rRNA gene sequencing have extensively examined the vaginal microbiota changes of pregnant women. However, no study has examined these changes considering the time of day at which vaginal fluid samples were collected from near-term pregnant women.

Objective

To describe the vaginal microbiota of Japanese near-term pregnant women with normal pregnancy outcomes and potential vaginal microbiota changes from wake-up to bedtime.

Study design

In this prospective observational study, vaginal swab specimens were obtained from healthy near-term pregnant women twice on the same day, after waking up and before bedtime. All specimens were examined for total bacterial cell count per gram of vaginal fluid, Nugent score, pH, and vaginal microbiota analysis using 16S rRNA gene sequencing. Initially, the wake-up and bedtime samples of all participants were analyzed at the genus level using next-generation sequencing. Subsequently, all samples were analyzed at the genus and species levels using Sanger sequencing.

Results

Sixteen pregnant women were enrolled in this study. The median age of the participants was 32.5 years, and the median gestational age was 38 weeks. Median bacterial counts in vaginal fluids at wake-up and bedtime were 3.9 × 109/g and 3.6 × 109/g, respectively, with no significant difference. Vaginal microbiota analyses based on 16S rRNA genes showed that the vaginal microbiota in pregnant women with no abnormalities during pregnancy was limited to a single flora dominated by Lactobacillus spp. and included pregnant women with highly diverse vaginal microbiota. Genus-level analysis using next-generation sequencing showed that the vaginal microbiota differed between wake-up and bedtime in more diverse samples but not in less diverse samples. However, these differences were small compared to individual differences. The dominant genera in each sample had similar relative abundances in both wake-up and bedtime samples. However, the non-dominant genus Streptococcus spp. was significantly more frequently detected in bedtime samples. In species-level analyses, the proportions of dominant and non-dominant species showed little change between wake-up and bedtime.

Conclusions

The vaginal microbiota of pregnant women with normal pregnancy outcomes was not necessarily dominated by Lactobacillus spp. Further studies are required to define the vaginal microbiota in healthy pregnant women. When vaginal fluid samples were collected from the same pregnant women at wake-up and bedtime under the same conditions, the differences between wake-up and bedtime samples were greater for women with high diversity of the vaginal microbiota than for those with low diversity. However, these differences were not sufficiently large to exceed individual differences, and almost no change in the abundances of the dominant genera was observed. Since the relative abundance of Streptococcus spp., a non-dominant species of the vaginal microbiota tends to change between wake-up and bedtime, it might be necessary to collect samples before bedtime to detect group B Streptococci.

Species-level characterization of the cervicovaginal microbiota and its role in human papillomavirus-associated cervical carcinogenesis

The cervicovaginal microbiome may contribute to human papillomavirus (HPV)-associated cervical carcinogenesis, but studies have been limited by low-resolution analysis methods. Using a high-resolution bioinformatics pipeline, we evaluated the relationship of the cervicovaginal microbiome with HPV and cervical intraepithelial neoplasia (CIN). The cervicovaginal microbiome of 186 women was characterized by sequencing 16S rRNA regions (V3-V4 and V5-V6) and annotated with the high-resolution ANCHOR pipeline. Samples were genotyped for HPV using the Roche-Cobas 4800 assay. We fitted logistic regression models using stepwise forward selection to select species (presence/absence) as correlates of CIN1+ and constructed a linear microbiome-based score using the regression coefficients. An HPV-based score was calculated from a separate logistic regression model to detect CIN1+ . Receiver operating characteristic curve analyses were performed; the area under the curve (AUC) and 95% confidence intervals (CI) were compared between scores. Overall, 66.7% of participants were HPV-positive. 77 unique species were identified: 8 using V3-V4, 48 using V5-V6, and 21 shared. Twelve species were retained via stepwise selection. The AUCs for the microbiome-, and HPV-based scores were 0.7656 (95% CI 0.6885-0.8426), and 0.7529 (95% CI 0.6855-0.8204), respectively. Bacterial species may be involved in cervical carcinogenesis as the microbiome- and HPV-based scores performed similarly for CIN1+ detection.

