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Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-6085-6749
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2014 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, 4398- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2014. Vol. 4, 4398- p.
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Medical and Health Sciences
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URN: urn:nbn:se:uu:diva-223522DOI: 10.1038/srep04398ISI: 000332937300007OAI: oai:DiVA.org:uu-223522DiVA: diva2:715082
Available from: 2014-04-30 Created: 2014-04-22 Last updated: 2017-12-05Bibliographically approved

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Ameur, AdamBunikis, IgnasHäggqvist, SusanaLindau, CeciliaLindberg, Julia HedlundGustavsson, IngerGyllensten, Ulf
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