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NAAT for chlamydia may be performed on swab specimens sampled from the cervix (women) or urethra (men), on self-collected vaginal swabs, or on voided urine.

At present, the NAATs have regulatory approval only for testing urogenital specimens, although rapidly evolving research indicates that they may give reliable results on rectal specimens.

If left untreated, chlamydia in men can spread to the testicles causing epididymitis, which in rare cases can lead to sterility if not treated.

Newborns can also develop chlamydia eye infection through childbirth (see below).

The diagnosis of genital chlamydial infections evolved rapidly from the 1990s through 2006.

Nucleic acid amplification tests (NAAT), such as polymerase chain reaction (PCR), transcription mediated amplification (TMA), and the DNA strand displacement amplification (SDA) now are the mainstays.

Because of improved test accuracy, ease of specimen management, convenience in specimen management, and ease of screening sexually active men and women, the NAATs have largely replaced culture, the historic gold standard for chlamydia diagnosis, and the non-amplified probe tests.

The latter test is relatively insensitive, successfully detecting only 60–80% of infections in asymptomatic women, and often giving falsely positive results.

Chlamydia may also cause reactive arthritis—the triad of arthritis, conjunctivitis and urethral inflammation—especially in young men.iron, or vitamins, this has a negative consequence for Chlamydiae since the organism is dependent on the host cell for these nutrients.Long-term cohort studies indicate that approximately 50% of those infected clear within a year, 80% within two years, and 90% within three years.A different serovar of Chlamydia trachomatis is also the cause of lymphogranuloma venereum, an infection of the lymph nodes and lymphatics.It usually presents with genital ulceration and swollen lymph nodes in the groin, but it may also manifest as rectal inflammation, fever or swollen lymph nodes in other regions of the body.

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