Efficacy of Dequalinium Chloride vs Metronidazole for the Treatment of Bacterial Vaginosis: A Randomized Clinical Trial

Importance

Bacterial vaginosis (BV) is a common cause of vaginal infection. First-line treatments of BV are metronidazole and clindamycin. Due to the increase in antibiotic resistance, effective nonantibiotic treatments for BV are needed.

Objective

To examine whether dequalinium chloride, a broad-spectrum antiseptic, is noninferior to oral metronidazole for the treatment of BV.

Design, Setting, and Participants

This phase 4, multicenter, triple-blind, double-dummy, parallel, noninferiority randomized clinical trial was conducted from July 29, 2021, to August 25, 2022, with a 1-month follow-up. Participants were premenopausal women 18 years or older with BV from 11 gynecologic practices and 1 hospital in Poland, Slovakia, and the Czech.

Intervention

Patients were randomized to treatment with dequalinium chloride vaginal tablets (10 mg once daily for 6 days) or oral metronidazole (500 mg twice daily for 7 days). Double-dummy medication kits contained vaginal and oral tablets with placebo and active medication.

Main Outcomes and Measures

The main outcome was the noninferiority margin (of 15 percentage points) in the absolute difference in clinical cure rates between dequalinium chloride and metronidazole 7 to 11 days after start of treatment (visit 1). Noninferiority was met if the lower 95% CI for the difference in clinical cure rate was less than 15 percentage points at visit 1.

Results

A total of 147 women (mean [SD] age, 36.7 [9.0] years) were treated with dequalinium chloride (n = 72) or metronidazole (n = 75). The clinical cure rates at visit 1 were 64 of 69 (92.8%) for dequalinium chloride vs 69 of 74 (93.2%) for metronidazole in the intention-to-treat population, whereas in the per-protocol population, cure rates were 54 of 58 (93.1%) for dequalinium chloride vs 48 of 53 (90.6%) for metronidazole. The treatment differences of -0.5 percentage points (95% CI, -10.8 to 9.8 percentage points; P = .002) in the intention-to-treat population and 2.5 percentage points (95% CI, -9.4 to 14.4 percentage points; P = .001) in the per-protocol population confirmed the noninferiority of dequalinium chloride. The tolerability of dequalinium chloride was rated as very good by 30 of 50 patients (60.0%) but only by 21 of 54 (38.9%) for metronidazole. Three patients in the metronidazole group suspended treatment due to an adverse event.

Conclusions and Relevance

This randomized clinical trial showed that dequalinium chloride was not inferior to metronidazole for the treatment of BV. Dequalinium chloride had a similarly high cure rate but with better tolerability and fewer adverse events. With a similar efficacy to metronidazole and clindamycin, dequalinium chloride warrants consideration as first-line treatment for BV to help reduce antibiotic consumption.

Trial Registration

EudraCT: 2020-002489-15.

Alterations in gut and genital microbiota associated with gynecological diseases: a systematic review and meta-analysis

BACKGROUND

Increasing number of studies have demonstrated certain patterns of microbial changes in gynecological diseases; however, the interaction between them remains unclear. To evaluate the consistency or specificity across multiple studies on different gynecological diseases and microbial alterations at different sites of the body (gut and genital tract), we conducted a systematic review and meta-analysis.

METHODS

We searched PubMed, Embase, Web of Science, and Cochrane Library up to December 5, 2022(PROSPERO: CRD42023400205). Eligible studies focused on gynecological diseases in adult women, applied next-generation sequencing on microbiome, and reported outcomes including alpha or beta diversity or relative abundance. The random-effects model on standardized mean difference (SMD) was conducted using the inverse-variance method for alpha diversity indices.

RESULTS

Of 3327 unique articles, 87 eligible studies were included. Significant decreases were found in gut microbiome of patients versus controls (observed species SMD=-0.35; 95%CI, -0.62 to -0.09; Shannon index SMD=-0.23; 95%CI, -0.40 to -0.06), whereas significant increases were observed in vaginal microbiome (Chao1 SMD = 1.15; 95%CI, 0.74 to 1.56; Shannon index SMD = 0.51; 95%CI, 0.16 to 0.86). Most studies of different diagnostic categories showed no significant differences in beta diversity. Disease specificity was observed, but almost all the changes were only replicated in three studies, except for the increased Aerococcus in bacterial vaginosis (BV). Patients with major gynecological diseases shared the enrichment of Prevotella and depletion of Lactobacillus, and an overlap in microbes was implied between BV, cervical intraepithelial neoplasia, and cervical cancer.

