A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research

Chlamydia trachomatis causes common sexually transmitted infections. The use of whole-genome sequencing for its classification and surveillance is limited due to technical challenges and the lack of standardized typing frameworks. In particular, core-genome multilocus sequence typing (cgMLST), a scalable and portable approach widely applied to other bacterial pathogens, remains little explored for C. trachomatis. Here, we compiled and curated a diverse C. trachomatis genome dataset (1230 samples from 26 countries), including publicly available and newly generated assemblies, to develop a cgMLST system (n = 846 loci) optimized for standardized local deployment. Benchmarking assays demonstrated its high typeability and clustering congruence with core-SNP approaches and the existing online cgMLST schema (PubMLST). Our cgMLST framework recapitulated the four major evolutionary lineages of C. trachomatis and enabled in-depth exploration of global phylogenomic diversity and evolution, including intra-lineage diversity for detection and tracking of contemporary strains. By enabling a direct link between loci/alleles and specific phylogenomic/phenotypic traits, this cgMLST approach also elucidated the C. trachomatis genome-wide recombination landscape and identified lineage-specific alleles (and disrupted loci) with potential diagnostic and/or functional relevance. Our cgMLST schema is publicly available for local implementation accompanied by a hierarchical cgMLST-based nomenclature, promoting harmonized genogroup tracking across laboratories and countries. The use of whole-genome sequencing for classification and surveillance of the pathogen Chlamydia trachomatis is limited due to the lack of standardized typing frameworks. Here, the authors present a core-genome multilocus sequence typing system, accompanied by a hierarchical nomenclature, optimized for standardized local implementation.