Clinical Microbiology and Antimicrobial Chemotherapy. 2026; 28(2):148-169
To develop a molecular typing scheme for Chlamydia trachomatis to enable molecular epidemiological monitoring of this pathogen in the Russian Federation.
A set of conserved and accessory genes from 430 C. trachomatis isolates of diverse geographical and phylogenetic origins was analyzed to identify loci involved in the intraspecies clustering of the pathogen. Whole-genome sequencing data for the isolates in FASTA and FASTQ formats were obtained from the PubMLST database. To generate genetic profiles of the studied C. trachomatis isolates based on the selected loci, a bioinformatics data processing pipeline was employed, which included sequence alignment to reference genomes, analysis of single nucleotide polymorphisms within the loci, annotation and identification of orthologs, and extraction of the selected loci into an individual isolate genetic profile. Visualization of the phylogenetic analysis of the studied C. trachomatis isolates was performed using R- and Python-based analytical packages.
A panel of 188 genes involved in the intraspecies clustering of C. trachomatis was compiled, forming the basis of a novel molecular typing scheme for this pathogen intended for molecular epidemiological surveillance. The bioinformatics analysis of genetic profiles from 430 isolates of various geographical and phylogenetic origins demonstrated that the discriminatory power of the developed typing scheme is comparable to that of cgMLST, despite the latter using a much larger number of loci in the analysis.
The developed molecular typing scheme enables effective molecular epidemiological analysis of the causative agent of chlamydial infection. The development of a reagent kit for DNA library preparation followed by NGS sequencing will facilitate the efficient implementation of this typing scheme in surveillance practice and allow the creation of a profile database for domestic C. trachomatis isolates.