We detected Chlamydia trachomatis biovar L2 in vaginal swab specimens of 7 women with vaginal discharge in South Africa. Whole-genome sequencing directly from clinical specimens identified a closely related cluster of strains. The clinical role of this infection in the context of syndromic management should be clarified.
Keywords: Chlamydia trachomatis; South Africa; bacteria; biovar L2; genital infection; lymphogranuloma venereum; serovar L; sexually transmitted infections.