Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
Identifieur interne : 000093 ( Main/Merge ); précédent : 000092; suivant : 000094Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing
Auteurs : Adam Ameur [Suède] ; Tracy L. Meiring [Afrique du Sud] ; Ignas Bunikis [Suède] ; Susana H Ggqvist [Suède] ; Cecilia Lindau [Suède] ; Julia Hedlund Lindberg [Suède] ; Inger Gustavsson [Suède] ; Zizipho Z. A. Mbulawa [Afrique du Sud] ; Anna-Lise Williamson [Afrique du Sud] ; Ulf Gyllensten [Suède]Source :
- Scientific Reports [ 2045-2322 ] ; 2014.
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.
Url:
DOI: 10.1038/srep04398
PubMed: 24637939
PubMed Central: 3957130
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PMC:3957130Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>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.</p>
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