title: Typing of Chlamydia trachomatis strains from urine samples by amplification and sequencing the major outer membrane protein gene (omp1).
abstract: OBJECTIVE
  To develop a novel protocol for the extraction, amplification, and sequencing of Chlamydia trachomatis MOMP gene (omp1) from urine, a non-invasive source, and apply it to an epidemiological study on the distribution of C trachomatis strains in a population of pregnant women in Thailand.
  
  
  METHODS
  The C trachomatis DNA was extracted from culture stocks and urine using a slightly modified commercially available kit, the High Pure PCR Template Preparation Kit (Roche Molecular Biochemicals, IN, USA). The PCR and sequencing primers used for the amplification and sequencing of the omp1 were designed based on the nucleotide sequence of multiple C trachomatis strains found in GenBank. The protocol for the extraction, amplification, and sequencing was tested on laboratory culture stocks of reference strains of all C trachomatis serovars and on urine samples collected in a cross sectional study designed to assess the prevalence of C trachomatis infections in the cities of Bangkok and Chiang Rai, Thailand.
  
  
  RESULTS
  The omp1 gene was successfully amplified and sequenced from 18 laboratory C trachomatis reference strains and from 45 C trachomatis positive urine clinical samples collected from asymptomatic pregnant women. Among clinical samples, we found nine different C trachomatis genotypes: F (11, 25%), D (10, 22.6%), H (5, 11.7%), K (5, 11.7%), E (4, 9.3%), Ia (3, 7%), B (3, 7%), Ja (2, 4.5%), and G (1, 2.3%). One specimen generated an omp1 DNA sequence pattern indicating the presence of a mixed infection with at least two different serovars.
  
  
  CONCLUSIONS
  Urine is a convenient and reliable source for genotyping C trachomatis strains. A clear advantage of urine over traditional samples, such as cervical swabs, is that urine is a non-invasive source which makes collection easier and thus facilitates the enrolment of patients in clinical and epidemiological studies. In addition to typing, urine is increasingly used for diagnosis of C trachomatis infection by several commercially available nucleic acid amplification assays which represents a distinct advantage for collecting, transport, storage, and laboratory handling of samples.
authors.affiliation: National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: C I
authors.initials: CI
authors.lastname: Bandea
authors.forename: K
authors.initials: K
authors.lastname: Kubota
authors.forename: T M
authors.initials: TM
authors.lastname: Brown
authors.forename: P H
authors.initials: PH
authors.lastname: Kilmarx
authors.forename: V
authors.initials: V
authors.lastname: Bhullar
authors.forename: S
authors.initials: S
authors.lastname: Yanpaisarn
authors.forename: P
authors.initials: P
authors.lastname: Chaisilwattana
authors.forename: W
authors.initials: W
authors.lastname: Siriwasin
authors.forename: C M
authors.initials: CM
authors.lastname: Black
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques / Q000379:methods*; D002690:Chlamydia Infections / Q000453:epidemiology / Q000382:microbiology; D002692:Chlamydia trachomatis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D003430:Cross-Sectional Studies; D005260:Female; D005798:Genes, Bacterial; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D018272:Porins; D011247:Pregnancy; D011251:Pregnancy Complications, Infectious / Q000453:epidemiology / Q000382:microbiology; D015995:Prevalence; D013785:Thailand / Q000453:epidemiology; D014556:Urine / Q000382:microbiology*
chemical_list: D001425:Bacterial Outer Membrane Proteins; D018272:Porins; C071677:omp1 protein, Chlamydia trachomatis