CONCLUSIONS

These findings demonstrated an association between alterations in gut and genital microbiota and gynecological diseases. The most observed results were shared alterations across diseases rather than disease-specific alterations. Therefore, further investigation is required to identify specific biomarkers for diagnosis and treatment in the future.

A Landscape View of the Female Genital Tract Microbiome in Healthy Controls and Women With Reproductive Health Conditions Associated With Ectopic Pregnancy

Disruption of the female genital microbiome is associated with several pregnancy complications, including miscarriage, preterm onset of labour, and tubal pregnancy. Ectopic pregnancy is a known cause of maternal morbidity and mortality, but early diagnosis and treatment of ectopic pregnancy remain a challenge. Despite growing established associations between genital microbiome and female reproductive health, few studies have specifically focused on its link with ectopic pregnancy. Therefore, the current review aims to provide a comprehensive account of the female genital microbiome in healthy and fertile women compared to those in ectopic pregnancy and its associated risk factors. The microbial diversity from various sites of the female genital tract was explored for a reliable proxy of female reproductive health in sequencing-based ectopic pregnancy research. Our report confirmed the predominance of Lactobacillus in the vagina and the cervix among healthy women. The relative abundance decreased in the vaginal and cervical microbiome in the disease state. In contrast, there were inconsistent findings on the uterine microbiome across studies. Additionally, we explore a spectrum of opportunities to enhance our understanding of the female genital tract microbiome and reproductive conditions. In conclusion, this study identifies gaps within the field and emphasises the need for visionary solutions in metagenomic tools for the early detection of ectopic pregnancy and other gynaecological diseases.

Cultivable Microbiome Approach Applied to Cervical Cancer Exploration

Traditional microbiological methodology is valuable and essential for microbiota composition description and microbe role assignations at different anatomical sites, including cervical and vaginal tissues; that, combined with molecular biology strategies and modern identification approaches, could give a better perspective of the microbiome under different circumstances. This pilot work aimed to describe the differences in microbiota composition in non-cancer women and women with cervical cancer through a culturomics approach combining culture techniques with Vitek mass spectrometry and 16S rDNA sequencing. To determine the possible differences, diverse statistical, diversity, and multivariate analyses were applied; the results indicated a different microbiota composition between non-cancer women and cervical cancer patients. The Firmicutes phylum dominated the non-cancer (NC) group, whereas the cervical cancer (CC) group was characterized by the predominance of Firmicutes and Proteobacteria phyla; there was a depletion of lactic acid bacteria, an increase in the diversity of anaerobes, and opportunistic and non-typical human microbiota isolates were present. In this context, we hypothesize and propose a model in which microbial composition and dynamics may be essential for maintaining the balance in the cervical microenvironment or can be pro-oncogenesis microenvironmental mediators in a process called Ying-Yang or have a protagonist/antagonist microbiota role.

Prevalence of Gardnerella vaginalis infection and antibiotic resistance pattern of isolates of gynecology clinic patients at Shahriar Noor Hospital from January to June 2020 by PCR and culture methods

Background and Objectives

Gardnerella vaginalis is one of the most important causes of prevalent genital infections that pose serious risks. This study aimed to determine the prevalence of Gardnerella vaginalis and antibiotic resistance pattern of isolates of patients referred to the gynecology clinic of Shahriar Noor Hospital by PCR and culture methods.

Materials and Methods

The study was conducted on 500 patients who had suffered from a vaginal infection. The demographic data of patients were studied. For diagnosis of Gardnerella vaginalis isolates, cultivation in anaerobic conditions, biochemical tests, PCR and Gardnerella vaginalis antibiotic susceptibility test to metronidazole and clindamycin were performed. Data analysis was performed utilizing SPSS statistical software version 19 and the Chi-square test.

