Diagnosis and management of chlamydia: a guide for GPs

Chlamydia is a common sexually-transmitted infection caused by Chlamydia trachomatis bacteria. This article discusses its diagnosis and treatment, and considers the GP’s role in management.

Chlamydia is the most common sexually-transmitted infection (STI) in the UK, with 203,116 new diagnoses in England in 2017, of which 126,828 (62%) were in young people aged 15–24 years.1 Chlamydia is transmitted primarily through penetrative sex and infects the urethra and endocervix. It can also infect the throat and the rectum, and in some cases the conjunctiva. It is very infectious, with a concordance of up to 75% between sexual partners. There are many risk factors for chlamydia infection, including being under the age of 25 years, having a new sexual partner and inconsistent use of condoms.

If a woman contracts chlamydia during pregnancy it can be transmitted to the baby at delivery, causing conjunctivitis or pneumonia.

Classification of chlamydia infections

There are three species of chlamydia bacteria that can cause disease in humans:
Chlamydia psittaci – the natural host is birds, especially parrots, but it can be transmitted to humans, causing psittacosis
Chlamydia pneumoniae – causes respiratory disease in humans
Chlamydia trachomatis – several different serovars can cause disease (including STIs) in humans, as detailed in Figure 1.

(Click figure for full size image)
Figure 1. Infections caused by the serovars of Chlamydia trachomatis


The majority of genital chlamydia infections are asymptomatic, but they can cause significant symptoms. In women, chlamydia can cause vaginal discharge, dysuria, abdominal and pelvic pain, post-coital and intermenstrual bleeding, and deep dyspareunia. In men, chlamydia can cause dysuria, urethral irritation and urethral discharge. Rectal chlamydia is nearly always asymptomatic, but can be associated with anal discharge and discomfort. If a patient presents with proctitis then a diagnosis of lymphogranuloma venereum (LGV) should be considered.


Although an uncomplicated chlamydia infection that is treated promptly carries very little morbidity, if left untreated it can lead to multiple complications. In women, it can lead to chronic pelvic pain, pelvic inflammatory disease (PID), ectopic pregnancy, tubal infertility and sexually acquired reactive arthritis (SARA). In men, it can lead to epididymo-orchitis and SARA. The cost of treating one episode of PID has been estimated to be around £163, which in London alone, with 7000 cases per year, would equate to more than £1 million a year.2


The gold-standard test for chlamydia is a nucleic acid amplification test (NAAT). Enzyme immunoassay (EIA) tests are rarely performed now, as they are not as sensitive or specific as NAAT.

Asymptomatic men should be offered a first-catch urine test and asymptomatic women should be offered a vulvo-vaginal self-swab. If women are symptomatic and having a speculum examination anyway, then a cervical swab can be done, but vulvo-vaginal self-swabs have been shown to be more sensitive, even in symptomatic women.3 It is important to remember that chlamydia can cause dysuria in both men and women, so that if a patient has a midstream specimen of urine (MSU) that shows ‘sterile pyuria’ then a chlamydia test should be considered.

Both rectal and throat swabs can be taken by the patient, and this can be offered for asymptomatic patients. A recent review found that rectal chlamydia in heterosexual women was common, in that 68.1% of those who had urogenital chlamydia also had rectal chlamydia, and this was not associated with reported anal intercourse.4

Patients with proctitis should have an LGV test performed at the same time as their chlamydia test. This should be done at proctoscopy, and patients should ideally be seen in a genitourinary medicine (GUM) clinic. In addition, asymptomatic HIV-positive men who have sex with men (MSM) who have a positive chlamydia diagnosis should have a test for LGV, as they are more likely to have LGV than those who are HIV negative.

Anyone under 25 years old who is sexually active should have an annual chlamydia screen, along with a screen when changing sexual partners. Most local authorities also now offer online STI testing kits (see Box 1).

Box 1. Online sexually-transmitted infection (STI) testing

The UK’s National Chlamydia Screening Programme (NCSP) aims to increase early detection and control the transmission of chlamydia infection through opportunistic screening of young people (see Box 2).

