Chlamydia are tiny gram negative bacteria; they are notoriously difficult to culture because, like viruses, they are dependent on a host cell for energy. Chlamydia swabs from mucous membranes are inoculated into a host cell culture for growth. The cell line is incubated for 48-72 hours, and then stained and examined for evidence of chlamydia. The issue here is that urine is toxic to the host cell lines; hence urethral swab collection is preferred to urine collection if chlamydia is suspected.
An interesting side note is that chlamydia have a toxic reaction to something in wood, so using wooden handled swabs can cause a false negative reading. Plastic handled swabs with untreated polyester heads need to be used.
In the modern lab setting, a urine sample would typically be handled using a PCR (polymerase chain reaction) test or a rapid immunoassay test. The RIT is preferred because it is very fast, has high reliability, and works very well on urine specimens.