title: Genotyping of Chlamydia trachomatis directly from urogenital and conjunctiva samples using an ompA gene pyrosequencing-based assay.
abstract: The aim of the present study was to develop and validate a multitarget pyrosequencing-based protocol for basic Chlamydia trachomatis genotyping directly from clinical samples and to characterize the distribution of genotypes among Slovenian sexually active population. The newly developed combination of assays that targets the variable domains VD-I and VD-IV of the C. trachomatis ompA gene, was optimized and validated with 11 reference C. trachomatis strains and by comparison to complete ompA conventional sequencing. In addition, 183 clinical specimens which were previously diagnosed as C. trachomatis positive were evaluated by pyrosequencing. The pyrosequencing products showed a 100% match to corresponding sections of the respective conventional ompA sequences. Based on our results the most frequent genotype in urogenital samples was E (51.1%) followed by F (21.4%), G and K (6.9%), D (6.1%), H (3.8%), J (2.3%) and Ia and Ja (0.8%). In conjunctiva samples the genotype distribution was E (63.3%), D and F (13.3%), K (6.7%) and G (3.3%). Pyrosequencing thus proved itself to be a rapid method for C. trachomatis typing, which is important for better understanding the pathogenesis and epidemiology of this pathogen.
authors.affiliation: Institute of Microbiology and Immunology, Medical Faculty Ljubljana, University of Ljubljana, Ljubljana, Slovenia. darja.kese@mf.uni-lj.si
authors.forename: Darja
authors.initials: D
authors.lastname: Kese
authors.forename: Marko
authors.initials: M
authors.lastname: Potocnik
authors.forename: Mojca
authors.initials: M
authors.lastname: Maticic
authors.forename: Rok
authors.initials: R
authors.lastname: Kogoj
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D002692:Chlamydia trachomatis / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D003228:Conjunctiva / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005260:Female; D005838:Genotype; D006801:Humans; D008219:Lymphogranuloma Venereum / Q000382:microbiology*; D008297:Male; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D014141:Trachoma / Q000382:microbiology*; D014566:Urogenital System / Q000382:microbiology*
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004269:DNA, Bacterial; C078167:OMPA outer membrane proteins