To Diagnosis: PCR; for monitoring then treatment, Cell CULTURE. In women endocervical swab or urine sample. For men, urethral sample, semen or urine

Hi 

There are several techniques and they dependent on your objectives. Serological Screening: by detecting IgG antibodies against C. trachomatis MOMPS and HSP60 and Microimmunofluorescent (MIF) to differentiate between the species. 

Confirmation of the diagnosis/current infection by PCR (conventional or quantitative) form samples collected from cervical swab/urethral swab/urine sample. You can also perform cell culture.

Wishes,

Bassem

 It is OK for diagnosis by PCR and the sample to be used is Urine, Urethral swab or Urine. But some researcher have shown different prevalence in different samples. some people claim PCR of urine  is the best and some for seman sample. In ELISA Chlamydia specific IgA is better in seminal fluid where as IgG is better for Serum sample. For a better prevalence can we take all three sample (urine,seminal fluid and serum) and do the antibody and PCR test ? 

Cell culture using McCoy cells is considered the gold standard for chlamydia diagnosis. There are also several U.S. FDA approved molecular test for chlamydia trachomatis like BD ProbeTec C. trachomatis (CT) Qx Amplified DNA Assay using SDA method, APTIMA CT Assay PACE 2 CT; Probe Competition Assay (CT confirmation test) using TC,TMA,DKA and HPA method, AMPLICOR CT/NG Test for C. trachomatis using PCR and COBAS AMPLICOR CT/NG Test for C. trachomatis using PCR. Today the approved specimens for chlamydia testing via molecular assays include a swab of urehral exudate or a first-void urine sample.

Mahon, C.R., Lehman, D.C., Manuselis, G. (2014). Textbook of Diagnostic Microbiology (5th ed.). New York: Saunders.