Periodic Reporting for period 1 - MUMVIP (Metabolic Profiling of the Vaginal Microbiome for Reproductive Health)
Reporting period: 2019-04-01 to 2020-12-31
Summary of the context and overall objectives of the project
There is ever increasing evidence that the vaginal microbiome plays an important role in reproductive health. Studies have shown that dysbiotic states can culminate in bacterial vaginosis, urinary tract infections and premature birth. Although the microbiome is usually characterised by 16S rRNA sequencing, the methodology is time consuming and expensive. Here we describe the development of desorption ionisation mass spectrometry (DESI-MS) based technique which characterises microbial community structures based upon metabolomic analysis directly from a vaginal swab sample. This method was tested on two different clinically relevant applications. Firstly, for stratifying patients at higher risk of pre-term birth (PTB) and secondly, assessing the potential success rates of in vitro fertilisation (IVF) treatments. The potential of the technology was assessed using three longitudinal cohort studies.
For the stratification of PTB risk, the cervicovaginal metabolome was characterised in two carefully phenotyped, independent patient cohorts sampled longitudinally through pregnancy (VMET, n=160; 455 swabs; VMET II, n= 205; 573 swabs). Integration of DESI-MS metabolic signatures with metataxonomic and immuno-profiling data resulted in the identification of metabolic signatures that robustly reflect vaginal microbiota composition (VMC) and local inflammatory status. Vaginal microbiota instability and innate immune activation, as predicted using DESI-MS, was associated with increased risk of subsequent preterm birth, including in women receiving cervical cerclage for preterm birth prevention.
To stratify pregnancy outcome, the cervicovaginal metabolome was characterised in a patient cohort of women sampled longitudinally across six different stages of IVF-treatment (ARTEMIS, n=52; 181 swabs). Patients were further classified into pregnant (n=19) and non-pregnant (n=34) IVF-treatment group based on their pregnancy status following 6-8 weeks after the end of the IVF-treatment. Integration of DESI-MS metabolic signatures with metataxonomic 16S rRNA gene sequencing data resulted in the identification of metabolic signatures that robustly reflect vaginal microbiota composition (VMC). Differences in the vaginal metabolome were also found across different stages of IVF-treatment in response to hormonal treatment therapy as determined by measured progesterone and oestrogen blood concentration levels. Furthermore, DESI-MS enabled the discrimination between pregnant and non-pregnant IVF-treatment outcome patients across all stages of IVF-treatment and independently of the VMC status.
Finally, a market assessment has been performed to identify the addressable demand of patients (n= 948) and gynaecology healthcare providers (n=45) and current diagnostic gaps with the help of an online survey questionnaire. The survey results confirmed bacterial vaginosis (BV) infection as a major burden to women, since the majority of female participant’s reported an experienced history of this disease (90%) and its associated long-term treatment (71%). Consequently, significant associations were found between patient’s willingness to pay more for vaginal infection screening and frequency of recurrent BV/yeast infection [p< 0.00001] history of vaginal infection treatment [p<0.00017] and interest in performing frequent annual testing [p< 0.0001]. Willingness to pay for the screening test was found weakly associated with household income [p=0.067] and independent of pregnancy status (pregnant, non-pregnant) history of pregnancy complications or IVF-treatment. Additionally, a strong demand in the use of probiotic treatment (53.8%) and the option of self-testing (43%) for vaginal infection screening was identified as a new source of future development for the DESI-MS technology to satisfy customers expectations. Results obtained from the female healthcare provider survey have confirmed the importance of VMC for PTB risk stratification (61.9%) and the need for more accurate diagnostic tools which help clinicians to discriminate between BV, yeast or Trichominas infection. The healthcare provider’s three most commonly used diagnostic tools for bacterial infection were culture, gram stain and PCR and therefore should be used in the future against direct on swab DESI-MS for validation purposes. The development of new POC diagnostic tools for Chlamydia and HIV detection were additionally highlighted as a diagnostic gap by the healthcare provider. Finally, matching cost expectations were identified in both patient and healthcare provider with <£20 per test for vaginal infection screening and will be used as a target price point.
Direct swab analysis by DESI-MS offers a novel point-of-care platform for monitoring vaginal microbiome dynamics in health and disease. DESI-MS could be used as a clinical stratification tool to identify those women (non-pregnant or pregnant) who exhibit a perturbed vaginal dysbiotic state characterised by Lactobacillus spp. depletion and an overgrowth of mixed anaerobic bacteria. Vaginal dysbiosis in general affects more than 70% of the female population at least once and 20-30% chronically suffer from the associated symptoms, leading to compromised quality of life and emotional/psychological problems. As reported by previous studies, it is also an increased risk factor for the development of life-threatening diseases including cervical cancer, ectopic pregnancy, preterm birth and PPROM with adverse short-term maternal and neonatal outcomes. Additionally, vaginal dysbiosis is associated with reduced fertility success rates and increased susceptibility for sexual transmitted infections. A robust diagnostic assay available for both patients and healthcare providers at an affordable price range would assist in improved detected of these conditions, monitoring of treatment responses and potentially, the identification of new drugable targets. Due to the high prevalence of the condition, the introduction of the proposed method could have society-level effects with direct impact on the economy through the improvement of the health status of hundreds of millions of women worldwide. Further socio-economic impacts are associated with the deeper understanding of the metabolic and signalling pathways governing the underlying host-microbiome interactions. The discovery of biomarkers and pathways will open up the opportunity to better understand the diseases and develop efficient therapeutic interventions.
