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.
authors: Division of Global and Tropical Health, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
authors: P
authors: P
authors: Andersson
authors: M
authors: M
authors: Klein
authors: R A
authors: RA
authors: Lilliebridge
authors: P M
authors: PM
authors: Giffard
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D002690:Chlamydia Infections / Q000382:microbiology*; D002692:Chlamydia trachomatis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D005260:Female; D006194:Gardnerella vaginalis / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054892:Metagenome; D019535:Mycoplasma hominis / Q000235:genetics / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide; D001443:Prevotella melaninogenica / Q000235:genetics / Q000302:isolation & purification; D016415:Sequence Alignment; D014621:Vagina / Q000382:microbiology*
keywords: Chlamydia trachomatis; metagenomics; whole genome sequencing