Results

Among the 500 patients, 173 were diagnosed with Gardnerella vaginitis. There was a significant relationship between age group, level of education, and contraceptive method with Gardnerella vaginosis incidence. Performing antibiotic susceptibility tests showed that the resistance of Gardnerella vaginalis isolated strains to metronidazole and clindamycin was 86.12% and 17.34%, respectively.

Conclusion

The high prevalence of Gardnerella vaginalis infections confirms the critical role of the bacterium in the occurrence of bacterial vaginosis. Therefore, it is necessary to check the prevalence of bacterial infections to recommend the correct medical treatment in different societies.

The association between symptom or microscopy based diagnosis of bacterial vaginosis (BV) and response to treatment in women with recurrent BV

BACKGROUND

Bacterial vaginosis (BV) is a common condition, yet accurate diagnosis remains a challenge. We explored symptom and microscopy-based diagnosis of BV and assessed the influence of these diagnostic approaches on treatment response.

METHODS

BV diagnosis based on patient-reported symptoms, and vaginal swab gram stain microscopy at local laboratories and a central laboratory were compared for women recruited into the VITA trial in England. Multivariable analysis was used to assess the association between the method of diagnosis and symptom resolution 2 weeks after metronidazole treatment.

RESULTS

517 women presenting with vaginal discharge (470/517 [91%]) and/or malodour (440/517 [85%]) were included. The accuracy of patients' vaginal symptoms compared to local laboratory microscopy for BV diagnosis were -discharge, sensitivity 90% and specificity 5%; malodour, sensitivity 84% and specificity 12%, and compared to a central laboratory diagnosis were -discharge, sensitivity 91% and specificity 8%; malodour, sensitivity 88% and specificity 18%. 143/204 (70%) participants reported symptom resolution after treatment and this was associated with a positive baseline local laboratory diagnosis (adjusted relative risk-aRR 1.64 [1.02 to 2.64]), but not with a positive central laboratory diagnosis (aRR 1.14 [0.95 to 1.37]). Symptom resolution occurred in 75% (83/111) of women who were symptom positive/central laboratory BV positive compared to 65% (58/89) who were symptom positive/microscopy negative.

CONCLUSION

Symptoms correlated poorly with microscopy-based BV diagnosis but two-thirds of women with a symptom positive/microscopy negative diagnosis experienced symptom resolution following metronidazole treatment. Further studies are needed to determine the optimal investigation and treatment for microscopy-negative women with typical BV symptoms.

Compositional Changes in the Vaginal Bacterial Microbiome of Healthy Pregnant Women across the Three Gestational Trimesters in Ismailia, Egypt

The composition of the vaginal microbiome may lead to adverse pregnancy outcomes. Normal pregnancy is associated with changes in the vaginal bacterial community composition, which tend to be more enriched with one or two Lactobacillus species promoting a healthy vagina and favorable birth outcomes. The aim of the current study was to determine compositional changes in the healthy vaginal microbiome composition during the three trimesters of pregnancy in Ismailia, Egypt using Illumina MiSeq sequencing of the V3-V4 region of the 16S rRNA. The phylum Firmicutes and the genus Lactobacillus dominated across the three trimesters of pregnancy. L. iners was the most abundant species. However, L. coleohominis and L. reuteri represented the least dominant vaginal lactobacilli. Core microbiome analyses showed the Lactobacillus genus and L. iners species to have the highest prevalence in all the samples of our study groups. The phylum Firmicutes was found to be negatively correlated with almost all other vaginal phyla during pregnancy. Likewise, a negative correlation between Lactobacillus and almost all other genera was detected, including significant negative correlations with Dialister and Prevotella. Furthermore, negative correlations of L. iners were detected with almost all other species, including a significant negative correlation with L. helveticus, G. vaginalis, S. anginosus, and S. agalactiae.

Natural progress history of asymptomatic bacterial vaginosis in Chinese Han women and associated risk factors

OBJECTIVE

Asymptomatic bacterial vaginosis (aBV) is prevalent in the general population, while a previous study only investigated the natural history of aBV in women at high-risk. This stage study was to investigate the natural history of aBV in Chinese Han women at general risk and examine risk factors associated with different outcomes.

