Chlamydia trachomatis isolated from cervicovaginal samples in Sapporo, Japan, reveals the circulation of genetically diverse strains

Abstract

Background: This study was conducted to understand the molecular epidemiology of circulating Chlamydia trachomatis (Ct) strains in Sapporo, Japan.

Methods: A total of 713 endocervical samples collected from April 2016 to March 2019 were screened for Ct. The obtained Ct positive samples were analyzed by ompA genotyping and multilocus sequence analysis (MLSA).

Results: Eighty-three (11.6%) samples were positive for Ct plasmid DNA. Sequence analysis of the ompA gene from the 61 positive cases revealed eight genotypes: F (40.9%), E (19.6%), D (14.7%), G (9.8%), H (6.5%), I (3.2%), K (3.2%), and J (1.6%). The globally dominant genotype E and F strains were highly conserved with 13 ompA genetic variants being detected, whereas genotype D strains were the most diverse. Genetic characterization of D strains revealed that D1 genetic variants may be potentially specific to Sapporo. MLSA revealed 13 unique sequence types (STs) including four novel STs from 53 positive samples, with the globally dominant STs 39 and 19 being predominant. STs 39, 34, and 21 were exclusively associated with genotypes E and F indicating their global dominance. Novel ST70 and ST30 were specifically associated with genotype D.

Conclusion: Our study has revealed the circulation of genetically diverse Ct strains in the women population of Sapporo, Japan. We suggest identifying a transmission network of those successful strains and implementing public health prevention strategies to control the spread of Ct in Sapporo.

Keywords: Chlamydia trachomatis; Genotypes; Multilocus sequence analysis; ompA.

Fig. 1

Mid-rooted phylogenetic tree generated by the neighbor-joining method of the C. trachomatis ompA nucleotide sequences from 61 clinical strains isolated from Sapporo and 15 reference sequences available from the GenBank database. The sequence of C. muridarum was used as an outgroup. The clinical samples and their corresponding genotypes (number of samples, %) are represented by identical colors. The scale bar represents the number of nucleotide substitutions per site

Fig. 2

Multilocus sequence analysis (MLSA)-based mid-rooted phylogenetic tree of the concatenated nucleotide sequences of seven MLST loci of 53 C. trachomatis strains isolated from Sapporo. Reference sequences were obtained from the Chlamydiales MLST database https://pubmlst.org/bigsdb?db=pubmlst_chlamydiales_seqdef&page=profiles. Each clinical strain is represented by its identification number (ompA genotype/collection year). Two red lines divide the tree into two distinct groups: cluster 1 and cluster 2. Sequence types (STs) are shown in colored boxes to represent the corresponding clinical strains. The scale bar represents the number of nucleotide substitutions per site

Fig. 3

Phylogenetic tree of the C. trachomatis ompA D genotype sequences from nine clinical strains isolated in this study, 12 clinical strains from Sapporo from a previous study (4), four reference strains, and other clinical strains from the USA, Russia, Sweden, Thailand, and India. The strains isolated in this study are indicated by their identification number whereas other strains are indicated by their GenBank accession numbers. Strains represented in red indicate overall Sapporo D genotypes, whereas strains represented in fuchsia indicate Sapporo D1 genetic variants. The neighbor-joining method with a bootstrap value of 1000 replicates was used to construct the phylogenetic tree. The scale bar represents the number of nucleotide substitutions per site