Background Chlamydia trachomatis is reported to be the most common sexually transmitted infection (STI) in developed countries; this data depends on the sensitivity and specificity of the diagnostic test employed. Even when Nucleic acid amplification tests (NAATs) are used to detect C.trachomatis infection, the occurrence of variant strains which lack the cryptic plasmid or possess deletion mutations may be responsible for negative test results, as was detected in Sweden recently. The present study was undertaken to establish the true prevalence of C.trachomatis infection among males with urethritis using not only a well tested NAAT but also Direct Fluorescent Antibody test (DFA).

Methods A total of 34 male patients reporting to the STI OPD of the Lok Nayak Hospital with urethritis were included in this study. Gram staining and culture was done for detection of Neisseria gonorrhoeae and DFA and real-time PCR using COBAS^® TaqMan^® CT Test, v2.0 to detect the presence of C.trachomatis.

Results Among the 34 males, 55.9% cases were positive for N.gonorrhoeae by culture. DFA for C.trachomatis was positive in 17.6% cases, 5 out of 6 DFA positive cases were also positive for N.gonorrhoeae. PCR for C.trachomatis has so far been done in 19 cases, including 4 of the DFA positive cases, and none of them yielded a positive result. Neither C.trachomatis nor N.gonorrhoeae was found in 41.1% cases.

Conclusion C.trachomatis was detected only in 17.6% men with urethritis and that too only by DFA and none by PCR. This could be either an actual low prevalence of C.trachomatis or it may be due to the occurrence of new variant strains not detected by the molecular diagnostic test used by us. Sequencing of C.trachomatis isolated from patient specimens will be required to detect mutants that could be responsible for underdiagnosis, when relying only on NAATs.