Putative azithromycin resistance mutations in Chlamydia trachomatis are globally distributed but arose before azithromycin was discovered.

Azithromycin is widely used to treat Chlamydia trachomatis infections, yet the extent of resistance to the drug across the species has not been addressed. We surveyed mutations and substitutions linked to putative azithromycin resistance across 1,349 high-quality C. trachomatis genomes. Mutations in the rplV gene encoding three non-synonymous substitutions, compared with the canonical C. trachomatis reference strain D//TW-3/Cx sequence, were found to be common but largely conserved within phylogenetic lineages causing prevalent urogenital and anorectal infections and lymphogranuloma venereum. However, no mutations were identified in the ocular lineage. Time-scaled phylogenetic analysis suggested that these mutations predate the clinical introduction of azithromycin. In contrast, no consistent resistance-associated patterns were observed in 23S rRNA or rplD genes. This large-scale genomic surveillance provides critical insights into the evolutionary trends of putative azithromycin resistance in C. trachomatis and underscores the importance of integrating genomic monitoring with phenotypic susceptibility testing to accurately assess and manage antimicrobial resistance.