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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Meiring</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4">These authors contributed equally to this work.</nlm:aff></affiliation></author><author><name sortKey="Bunikis, Ignas" sort="Bunikis, Ignas" uniqKey="Bunikis I" first="Ignas" last="Bunikis">Ignas Bunikis</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="H Ggqvist, Susana" sort="H Ggqvist, Susana" uniqKey="H Ggqvist S" first="Susana" last="H Ggqvist">Susana H Ggqvist</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lindau, Cecilia" sort="Lindau, Cecilia" uniqKey="Lindau C" first="Cecilia" last="Lindau">Cecilia Lindau</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lindberg, Julia Hedlund" sort="Lindberg, Julia Hedlund" uniqKey="Lindberg J" first="Julia Hedlund" last="Lindberg">Julia Hedlund Lindberg</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Gustavsson, Inger" sort="Gustavsson, Inger" uniqKey="Gustavsson I" first="Inger" last="Gustavsson">Inger Gustavsson</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mbulawa, Zizipho Z A" sort="Mbulawa, Zizipho Z A" uniqKey="Mbulawa Z" first="Zizipho Z. 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Meiring</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4">These authors contributed equally to this work.</nlm:aff></affiliation></author><author><name sortKey="Bunikis, Ignas" sort="Bunikis, Ignas" uniqKey="Bunikis I" first="Ignas" last="Bunikis">Ignas Bunikis</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="H Ggqvist, Susana" sort="H Ggqvist, Susana" uniqKey="H Ggqvist S" first="Susana" last="H Ggqvist">Susana H Ggqvist</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lindau, Cecilia" sort="Lindau, Cecilia" uniqKey="Lindau C" first="Cecilia" last="Lindau">Cecilia Lindau</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Lindberg, Julia Hedlund" sort="Lindberg, Julia Hedlund" uniqKey="Lindberg J" first="Julia Hedlund" last="Lindberg">Julia Hedlund Lindberg</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Gustavsson, Inger" sort="Gustavsson, Inger" uniqKey="Gustavsson I" first="Inger" last="Gustavsson">Inger Gustavsson</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mbulawa, Zizipho Z A" sort="Mbulawa, Zizipho Z A" uniqKey="Mbulawa Z" first="Zizipho Z. A." last="Mbulawa">Zizipho Z. A. Mbulawa</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Health Laboratory Service</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Williamson, Anna Lise" sort="Williamson, Anna Lise" uniqKey="Williamson A" first="Anna-Lise" last="Williamson">Anna-Lise Williamson</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3"><institution>National Health Laboratory Service</institution>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4">These authors contributed equally to this work.</nlm:aff></affiliation></author><author><name sortKey="Gyllensten, Ulf" sort="Gyllensten, Ulf" uniqKey="Gyllensten U" first="Ulf" last="Gyllensten">Ulf Gyllensten</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University</institution>,<country>Sweden</country></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation><nlm:aff id="a4">These authors contributed equally to this work.</nlm:aff></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Arroyo, L S" uniqKey="Arroyo L">L. S. Arroyo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barzon, L" uniqKey="Barzon L">L. Barzon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conway, C" uniqKey="Conway C">C. Conway</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Militello, V" uniqKey="Militello V">V. Militello</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johansson, H" uniqKey="Johansson H">H. Johansson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meiring, T L" uniqKey="Meiring T">T. L. Meiring</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fettweis, J M" uniqKey="Fettweis J">J. M. Fettweis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gao, W" uniqKey="Gao W">W. Gao</name></author><author><name sortKey="Weng, J" uniqKey="Weng J">J. Weng</name></author><author><name sortKey="Gao, Y" uniqKey="Gao Y">Y. Gao</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, S K" uniqKey="Li S">S. K. Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rothberg, J M" uniqKey="Rothberg J">J. M. Rothberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Doorslaer, K" uniqKey="Van Doorslaer K">K. Van Doorslaer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Villiers, E M" uniqKey="De Villiers E">E. M. de Villiers</name></author><author><name sortKey="Fauquet, C" uniqKey="Fauquet C">C. Fauquet</name></author><author><name sortKey="Broker, T R" uniqKey="Broker T">T. R. Broker</name></author><author><name sortKey="Bernard, H U" uniqKey="Bernard H">H. U. Bernard</name></author><author><name sortKey="Zur Hausen, H" uniqKey="Zur Hausen H">H. zur Hausen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mbulawa, Z Z" uniqKey="Mbulawa Z">Z. Z. Mbulawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mbulawa, Z Z" uniqKey="Mbulawa Z">Z. Z. Mbulawa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mbulawa, Z Z" uniqKey="Mbulawa Z">Z. Z. Mbulawa</name></author><author><name sortKey="Johnson, L F" uniqKey="Johnson L">L. F. Johnson</name></author><author><name sortKey="Marais, D J" uniqKey="Marais D">D. J. Marais</name></author><author><name sortKey="Coetzee, D" uniqKey="Coetzee D">D. Coetzee</name></author><author><name sortKey="Williamson, A L" uniqKey="Williamson A">A. L. Williamson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mbulawa, Z Z" uniqKey="Mbulawa Z">Z. Z. Mbulawa</name></author><author><name sortKey="Marais, D J" uniqKey="Marais D">D. J. Marais</name></author><author><name sortKey="Johnson, L F" uniqKey="Johnson L">L. F. Johnson</name></author><author><name sortKey="Coetzee, D" uniqKey="Coetzee D">D. Coetzee</name></author><author><name sortKey="Williamson, A L" uniqKey="Williamson A">A. L. Williamson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gustavsson, I" uniqKey="Gustavsson I">I. Gustavsson</name></author><author><name sortKey="Juko Pecirep, I" uniqKey="Juko Pecirep I">I. Juko-Pecirep</name></author><author><name sortKey="Backlund, I" uniqKey="Backlund I">I. Backlund</name></author><author><name sortKey="Wilander, E" uniqKey="Wilander E">E. Wilander</name></author><author><name sortKey="Gyllensten, U" uniqKey="Gyllensten U">U. Gyllensten</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marincevic Zuniga, Y" uniqKey="Marincevic Zuniga Y">Y. Marincevic-Zuniga</name></author><author><name sortKey="Gustavsson, I" uniqKey="Gustavsson I">I. Gustavsson</name></author><author><name sortKey="Gyllensten, U" uniqKey="Gyllensten U">U. Gyllensten</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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