For the stratification of PTB risk, the cervicovaginal metabolome was characterised in two carefully phenotyped, independent patient cohorts sampled longitudinally through pregnancy (VMET, n=160; 455 swabs; VMET II, n= 205; 573 swabs). Integration of DESI-MS metabolic signatures with metataxonomic and immuno-profiling data resulted in the identification of metabolic signatures that robustly reflect vaginal microbiota composition (VMC) and local inflammatory status. Vaginal microbiota instability and innate immune activation, as predicted using DESI-MS, was associated with increased risk of subsequent preterm birth, including in women receiving cervical cerclage for preterm birth prevention.
To stratify pregnancy outcome, the cervicovaginal metabolome was characterised in a patient cohort of women sampled longitudinally across six different stages of IVF-treatment (ARTEMIS, n=52; 181 swabs). Patients were further classified into pregnant (n=19) and non-pregnant (n=34) IVF-treatment group based on their pregnancy status following 6-8 weeks after the end of the IVF-treatment. Integration of DESI-MS metabolic signatures with metataxonomic 16S rRNA gene sequencing data resulted in the identification of metabolic signatures that robustly reflect vaginal microbiota composition (VMC). Differences in the vaginal metabolome were also found across different stages of IVF-treatment in response to hormonal treatment therapy as determined by measured progesterone and oestrogen blood concentration levels. Furthermore, DESI-MS enabled the discrimination between pregnant and non-pregnant IVF-treatment outcome patients across all stages of IVF-treatment and independently of the VMC status.
Finally, a market assessment has been performed to identify the addressable demand of patients (n= 948) and gynaecology healthcare providers (n=45) and current diagnostic gaps with the help of an online survey questionnaire. The survey results confirmed bacterial vaginosis (BV) infection as a major burden to women, since the majority of female participant’s reported an experienced history of this disease (90%) and its associated long-term treatment (71%). Consequently, significant associations were found between patient’s willingness to pay more for vaginal infection screening and frequency of recurrent BV/yeast infection [p< 0.00001] history of vaginal infection treatment [p<0.00017] and interest in performing frequent annual testing [p< 0.0001]. Willingness to pay for the screening test was found weakly associated with household income [p=0.067] and independent of pregnancy status (pregnant, non-pregnant) history of pregnancy complications or IVF-treatment. Additionally, a strong demand in the use of probiotic treatment (53.8%) and the option of self-testing (43%) for vaginal infection screening was identified as a new source of future development for the DESI-MS technology to satisfy customers expectations. Results obtained from the female healthcare provider survey have confirmed the importance of VMC for PTB risk stratification (61.9%) and the need for more accurate diagnostic tools which help clinicians to discriminate between BV, yeast or Trichominas infection. The healthcare provider’s three most commonly used diagnostic tools for bacterial infection were culture, gram stain and PCR and therefore should be used in the future against direct on swab DESI-MS for validation purposes. The development of new POC diagnostic tools for Chlamydia and HIV detection were additionally highlighted as a diagnostic gap by the healthcare provider. Finally, matching cost expectations were identified in both patient and healthcare provider with <£20 per test for vaginal infection screening and will be used as a target price point.
Direct swab analysis by DESI-MS offers a novel point-of-care platform for monitoring vaginal microbiome dynamics in health and disease. DESI-MS could be used as a clinical stratification tool to identify those women (non-pregnant or pregnant) who exhibit a perturbed vaginal dysbiotic state characterised by Lactobacillus spp. depletion and an overgrowth of mixed anaerobic bacteria. Vaginal dysbiosis in general affects more than 70% of the female population at least once and 20-30% chronically suffer from the associated symptoms, leading to compromised quality of life and emotional/psychological problems. As reported by previous studies, it is also an increased risk factor for the development of life-threatening diseases including cervical cancer, ectopic pregnancy, preterm birth and PPROM with adverse short-term maternal and neonatal outcomes. Additionally, vaginal dysbiosis is associated with reduced fertility success rates and increased susceptibility for sexual transmitted infections. A robust diagnostic assay available for both patients and healthcare providers at an affordable price range would assist in improved detected of these conditions, monitoring of treatment responses and potentially, the identification of new drugable targets. Due to the high prevalence of the condition, the introduction of the proposed method could have society-level effects with direct impact on the economy through the improvement of the health status of hundreds of millions of women worldwide. Further socio-economic impacts are associated with the deeper understanding of the metabolic and signalling pathways governing the underlying host-microbiome interactions. The discovery of biomarkers and pathways will open up the opportunity to better understand the diseases and develop efficient therapeutic interventions.