title: Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples.
abstract: BACKGROUND
  Genital chlamydia infection is the most commonly diagnosed sexually transmitted infection in the UK. C. trachomatis genital infections are usually caused by strains which fall into two pathovars: lymphogranuloma venereum (LGV) and the genitourinary genotypes D-K. Although these genotypes can be discriminated by outer membrane protein gene (ompA) sequencing or multi-locus sequence typing (MLST), neither protocol affords the high-resolution genotyping required for local epidemiology and accurate contact-tracing.
  
  
  RESULTS
  We evaluated variable number tandem repeat (VNTR) and ompA sequencing (now called multi-locus VNTR analysis and ompA or "MLVA-ompA") to study local epidemiology in Southampton over a period of six months. One hundred and fifty seven endocervical swabs that tested positive for C. trachomatis from both the Southampton genitourinary medicine (GUM) clinic and local GP surgeries were tested by COBAS Taqman 48 (Roche) PCR for the presence of C. trachomatis. Samples tested as positive by the commercial NAATs test were genotyped, where possible, by a MLVA-ompA sequencing technique. Attempts were made to isolate C. trachomatis from all 157 samples in cell culture, and 68 (43%) were successfully recovered by repeatable passage in culture. Of the 157 samples, 93 (i.e. 59%) were fully genotyped by MLVA-ompA. Only one mixed infection (E & D) in a single sample was confirmed. There were two distinct D genotypes for the ompA gene. Most frequent ompA genotypes were D, E and F, comprising 20%, 41% and 16% of the type-able samples respectively. Within all genotypes we detected numerous MLVA sub-types.
  
  
  CONCLUSIONS
  Amongst the common genotypes, there are a significant number of defined MLVA sub-types, which may reflect particular background demographics including age group, geography, high-risk sexual behavior, and sexual networks.
authors.affiliation: Molecular Microbiology and Infection, School of Medicine, University of Southampton, Southampton, United Kingdom.
authors.forename: Yibing
authors.initials: Y
authors.lastname: Wang
authors.forename: Rachel J
authors.initials: RJ
authors.lastname: Skilton
authors.forename: Lesley T
authors.initials: LT
authors.lastname: Cutcliffe
authors.forename: Emma
authors.initials: E
authors.lastname: Andrews
authors.forename: Ian N
authors.initials: IN
authors.lastname: Clarke
authors.forename: Pete
authors.initials: P
authors.lastname: Marsh
mesh_terms: D000293:Adolescent; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001483:Base Sequence; D002692:Chlamydia trachomatis / Q000235:genetics* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D010865:Pilot Projects; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics; D055815:Young Adult
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004269:DNA, Bacterial; D005819:Genetic Markers; C078167:OMPA outer membrane proteins