Microbiome analysis to develop Gardnerella vaginalis abundance threshold to profile and detect potential STI pathogens

BackgroundGlobally, since the 1990s the rate of curable sexually transmitted bacterial infections (STIs) has increased. In 2018, there were 447,694 new diagnoses in the UK, a 5% increase from 2017. The successful diagnosis of Chlamydia and Gonorrhoea in the laboratory remains relatively low at approx. 10% leaving patients at risk from untreated infections. Rapid diagnosis, appropriate treatment and infection control measures are, therefore, particularly important. This study has developed a threshold and detected key pathogens that are effective and reliable in the diagnostics of STIs.Methods and findingsIn the study, 180 urine, vaginal and cervical samples were blindly analysed. Chlamydia and Gonorrhoea were found in only 6.7% of samples, while Gardnerella vaginalis occurred in 94%. Establishing an abundance threshold of >=1% for G. vaginalis, is a means by which to highlight abnormalities that may cause Bacterial Vaginosis (BV). This finding is supported by Lactobacillus spp., which significantly decreased (P < 0.001) to 17.5% in the presence of G. vaginalis and increased to 87.8% in its absence. Prevotella amnii and Sneathia amnii, which are also linked to BV, showed significant differences in abundance (P < 0.01) in the presence of G. vaginalis. The overall outcome was that 63.9% of samples were diagnosed with STIs, leaving 36.1% unknown. The 16S rRNA gene sequences generated were analysed using the Open Source, Mothur and the Ribosomal Database Project database to identify taxonomy. All statistical analysis was carried out using non-parametric methods