High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis

Abstract

Genotyping of Chlamydia trachomatis is limited by the low sequence variation in the genome, and no adequate method is available for analysis of the spread of chlamydial infections in the community. We have developed a multilocus sequence typing (MLST) system based on five target regions and compared it with analysis of ompA, the single gene most extensively used for genotyping. Sequence determination of 16 reference strains, comprising all major serotypes, serotypes A to L3, showed that the number of genetic variants in the five separate target regions ranged from 8 to 16. The genetic variation in 47 clinical C. trachomatis isolates of representative serotypes (14 serotype D, 12 serotype E, 11 serotype G, and 10 serotype K strains) was analyzed; and the MLST system detected 32 variants, whereas 12 variants were detected by using ompA analysis. Specimens of the predominant serotype, serotype E, were differentiated into seven genotypes by MLST but into only two by ompA analysis. The MLST system was applied to C. trachomatis specimens from a population of men who have sex with men and was able to differentiate 10 specimens of one predominant ompA genotype G variant into four distinct MLST variants. To conclude, our MLST system can be used to discriminate C. trachomatis strains and can be applied to high-resolution molecular epidemiology.

FIG. 1.

Schematic view of the five MLST regions. Each region is named after the dominant gene. Lengths are approximate since there are minor deletions/insertions. The hctB region has a repetitive element (gray).

FIG. 2.

Variable positions found in the CT058 target region when 16 reference strains of serotypes A to L3 and 47 clinical specimens of serotypes D, E, G, and K were analyzed. Some strains carry multiple variations.

FIG. 3.

A contact-tracing chain of males (squares) and females (rounded), with sampling dates. Negative cases are indicated with white boxes. All positive cases were infected by serotype E and had identical ompA sequences. MLST was able to separate them, and the two variants are presented with different allele numbers in two samples. *, no sequence was obtained from the target region.