Researchers developed a core-genome multilocus sequence typing schema for Chlamydia trachomatis to standardize genomic surveillance across local laboratory environments, according to a study published in Nature Communications.
The team curated a dataset of 1,230 genome assemblies from 26 countries, spanning isolate collection dates between 1957 and 2023. To expand modern representation, the authors attempted whole-genome sequencing on 163 samples from the Portuguese National Reference Laboratory collection. Of 148 samples processed via targeted enrichment, 45 yielded complete genome assemblies that passed quality controls, alongside 12 assemblies derived from cultured clinical isolates. The 57 newly sequenced genomes increased the dataset's European isolates by 17% and its anorectal samples by 56%.
The resulting typing schema comprises 846 loci, including 838 chromosomal coding sequences and eight plasmid sequences. Together, these loci cover approximately 85% to 88% of the expected genome size and capture 26,528 unique alleles. When benchmarked against the existing online PubMLST schema using the chewBBACA allele caller, the new framework achieved a median locus calling rate of 99.2% per sample, compared to 96.7% for the older system. The earlier schema omitted several typing targets, including ompA, pmpH, and plasmid loci.
To support surveillance workflows, the researchers designed a three-tier hierarchical nomenclature system based on allelic differences. The system delineates isolates into four known evolutionary lineages at a 475-allelic-difference threshold, high-level genogroups at 75 allelic differences, and low-level genogroups at 25 allelic differences. Across the 1,230 evaluated genomes, this classification produced 473 unique nomenclature codes covering 179 high-level and 473 low-level genogroups.
The complete schema and accompanying analysis files are publicly hosted on Zenodo under DOI 10.5281/zenodo.17177579, with an adapted version available through the chewie-NS platform for local pipeline deployment.
