Introduction Chlamydia is the most common sexually transmitted disease worldwide. Many studies have been evaluated the prevalence of Chlamydia trachomatis (CT) infection while very rare studies assessed the genotype distribution in urine among males attending sexually transmitted diseases (STD) clinics (MSCs)in China. This study aimed to investigate the prevalence and molecular epidemiology of CT infection by urine samples among MSCs from different geographic areas of Guangdong province, China.

Methods A cross-sectional study was performed among MSCs from ten HIV surveillance sites of Guangdong province, China. CT DNA in male urines were extracted and detected by using the Roche cobas 4800 CT/NG. The ompA genes were amplified by nested polymerase chain reaction and sequenced. Urine leukocyte esterase test were performed.

Results Of the 1926 urine specimens, 1903 urines were successfully validated for detection of CT. Of the 1903 samples, one hundred and sixty-three (8.6%, 95% CI 8.2% to 9.0%) were found to be positive for CT. One hundred and thirty CT positive specimens were successfully genotyped by nested PCR, resulting in eight genotypes. The most prevalent genotypes were D, E, F, and J with proportions of 20.8%, 20.0%, 17.7%, 16.9%, respectively. There was no significant difference between age, geographic area, leukocyte esterase test and genotype distribution.

Conclusion There was a high prevalence of CT infection among males attending STD clinics in eastern area of Guangdong province, China. Promoting detection and molecular epidemiology research are needed for effective and comprehensive prevention and control programs.