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.
Highlights
Infections by human immunodeficiency virus (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 have combined sample preparation enriching for circular DNA of infectious www.nature.com/scientificreports agents using rolling circle amplification (RCA), with Ion Proton sequencing to characterize the vaginal microbiota of HIV infected women
The prevalence of human papillomavirus (HPV) is known to be substantially higher in HIV infected individuals[13], but previous studies have been limited to the range of HPV types included in the genotyping assays
Summary
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. Our method provides rapid detection of a broad range of pathogens and the ability to reconstruct complete genomes of novel infectious agents. Parallel sequencing (MPS) provides an unprecedented opportunity to detect known viral and bacterial pathogens and identify novel infectious agents. In a recent study of the DNA in plasma, HIV positive patients showed the presence of both viral and bacterial infections not present in healthy individuals[9]. No studies have used the latest MPS technology for characterization of the vaginal microbiota of HIV infected women. We have combined sample preparation enriching for circular DNA of infectious www.nature.com/scientificreports agents using rolling circle amplification (RCA), with Ion Proton sequencing to characterize the vaginal microbiota of HIV infected women
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