METHODS

Women of reproductive age with aBV were enrolled and prospectively followed up with for four months. Participants were classified into one of three outcomes: progress, self-cure or no-change. Univariate and multivariate analyses were used to determine the association between potential risk factors and outcomes.

RESULTS

A total of 3420 subjects were screened and 1014 women with aBV were enrolled. Eventually, 984 participants completed the study, with 30 patients dropped out. Among the 984 cases, 42 cases self-cured spontaneously, while 433 cases progressed and 509 cases did not change significantly. Of the 433 cases that progressed, several types of mixed infections were observed in addition to 196 symptomatic bacterial vaginosis. According to univariate analysis, frequent travel (OR, 95% CI, 2.73 [2.09 ~ 3.55]) and history of bacterial vaginosis (BV) (5.47, [4.15 ~ 7.21]) exhibited significant associations with aBV progression, while condom contraception (0.46 [0.36 ~ 0.61]) and lower Nugent score (0.49, [0.37 ~ 0.64]) demonstrated protective effects for self-cure. According to multivariate regression analysis, the risk factors for aBV progression were history of BV (6.67, [4.86 ~ 9.15]) and frequent travel (3.57, 2.59 ~ 4.92). Condom contraception (0.36, 0.26 ~ 0.49) exhibited a protective effect against aBV progression.

CONCLUSION

Without intervention, a large proportion of aBV would progress, compared to the very few patients whose aBV self-cured spontaneously. It is necessary to clinically intervene aBV patients. Condom utilization can be used as an effective method to improve the outcome of aBV.

Diagnosis of bacterial vaginosis: Comparison of Nugent´s and novel microscopic method

Background/Aim. Bacterial vaginosis (BV) is a common cause of vaginal discomfort in women. The aim of this study was to compare Nugent?s scoring system and novel microscopy method, introduced in our laboratory and used in BV diagnosis. Methods. This study included 705 pregnant and asymptomatic women between 24 and 28 weeks of pregnancy. The degree of agreement between methods was determined by the kappa (?) index. The sensitivity, specificity, positive and negative predictive value of the novel microscopy method was compared to Nugent?s score as standard. Results. Based on the scoring system of both methods, Nugent?s and novel microscopy method, BV was diagnosed in 21% and 25% of women, respectively. Despite the disparities among diagnostic criteria, which mainly concerned classification of intermediary samples, the degree of agreement between categories, determined by ? index, was satisfactory: Nugent?s vs. novel microscopy method (? = 0.68; good agreement), and Nugent?s vs. novel microscopy method without intermediary results (? = 0.83; very good agreement). We also demonstrated that compared to Nugent?s method, as the golden standard, the novel microscopy method had high sensitivity and specificity (ranging from 75%?99.3%) and positive and negative predictive values (ranging from 88.8%?99.5%). Our method is based on a relative number of bacterial morphotypes, either rod forms (? 1.5 ?m, lactobacilli) or non-rod forms (< 1.5 ?m, bacterial vaginosis associated bacteria) under 200? magnification, which extends the surface of examined preparation, but without prolongation of observer?s working time. Conclusion. The novel microscopy method in diagnosing BV corresponded well with Nugent?s scoring system which allows it to be an alternative method in diagnosing BV. Further-more, the novel microscopy method is based on a relative number of bacterial morphotypes that appeared to be flexible and can be reorganized in the way to categorize findings into only two groups: normal and BV, which makes it comparable to dichotomous Amsel?s clinical criterion.

Airway microbial communities, smoking and asthma in a general population sample

BACKGROUND

Normal airway microbial communities play a central role in respiratory health but are poorly characterized. Cigarette smoking is the dominant global environmental influence on lung function, and asthma has become the most prevalent chronic respiratory disease worldwide. Both conditions have major microbial components that are incompletely defined.

METHODS

We investigated airway bacterial communities in a general population sample of 529 Australian adults. Posterior oropharyngeal swabs were analyzed by sequencing of the 16S rRNA gene. The microbiota were characterized according to their prevalence, abundance and network memberships.

FINDINGS

The microbiota were similar across the general population, and were strongly organized into co-abundance networks. Smoking was associated with diversity loss, negative effects on abundant taxa, profound alterations to network structure and expansion of Streptococcus spp. By contrast, the asthmatic microbiota were selectively affected by an increase in Neisseria spp. and by reduced numbers of low abundance but prevalent organisms.

