Vaginal microbiome signatures in Chlamydia trachomatis infected women

Introduction: In healthy women, lactobacilli play a crucial role in maintaining the microbial homeostasis of the vaginal niche. In case of bacterial vaginosis (BV), a condition characterised by a depletion of lactobacilli and an increasing number of anaerobes, a higher risk of urogenital and sexually transmitted infections (STIs) is reported. The vaginal environment of healthy and BV-positive women have been extensively studied, leading to the identification of the microbial species dominating these opposite conditions and to the description of specific metabolic profiles. Besides that, less is known about the vaginal microbiome in case of STIs, as Chlamydia trachomatis (CT) infections. The aim of this study was to analyse the composition of the endogenous microbiota and the metabolic signatures of the vaginal niche in 3 different conditions: healthy, BV and CT infections. Methods: From July 2016, all the pre-menopausal women attending the STI Outpatients Clinic of Sant’Orsola-Malpighi Hospital in Bologna (Italy) and meeting one of the following criteria were enrolled: presence of vaginal symptoms or presence of risk factors for CT infection. Patients with vaginal candidiasis were excluded. For all the patients, a vaginal swab was collected for molecular CT detection (Versant CT/GC DNA 1.0 Assay; Siemens), whereas Amsel criteria were used for BV assessment. Moreover, for each woman, an additional vaginal swab stored in saline was collected and centrifuged. Cell pellets were examined with a DNA-microarray platform including 17 probe sets specific for the most representative vaginal bacterial groups and with a quantitative real-time PCR targeting 16s rRNA gene of Gardnerella vaginalis (GV). Cell-free supernatants were used for metabolomic analysis by means of 1H-NMR spectroscopy. NMR spectra were recorded with an AVANCE spectrometer (Bruker). Similarities among microbial and metabolic profiles of samples were investigated by means of a principal component analysis (PCA). Differences in GV DNA loads and metabolites concentrations were analysed by ANOVA test. The study was approved by the Hospital Ethical Committee. Results: Among all the women enrolled, 25 were considered healthy, 18 received a diagnosis of BV and 22 were positive for CT. PCA revealed that the vaginal microbiome of healthy and BV-subjects were clearly distinct and that CT-positive women were more similar to healthy women rather than to BV-positives, both for microbial composition and for metabolic profile. The mean GV DNA load was significantly different between the groups (p=0.03): healthy and CT positive women showed similar and lower mean loads compared to BV group. At a metabolic level, significantly higher concentrations of formate, ethanolamine and methylamine were found in BV-patients, while tryptophan and lactate were more present in healthy and CT-positive women. Conclusion: Specific microbial and metabolic signatures characterise different clinical conditions of the vaginal tract. In this context, CT-positive women are definitely more similar to healthy than BV-subjects.