Highly discriminative genotyping of Chlamydia trachomatis using omp1 and a set of variable number tandem repeats

Abstract

This article reports the development of a method for genotyping Chlamydia trachomatis, using PCR and sequencing of omp1, supplemented with three new variable number tandem repeat (VNTR) loci of C. trachomatis. Typeability, reproducibility and discriminatory power were assessed using four groups of samples: two groups (I and II) of C. trachomatis-positive patients and their positive partner(s), one group (III) of patients with recurrent or persistent C. trachomatis infections, and one group (IV) comprising samples containing a newly discovered mutant strain with a 377-bp deletion in the cryptic plasmid, the new variant C. trachomatis (nvCT). The VNTR loci (designated CT1335, CT1299, and CT1291) were all single nucleotide repeats chosen for maximal mutability and variation. In the study material, nine variants of CT1335, eight variants of CT1299 and five variants of CT1291 were found. The discriminatory power (D) of omp1 in the present material was D(omp1) = 0.69. Ds for VNTRs CT1335, CT1299 and CT1291 were 0.53, 0.74 and 0.74, respectively. The resolution power of the omp1-VNTR assay was 0.94. Stability over time of the VNTRs was investigated and found to be adequate for epidemiological studies. Using this genotyping assay, it was confirmed that the nvCT strain was indeed a clone. These results indicate that, with this novel method, strains of C. trachomatis can be individually identified, and epidemiological associations established.

Development and Evaluation of anompAQuantitative Real-Time PCR Assay forChlamydia trachomatisSerovar Determination

“…These have included multilocus sequence-based approaches (11,18) and use of a microsphere suspension array (8). A real-time PCR system offering typing of urogenital strains (D to K) and (L1 to L3) has been reported previously (9).…”

Genotyping and prevalence of Chlamydia trachomatis infection among women in Belém, Pará, northern Brazil

“…The availability of the whole genome sequence for C. trachomatis has led to the development of several new genotyping systems, such as multilocus sequence typing (MLST) and multilocus variable number tandem repeat analyses (MLVA), with a higher discriminating capacity [10][11][12]. However, these approaches have been used within the framework of the current ompA-based C. trachomatis classification system, as there is not yet a standardized nomenclature or classification system based on these novel typing methods [8].…”

Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries

“…In most countries, almost half of all urogenital chlamydia infections are of serotype E, and within this serotype the ompA E/Bour genotype predominates (4)(5)(6)(7)(8). Therefore, other typing methods were developed, such as multilocus variable-number tandem-repeat analysis (MLVA) (8,9) and multilocus sequence typing (MLST) (10)(11)(12).…”