INTERPRETATION

Our study shows that the healthy airway microbiota in this population were contained within a highly structured ecosystem, suggesting balanced relationships between the microbiome and human host factors. The marked abnormalities in smokers may contribute to chronic obstructive pulmonary disease (COPD) and lung cancer. The narrow spectrum of abnormalities in asthmatics encourages investigation of damaging and protective effects of specific bacteria.

FUNDING

The study was funded by the Asmarley Trust and a Wellcome Joint Senior Investigator Award to WOCC and MFM (WT096964MA and WT097117MA). The Busselton Healthy Ageing Study is supported by the Government of Western Australia (Office of Science, Department of Health) the City of Busselton, and private donations.

Comparative Effectiveness of Treatments for Bacterial Vaginosis: A Network Meta-Analysis

Bacterial vaginosis (BV) is a common vaginal dysbiosis in women of reproductive age. However, the cure rate for BV varies considerably and many women experience a relapse after the initial treatment. The present meta-analysis aimed to evaluate the clinical cure rates (CCRs) in randomized controlled trials (RCTs) through different therapies and administration routes. This meta-analysis included a final set of 25 eligible studies with a total of 57 RCTs and compared the effectiveness of BV treatments among non-pregnant and pregnant women. The initial range of CCRs varied greatly from 46.75% to 96.20% and the final pooled CCR was 75.5% (CI: 69.4-80.8) using the random model. The heterogeneity indices were Q = 418.91, I2 = 94.27%, and τ = 0.7498 (p < 0.0001). No publication bias was observed according to Funnel plot symmetry and Egger's linear regression test (p = 0.1097). To evaluate different variables, sub-group analysis, meta-regressions, and network meta-analysis were also realized. The highest P-scores in CCR were obtained by: (1) a combined therapy with local probiotic treatment and application of antibiotics by both administration route (oral clindamycin and local 5-nitroimidazole; P-score = 0.92); (2) a combined therapy with oral administration of 5-nitroimidazole and probiotic treatment (P-score = 0.82); (3) and a combined therapy with local administration of 5-nitroimidazole and oral probiotic treatment (P-score = 0.68). A clear-cut decision of the best BV treatment was not possible due to the heterogeneity of outcomes reported in the trials, indicating the necessity for a better characterization of RCTs. Finally, combined therapies suggested the reduction of the optimal concentration of antibiotics, and double phase treatments of antibiotics indicated an increment of CCRs in BV.

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection

Mounting evidence suggests that Lactobacillus species may not necessarily be the sine qua non of healthy cervicovaginal microbiota (CVM), especially among reproductive-age African women. A majority of African women have high-diversity non-Lactobacillus-dominated CVM whose bacterial functions remain poorly characterized. Functional profiling of the CVM is vital for investigating human host-microbiota interactions in health and disease. Here, we investigated the functional potential of L. iners-dominated and high-diversity non-Lactobacillus-dominated CVM of 75 African women with and without bacterial vaginosis (BV) and high-risk human papillomavirus (HR-HPV) infection. Functional contents were predicted using PICRUSt. Microbial taxonomic diversity, BV, and HR-HPV infection statuses were correlated with the inferred functional composition of the CVM. Differentially abundant inferred functional categories were identified using linear discriminant analysis (LDA) effect size (LEfSe) (p-value <0.05 and logarithmic LDA score >2.0). Of the 75 women, 56 (74.7%), 35 (46.7%), and 29 (38.7%) had high-diversity non-Lactobacillus-dominated CVM, BV, and HR-HPV infection, respectively. Alpha diversity of the inferred functional contents (as measured by Shannon diversity index) was significantly higher in women with high-diversity non-Lactobacillus-dominated CVM and BV than their respective counterparts (H statistic ≥11.5, q-value <0.001). Ordination of the predicted functional metagenome content (using Bray-Curtis distances) showed that the samples segregated according to the extent of microbial taxonomic diversity and BV (pseudo-F statistic ≥19.6, q-value = 0.001) but not HR-HPV status (pseudo-F statistic = 1.7, q-value = 0.159). LEfSe analysis of the inferred functional categories revealed that transport systems (including ABC transporters) and transcription factors were enriched in high-diversity CVM. Interestingly, transcription factors and sporulation functional categories were uniquely associated with high-diversity CVM, BV, and HR-HPV infection. Our predictive functional analysis reveals features unique to high-diversity CVM, BV and HR-HPV infections. Such features may represent important biomarkers of BV and HR-HPV infection. Our findings require proof-of-concept functional studies to examine the relevance of these potential biomarkers in women's reproductive health and disease.

