Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

Abstract

Infections by HIV increase the risk of acquiring secondary viral and bacterial infections and methods are needed to determine the spectrum of co-infections for proper treatment. We used rolling circle amplification (RCA) and Ion Proton sequencing to investigate the vaginal microbiome of 20 HIV positive women from South Africa. A total of 46 different human papillomavirus (HPV) types were found, many of which are not detected by existing genotyping assays. Moreover, the complete genomes of two novel HPV types were determined. Abundance of HPV infections was highly correlated with real-time PCR estimates, indicating that the RCA-Proton method can be used for quantification of individual pathogens. We also identified a large number of other viral, bacterial and parasitic co-infections and the spectrum of these co-infections varied widely between individuals. Our method provides rapid detection of a broad range of pathogens and the ability to reconstruct complete genomes of novel infectious agents.

Assessment ofAtopobium vaginaeandGardnerella vaginalisconcentrations in a cohort of pregnant South African women

“…The IVF category with its mixed flora is largely uncharacterised and complicates clinical approaches; IVF is however equally associated with poor obstetric outcomes and HIV as BVF, and has a profile more similar to that of BV than that of NVF 5 19 25. Although G. vaginalis was not significantly associated with HIV infection in our study, this species was abundant in HIV-positive women (77.8%), corresponding to previous findings in a similar population 26. The higher median concentrations of A. vaginae and G. vaginalis in HIV-positive women might contribute substantially to the spread of HIV, as these two species have been shown to induce and/or enhance the expression of HIV in vitro 27 28…”

HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria

“…In the present study we found that they were unable to establish a detectable colonization in the normal proximal gut but the resistance to their colonization disappeared when the CD4 counts dropped to below the normal limit in HIV infection. The bacteria do not seem related to oral sex as they were not present in the oral cavity as shown in the present study and were not reported to be present in the vagina by previous studies [29–31]. A food or environmental contaminant was unlikely as all subjects including both HIV-infected patients and HIV-negative controls were from New York metropolitan area.…”

“…Clinically, our knowledge of opportunistic pathogens in relation to HIV-related proximal gut problems is rather limited, and clinical signs and symptoms alone rarely suggest a specific etiology. Besides the distal gut microbiome, high-throughput sequencing has been used to examine the effects of HIV infection on the microbiomes in the vagina [29–31], lung [32], mouth [33, 34], Semen [35], and anus [36] as well as in normally sterile body sites such as the brain [37] and blood [38, 39], but not in the proximal gut. Unlike its distal counterpart, the status of microbiome in the proximal gut in HIV infection was only examined recently by analysis of gastric juice samples from only two HIV patients [40].…”

Molecular archeological evidence in support of the repeated loss of a papillomavirus gene

“…The sequences for HPV-x and HPV-y were obtained from the original authors32. Papillomaviruses are officially classified into distinct species by the International Committee for the Taxonomy of Viruses (ICTV)18.…”