Direct genotyping and nucleotide sequence analysis of VS1 and VS2 of the Omp1 gene of Chlamydia trachomatis from Moroccan trachomatous specimens

To determine the range of ocular strains of Chlamydia trachomatis circulati ng in southern Morocco, where trachoma is endemic, and to compare the value of the molecular methods for genotyping C. trachomatis, ocular specimens w ere subjected to a direct Omp1 PCR-restriction fragment length polymorphism (RFLP)-based analysis and direct sequencing. PCR-RFLP analysis shows that the Ba genotype represents the most frequent one (63%), followed by genotyp e A (45%), whereas no B or C genotypes were identified among the 53 out of 108 specimens that were strongly positive in the Omp1 CT1-CT5 PCR. Our resu lts further show that the notion of interfamily and intrafamily transmissio n is very likely. To confirm the genotype identity of C, trachomatis as det ermined by PCR-RFLP, 16 selected specimens were sequenced across variable s equence 1 (VS1) and 2 (VS2). No discrepancies were found between PCR-RFLP t yping and the genotype identity confirmed by nucleotide sequencing of the P CR product. Our results clearly indicate that both molecular methods of typ ing chlamydiae (i.e., PCR-RFLP and sequencing) are important and have speci fic applications for clinical epidemiological purposes. This is the case fo r individuals infected with more than one clonal population of C. trachomat is. The unambiguous nucleotide sequencing therefore defines an important ep idemiologic descriptor for the infected patient whether the source is from a clonal population of organisms or whether it represents a more dynamic pr ocess of strain dominance or genetic change. Furthermore, Omp1 genotyping a ffords the necessary approach to epidemiologic investigations in areas of t he world endemic for trachoma, where only one or two serovars are known to predominate. (C) 2001 Editions scientifiques et medicales Elsevier SAS.