Vaginotypes of the human vaginal microbiome

The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.

The effect of probiotic supplementation during pregnancy on the interaction network of vaginal microbiome

AIM

To evaluate the effect of probiotic supplementation on the vaginal microbiome and provide the effective evidences for clinical management of pregnant women.

METHODS

A total of 28 healthy pregnant women at 32 weeks of gestation were enrolled. The women were divided randomly to the probiotic group where they were prescribed with 2 g combined probiotics daily (13 cases) during the third trimester of pregnancy or to the control group (15 cases) on a voluntary basis. Their vaginal samples were taken for analyzing microbiome with the 16S rDNA amplicon sequencing of V4 region.

RESULTS

There was no significant difference on the clinical characteristics between the probiotic and control groups. The complexity of vaginal microbial network increased from 32 weeks of gestation to antepartum. Lactobacillus was the dominant microbiota. The probiotic supplementation had no obvious influence on the structure of the vaginal microbiome, whereas the relationships of some pivotal vaginal microbiota at the genus level changed in the probiotic group.

CONCLUSION

The vaginal microbiome varied during the third trimester of pregnancy. The features of the vaginal microbiota after probiotic supplementation had shifted and the interaction network had the tendency to be loose. The probiotic supplementation may be useful in regulating the interaction network of vaginal microbiome.

Bacterial Vaginosis: Current Diagnostic Avenues and Future Opportunities

A healthy female genital tract harbors a microbiome dominated by lactic acid and hydrogen peroxide producing bacteria, which provide protection against infections by maintaining a low pH. Changes in the bacterial compositions of the vaginal microbiome can lead to bacterial vaginosis (BV), which is often associated with vaginal inflammation. Bacterial vaginosis increases the risk of acquiring sexually transmitted infections (STIs) like human immunodeficiency virus (HIV) and affects women's reproductive health negatively. In pregnant women, BV can lead to chorioamnionitis and adverse pregnancy outcomes, including preterm premature rupture of the membranes and preterm birth. In order to manage BV effectively, good diagnostic procedures are required. Traditionally clinical and microscopic methods have been used to diagnose BV; however, these methods require skilled staff and time and suffer from reduced sensitivity and specificity. New diagnostics, including highly sensitive and specific point-of-care (POC) tests, treatment modalities and vaccines can be developed based on the identification of biomarkers from the growing pool of vaginal microbiome and vaginal metabolome data. In this review the current and future diagnostic avenues will be discussed.

Screening for Bacterial Vaginosis in Pregnant Adolescents and Women to Prevent Preterm Delivery: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force

IMPORTANCE

Preterm delivery results in adverse outcomes; identifying and treating bacterial vaginosis may reduce its occurrence.

OBJECTIVE

To update the evidence on screening and treatment of asymptomatic bacterial vaginosis in pregnancy for the US Preventive Services Task Force.

DATA SOURCES

MEDLINE, Cochrane Library, and trial registries through May 29, 2019; bibliographies from retrieved articles, experts, and surveillance of the literature through December 31, 2019.

STUDY SELECTION

Fair- or good-quality English-language studies evaluating diagnostic accuracy of tests feasible within primary care; randomized clinical trials (RCTs); nonrandomized controlled intervention studies (for harms only); or meta-analyses of metronidazole or clindamycin.

DATA EXTRACTION AND SYNTHESIS

Two reviewers independently assessed titles/abstracts and full-text articles, extracted data, and assessed study quality; when at least 3 similar studies were available, meta-analyses were conducted.

MAIN OUTCOMES AND MEASURES

Sensitivity, specificity, preterm delivery, maternal adverse effects, congenital birth defects, childhood cancer.

