title: 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.
authors.affiliation: 1] Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden [2].
authors.forename: Adam
authors.initials: A
authors.lastname: Ameur
authors.affiliation: 1] Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa [2].
authors.forename: Tracy L
authors.initials: TL
authors.lastname: Meiring
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden.
authors.forename: Ignas
authors.initials: I
authors.lastname: Bunikis
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden.
authors.forename: Susana
authors.initials: S
authors.lastname: Häggqvist
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Lindau
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden.
authors.forename: Julia Hedlund
authors.initials: JH
authors.lastname: Lindberg
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden.
authors.forename: Inger
authors.initials: I
authors.lastname: Gustavsson
authors.affiliation: 1] Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa [2] National Health Laboratory Service, South Africa.
authors.forename: Zizipho Z A
authors.initials: ZZ
authors.lastname: Mbulawa
authors.affiliation: 1] Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa [2] National Health Laboratory Service, South Africa [3].
authors.forename: Anna-Lise
authors.initials: AL
authors.lastname: Williamson
authors.affiliation: 1] Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Sweden [2].
authors.forename: Ulf
authors.initials: U
authors.lastname: Gyllensten
mesh_terms: D000293:Adolescent; D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001424:Bacterial Infections / Q000382:microbiology; D060085:Coinfection; D005260:Female; D016679:Genome, Viral; D005838:Genotype; D006678:HIV / Q000235:genetics / Q000302:isolation & purification; D015658:HIV Infections / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota / Q000235:genetics*; D058889:Molecular Typing; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D030361:Papillomavirus Infections / Q000821:virology*; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D012666:Semiconductors; D013019:South Africa; D014621:Vagina / Q000382:microbiology / Q000821:virology