Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen

Patiyan Andersson, Martin Klein, Rachael Lilliebridge, Philip Giffard

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    Ultra-deep Illumina sequencing was performed on whole genome amplified DNA derived from a Chlamydia trachomatis-positive vaginal swab. Alignment of reads with reference genomes allowed robust SNP identification from the C. trachomatis chromosome and plasmid. This revealed that the C. trachomatis in the specimen was very closely related to the sequenced urogenital, serovar F, clade T1 isolate F-SW4. In addition, high genome-wide coverage was obtained for Prevotella melaninogenica, Gardnerella vaginalis, Clostridiales genomosp. BVAB3 and Mycoplasma hominis. This illustrates the potential of metagenome data to provide high resolution bacterial typing data from multiple taxa in a diagnostic specimen.
    Original languageEnglish
    Pages (from-to)E405-E408
    Number of pages4
    JournalClinical Microbiology and Infection
    Volume19
    Issue number9
    DOIs
    Publication statusPublished - Sep 2013

    Fingerprint

    Bacterial Genomes
    Chlamydia trachomatis
    DNA Sequence Analysis
    Genotype
    Genome
    Bacterial Typing Techniques
    Prevotella melaninogenica
    Metagenome
    Gardnerella vaginalis
    Mycoplasma hominis
    High-Throughput Nucleotide Sequencing
    Single Nucleotide Polymorphism
    Plasmids
    Chromosomes
    DNA

    Cite this

    @article{6c9a5936ca84475fb1ed9b77e7098957,
    title = "Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen",
    abstract = "Ultra-deep Illumina sequencing was performed on whole genome amplified DNA derived from a Chlamydia trachomatis-positive vaginal swab. Alignment of reads with reference genomes allowed robust SNP identification from the C. trachomatis chromosome and plasmid. This revealed that the C. trachomatis in the specimen was very closely related to the sequenced urogenital, serovar F, clade T1 isolate F-SW4. In addition, high genome-wide coverage was obtained for Prevotella melaninogenica, Gardnerella vaginalis, Clostridiales genomosp. BVAB3 and Mycoplasma hominis. This illustrates the potential of metagenome data to provide high resolution bacterial typing data from multiple taxa in a diagnostic specimen.",
    keywords = "article, bacterial genome, Chlamydia trachomatis, chlamydiasis, Clostridiales, DNA sequence, female, Gardnerella vaginalis, gene amplification, human, metagenome, Mycoplasma hominis, nonhuman, nucleotide sequence, Prevotella melaninogenica, priority journal, single nucleotide polymorphism, vaginitis, virus genome, Bacteria (microorganisms)",
    author = "Patiyan Andersson and Martin Klein and Rachael Lilliebridge and Philip Giffard",
    year = "2013",
    month = "9",
    doi = "10.1111/1469-0691.12237",
    language = "English",
    volume = "19",
    pages = "E405--E408",
    journal = "Clinical Microbiology and Infection",
    issn = "1198-743X",
    publisher = "Wiley-Blackwell",
    number = "9",

    }

    Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen. / Andersson, Patiyan; Klein, Martin; Lilliebridge, Rachael; Giffard, Philip.

    In: Clinical Microbiology and Infection, Vol. 19, No. 9, 09.2013, p. E405-E408.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Sequences of multiple bacterial genomes and a Chlamydia trachomatis genotype from direct sequencing of DNA derived from a vaginal swab diagnostic specimen

    AU - Andersson, Patiyan

    AU - Klein, Martin

    AU - Lilliebridge, Rachael

    AU - Giffard, Philip

    PY - 2013/9

    Y1 - 2013/9

    N2 - Ultra-deep Illumina sequencing was performed on whole genome amplified DNA derived from a Chlamydia trachomatis-positive vaginal swab. Alignment of reads with reference genomes allowed robust SNP identification from the C. trachomatis chromosome and plasmid. This revealed that the C. trachomatis in the specimen was very closely related to the sequenced urogenital, serovar F, clade T1 isolate F-SW4. In addition, high genome-wide coverage was obtained for Prevotella melaninogenica, Gardnerella vaginalis, Clostridiales genomosp. BVAB3 and Mycoplasma hominis. This illustrates the potential of metagenome data to provide high resolution bacterial typing data from multiple taxa in a diagnostic specimen.

    AB - Ultra-deep Illumina sequencing was performed on whole genome amplified DNA derived from a Chlamydia trachomatis-positive vaginal swab. Alignment of reads with reference genomes allowed robust SNP identification from the C. trachomatis chromosome and plasmid. This revealed that the C. trachomatis in the specimen was very closely related to the sequenced urogenital, serovar F, clade T1 isolate F-SW4. In addition, high genome-wide coverage was obtained for Prevotella melaninogenica, Gardnerella vaginalis, Clostridiales genomosp. BVAB3 and Mycoplasma hominis. This illustrates the potential of metagenome data to provide high resolution bacterial typing data from multiple taxa in a diagnostic specimen.

    KW - article

    KW - bacterial genome

    KW - Chlamydia trachomatis

    KW - chlamydiasis

    KW - Clostridiales

    KW - DNA sequence

    KW - female

    KW - Gardnerella vaginalis

    KW - gene amplification

    KW - human

    KW - metagenome

    KW - Mycoplasma hominis

    KW - nonhuman

    KW - nucleotide sequence

    KW - Prevotella melaninogenica

    KW - priority journal

    KW - single nucleotide polymorphism

    KW - vaginitis

    KW - virus genome

    KW - Bacteria (microorganisms)

    UR - http://www.scopus.com/inward/record.url?scp=84882636123&partnerID=8YFLogxK

    U2 - 10.1111/1469-0691.12237

    DO - 10.1111/1469-0691.12237

    M3 - Article

    VL - 19

    SP - E405-E408

    JO - Clinical Microbiology and Infection

    JF - Clinical Microbiology and Infection

    SN - 1198-743X

    IS - 9

    ER -