RESULTS

Forty-four studies (48 publications) were included. No studies evaluated the benefits or harms of screening. Twenty-five studies (n = 15 785) evaluated the accuracy of screening tests; across individual studies and tests, sensitivity ranged from 0.36 to 1.0 and specificity ranged from 0.49 to 1.0. Among trials reporting findings from general obstetric populations (n = 7953), no significant association was observed between treatment and spontaneous delivery before 37 weeks (pooled absolute risk difference [ARD], -1.44% [95% CI, -3.31% to 0.43%]; 8 RCTs, n = 7571) or any delivery before 37 weeks (pooled ARD, 0.20% [95% CI, -1.13% to 1.53%]; 6 RCTs, n = 6307). Among 5 trials reporting findings among women with a prior preterm delivery, findings were inconsistent; 3 showed a significant beneficial effect, while 2 did not. Maternal adverse events from treatment were infrequent and minor (eg, candidiasis) but were slightly more common with active treatment compared with placebo across 8 RCTs. Two meta-analyses of observational studies reported no significant association between metronidazole exposure and congenital malformations (odds ratio, 0.96 [95% CI, 0.75 to 1.22]; odds ratio, 1.08 [95% CI, 0.90 to 1.29]). One cohort study reported no significantly increased incidence of childhood cancer among metronidazole-exposed children (adjusted relative risk, 0.81 [95% CI, 0.41 to 1.59]). However, studies of in utero exposure had important limitations.

CONCLUSIONS AND RELEVANCE

Accuracy of screening tests for bacterial vaginosis varies. The evidence suggests no difference in the incidence of preterm delivery and related outcomes from treatment for asymptomatic bacterial vaginosis in a general obstetric population but was inconclusive for women with a prior preterm delivery. Maternal adverse events from treatment appear to be infrequent and minor, but the evidence about harms from in utero exposure was inconclusive.

Microbiome-based body site of origin classification of forensically relevant blood traces

Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood trace originated are missing, but would be highly valuable in crime scene investigations. With this study, we introduce a taxonomy-independent deep neural network approach based on massively parallel microbiome sequencing, which delivers accurate body site of origin classification of forensically-relevant blood samples, such as menstrual, nasal, fingerprick, and venous blood. A total of 50 deep neural networks were trained using a large 16S rRNA gene sequencing dataset from 773 reference samples, including 220 female urogenital tract, 190 nasal cavity, 213 skin, and 150 venous blood samples. Validation was performed with de-novo generated 16S rRNA gene massively parallel sequencing (MPS) data from 94 blood test samples of four different body sites, and achieved high classification accuracy with AUC values at 0.992 for menstrual blood (N = 23), 0.978 for nasal blood (N = 16), 0.978 for fingerprick blood (N = 30), and 0.990 for venous blood (N = 25). The obtained highly accurate classification of menstrual blood was independent of the day of the menses, as established in additional 86 menstrual blood test samples. Accurate body site of origin classification was also revealed for 45 fresh and aged mock casework blood samples from all four body sites. Our novel microbiome approach works based on the assumption that a sample is from blood, as can be obtained in forensic practise from prior presumptive blood testing, and provides accurate information on the specific body source of blood, with high potentials for future forensic applications.

Understanding and interpreting community sequencing measurements of the vaginal microbiome

Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.

Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status

Recent research on vaginal microbiota relies on high throughput sequencing while microscopic methods have a long history in clinical use. We investigated the correspondence between microscopic findings of Pap smears and the vaginal microbiota composition determined by next generation sequencing among 50 asymptomatic women. Both methods produced coherent results regarding the distinction between Lactobacillus-dominant versus mixed microbiota, reassuring gynaecologists for the use of Pap smear or wet mount microscopy for rapid evaluation of vaginal bacteria as part of diagnosis. Cytologic findings identified women with bacterial vaginosis and revealed that cytolysis of vaginal epithelial cells is associated to Lactobacillus crispatus-dominated microbiota. Education and socio-economic status were associated to the vaginal microbiota variation. Our results highlight the importance of including socio-economic status as a co-factor in future vaginal microbiota studies.