Chlamydia trachomatis is a gram-negative bacteria. It is an intracellular organism, meaning it enters and replicates within cells before rupturing the cell and spreading to others. Chlamydia is the most common sexually transmitted infection in the UK and a significant cause of infertility.

Being young, sexually active and having multiple partners increase the risk of catching the infection. A large number of cases are asymptomatic (50% in men and 75% in woman). Asymptomatic patients can still pass the infection on.


National Chlamydia Screening Programme

Public Health England has set out a National Chlamydia Screening Programme (NCSP). This program aims to screen every sexually active person under 25 years of age for chlamydia annually or when they change their sexual partner. Everyone that tests positive should have a re-test three months after treatment. This re-testing is to ensure they have not contracted chlamydia again, rather than to check the treatment has worked.

In general, when a patient attends a GUM clinic for STI screening, as a minimum, they are tested for:

  • Chlamydia
  • Gonorrhoea
  • Syphilis (blood test)
  • HIV (blood test)



It can be tricky to get your head around the swabs used for sexual health screening. There are many different swab types and uses. The FSRH Clinical Guideline on vaginal discharge (2012) has helpful guidance on the investigation with different swabs in different clinical scenarios. There are two types of swabs involved in sexual health testing:

  • Charcoal swabs
  • Nucleic acid amplification test (NAAT) swabs


Charcoal swabs allow for microscopy (looking at the sample under the microscope), culture (growing the organism) and sensitivities (testing which antibiotics are effective against the bacteria). Charcoal swabs look like a long cotton bud that goes into a tube with a black transport medium at the end. The transport medium is called Amies transport medium, and contains a chemical solution for keeping microorganisms alive during transport.


Microscopy involves gram staining and examination under a microscopeA stain is used to highlight different types of bacteria with different colours. Charcoal swabs can be used for endocervical swabs and high vaginal swabs (HVS). Charcoal swabs can confirm:

  • Bacterial vaginosis
  • Candidiasis
  • Gonorrhoeae (specifically endocervical swab)
  • Trichomonas vaginalis (specifically a swab from the posterior fornix)
  • Other bacteria, such as group B streptococcus (GBS)


Nucleic acid amplification tests (NAAT) check directly for the DNA or RNA of the organism. NAAT testing is used to test specifically for chlamydia and gonorrhoea. They are not useful for other pelvic infections (except where specifically testing for Mycoplasma genitalium). In women, a NAAT test can be performed on a vulvovaginal swab (a self-taken lower vaginal swab), an endocervical swab or a first-catch urine sample. The order of preference is endocervical, vulvovaginal, and then urine. In men, a NAAT test can be performed on a first-catch urine sample or a urethral swab. It is worth noting that the NAAT swabs will specify on the packet whether the swabs are for endocervical, vulvovaginal or urethral use. A specific kit is used for first-catch urine NAAT testing.

Rectal and pharyngeal NAAT swabs can also be taken to diagnose chlamydia in the rectum and throat. Consider these swabs where anal or oral sex has occurred.

Where gonorrhoea is suspected or demonstrated on a NAAT test, an endocervical charcoal swab is required for microscopyculture and sensitivities.



The majority of cases of chlamydia in women are asymptomatic. Consider chlamydia in women that are sexually active and present with:

  • Abnormal vaginal discharge
  • Pelvic pain
  • Abnormal vaginal bleeding (intermenstrual or postcoital)
  • Painful sex (dyspareunia)
  • Painful urination (dysuria)


Consider chlamydia in men that are sexually active and present with:

  • Urethral discharge or discomfort
  • Painful urination (dysuria)
  • Epididymo-orchitis
  • Reactive arthritis


It is worth considering rectal chlamydia and lymphogranuloma venereum in patients presenting with anorectal symptoms, such as discomfort, discharge, bleeding and change in bowel habits.


Examination Findings

  • Pelvic or abdominal tenderness
  • Cervical motion tenderness (cervical excitation)
  • Inflamed cervix (cervicitis)
  • Purulent discharge



Nucleic acid amplification tests (NAAT) are used to diagnose chlamydia. This can involve a:

  • Vulvovaginal swab
  • Endocervical swab
  • First-catch urine sample (in women or men)
  • Urethral swab in men
  • Rectal swab (after anal sex)
  • Pharyngeal swab (after oral sex)



This section is based on the British Association for Sexual Health and HIV (BASHH) guidelines (published 2015, updated 2018). Always check local and national guidelines before treating patients. This is a summary to help with your learning and exam preparation.

First-line for uncomplicated chlamydia infection is doxycycline 100mg twice a day for 7 days.

The guidelines previously recommended a single dose of azithromycin 1g orally as an alternative. This recommendation has been removed due to Mycoplasma genitalium resistance to azithromycin, and azithromycin being less effective for rectal chlamydia infection.


Doxycycline is contraindicated in pregnancy and breastfeeding. Alternatives options listed in the BASHH guidelines (always check guidelines) for treatment in pregnant or breastfeeding women are:

  • Azithromycin 1g stat then 500mg once a day for 2 days
  • Erythromycin 500mg four times daily for 7 days
  • Erythromycin 500mg twice daily for 14 days
  • Amoxicillin 500mg three times daily for 7 days

test of cure is not routinely recommended. However, a test of cure should be used for rectal cases of chlamydia, in pregnancy and where symptoms persist.


Other factors to consider are:

  • Abstain from sex for seven days of treatment of all partners to reduce the risk of re-infection
  • Refer all patients to genitourinary medicine (GUM) for contact tracing and notification of sexual partners
  • Test for and treat any other sexually transmitted infections
  • Provide advice about ways to prevent future infection
  • Consider safeguarding issues and sexual abuse in children and young people



There are a large number of complications from infection with chlamydia:

  • Pelvic inflammatory disease
  • Chronic pelvic pain
  • Infertility
  • Ectopic pregnancy
  • Epididymo-orchitis
  • Conjunctivitis
  • Lymphogranuloma venereum
  • Reactive arthritis


Pregnancy-related complications include:

  • Preterm delivery
  • Premature rupture of membranes
  • Low birth weight
  • Postpartum endometritis
  • Neonatal infection (conjunctivitis and pneumonia)


Lymphogranuloma Venereum

Lymphogranuloma venereum (LGV) is a condition affecting the lymphoid tissue around the site of infection with chlamydia. It most commonly occurs in men who have sex with men (MSM). LGV occurs in three stages:

The primary stage involves a painless ulcer (primary lesion). This typically occurs on the penis in men, vaginal wall in women or rectum after anal sex.

The secondary stage involves lymphadenitis. This is swelling, inflammation and pain in the lymph nodes infected with the bacteria. The inguinal or femoral lymph nodes may be affected.

The tertiary stage involves inflammation of the rectum (proctitis) and anus. Proctocolitis leads to anal pain, change in bowel habit, tenesmus and discharge. Tenesmus is a feeling of needing to empty the bowels, even after completing a bowel motion.

Doxycycline 100mg twice daily for 21 days is the first-line treatment for LGV recommended by BASHH. Erythromycin, azithromycin and ofloxacin are alternatives.


Chlamydial Conjunctivitis

Chlamydia can infect the conjunctiva of the eye. Conjunctival infection is usually as a result of sexual activity, when genital fluid comes in contact with the eye, for example, through hand-to-eye spread. It presents with chronic erythema, irritation and discharge lasting more than two weeks. Most cases are unilateral.

Chlamydial conjunctivitis occurs more frequently in young adults. It can also affect neonates with mothers infected with chlamydia. Gonococcal conjunctivitis is a crucial differential diagnosis and should be tested.


Last updated July 2020