Comparison of urine, first and second endourethral swabs for PCR based detection of genital Chlamydia trachomatis infection in male patients

Objectives: To compare endourethral swabs and urine as diagnostic specimens for the detection of genital Chlamydia trachomatis infection using the polymerase chain reaction (PCR), in male patients attending a genitourinary clinic and to assess whether the first endourethral swab used solely for diagnosing gonococcal infection could be used for C trachomatis detection as well. Methods: Two endourethral swabs were taken from 80 male patients, in whom the likelihood of genital C trachomatis infection was high. The first swab was used for microscopy and culture for Neisseria gonorrhoeae, before being used for C trachomatis detection. First voided urine specimens were collected from 61 of these patients. All three specimens were processed for C trachomatis DNA detection using the Roche Cobas Amplicor PCR. A diagnosis of genital C trachomatis infection was made if any one of the specimens tested reproducibly positive. Samples from 13 patients showing discrepant PCR results between swabs and/or urine were retested by ligase chain reaction (LCR). Results:Chlamydia trachomatis DNA was detected in 35 (43.8%) of the 80 patients. In 17 of the 35 patients (48.6%), all the genital specimens were positive. However, in 18 (51.4%) patients, one or more of the genital specimens had negative PCR results. Among the 18 patients with discrepant results, urine was found to be a more sensitive diagnostic specimen than the second urethral swab picking up 13 out of 16 positives (81.3%) as opposed to five out of 18 (27.8%). There was no significant difference between the two swabs. Retesting by LCR, of the samples from 13 of the 18 patients with discrepant PCR results confirmed them all as true positives, although as with PCR, not all specimens in the set were concordantly positive. LCR detected all the 13 positives in urine, while there was no difference in the detection rate between the first and the second urethral swabs. Conclusions: Urine appeared to be a better diagnostic specimen than the conventional second endourethral swab for C trachomatis detection by PCR in this cohort of male patients. There was no difference between the first swab, intended primarily for N gonorrhoeae testing and the second swab intended for C trachomatis detection. This raises questions over the need for the conventional second swab for detecting C trachomatis.