High treatment failure rate is better explained by resistant gene detection than by minimal inhibitory concentrations in patients with urogenital Chlamydia trachomatis infection.

•Minimum inhibitory concentrations (MICs) of macrolides and tetracyclines against Chlamydia trachomatis were comparable in the treatment success and treatment failure groups.•The occurrence of gene mutations in 23S rRNA and tet(M) acquisition are better associated with clinical treatment outcomes of C. trachomatis infection than MICs.•The A2057G, C2452A, and T2611C gene mutations of 23S rRNA were detected in C. trachomatis clinical isolates with azithromycin treatment.•The detection of resistance genes may be a preferable assay for the prediction of treatment results compared with in vitro drug susceptibility tests.