Box 2. National Chlamydia Screening Programme

Differential diagnosis

The differential diagnosis of conditions whose symptoms may resemble chlamydia is summarised in Table 1.

Table 1. Differential diagnosis of conditions with symptoms that resemble chlamydia

Treatment options

First-line treatment

For uncomplicated urogenital, throat and rectal infection, the recommended first-line treatment is doxycycline 100mg twice daily orally for seven days. In patients who are allergic to tetracyclines, use azithromycin 1g orally as a single dose, then 500mg per day for two days.

Second-line treatment

The recommended second-line treatment options are: erythromycin 500mg twice daily for 10–14 days; or ofloxacin 200mg twice daily or 400mg once daily for seven days.7

HIV-positive patients

Treatment for urogenital and pharyngeal infection in HIV-positive patients remains the same as for HIV-negative patients. Rectal infection should be treated as if it were LGV (unless a negative LGV result is available) – with three weeks of doxycycline 100mg twice daily.


Doxycycline and ofloxacin are contraindicated in pregnancy. Recommended treatments are either: azithromycin 1g orally as a single dose, then 500g a day for two days; or erythromycin 500mg four times daily for seven days; or erythromycin 500mg twice daily for 14 days; or amoxicillin 500mg three-times daily for seven days.

Partner notification and test of cure

Because chlamydia can be asymptomatic in so many patients, and because the complications can cause such significant morbidity, it is vital that prompt and comprehensive partner notification is undertaken for all positive diagnoses. This has traditionally been done in GUM clinics but can also be done by the GP or practice nurse, with the appropriate training.

For male patients with symptoms, all sexual partners within the four weeks preceding any symptoms and since the diagnosis should be contacted. For all other patients, all sexual partners in the six months prior to diagnosis should be contacted. All those contacts should be tested for chlamydia and offered epidemiological treatment and a full STI screen.

In addition, patients and any sexual partners should abstain from any sexual activity until treatment has been completed. This means abstaining during the week that they are taking doxycycline, or a week after completing the course of azithromycin.

A test of cure, in which you check if the treatment is working by retesting the patient, is not routinely recommended for chlamydia but one should be done three weeks after completing treatment in the following situations:
• In rectal infection if an extended course of azithromycin has been used as treatment8
• In pregnancy
• When symptoms persist
• Where poor compliance or LGV is suspected.

Routine retesting should also be done three to six months after treatment in patients under the age of 25 years.

GP’s role in management

GPs are well placed to screen for chlamydia, treat uncomplicated infections and undertake basic partner notification. It is also important to test for other STIs in the event that the chlamydia test is positive – a basic STI screen consists of tests for chlamydia, gonorrhoea, HIV and syphilis. While it is true that some patients would rather attend a sexual health clinic for any STI-related concerns, there is no reason why they shouldn’t be able to access their GP for STI screens and treatment. Additionally, GPs should consider chlamydia (or other STIs) both as a differential diagnosis in patients with related symptoms and as a screening test in asymptomatic patients, particularly those who are under 25 years.

If a baby presents with a sticky eye within 30 days of birth, a chlamydia diagnosis should be considered. If the chlamydia test is then positive, it is important to remember that, alongside the baby, the mother and her partner(s) will also need to be tested and treated.


Chlamydia is an infection that is easily missed, but also easily treated. Due to it being an STI there are additional aspects to consider with treatment, such as partner notification and repeat testing to ensure the infection has been eradicated, but all of these things can, and should, be done by GPs where appropriate.

Declaration of interests

None to declare.

Dr Draeger is currently on a career break from clinical medicine and is currently working as a sex education trainer and freelance medical writer; she previously worked as a consultant in genitourinary medicine at Lewisham and Greenwich NHS Trust


1. Public Health England. Sexually transmitted infections and screening for chlamydia in England, 2017. Health Protection Report volume 12, number 20. June 2018. Available from: https://www.gov.uk/government/statistics/sexually-transmitted-infections-stis-annual-data-tables
2. Aghaizu A, et al. What is the cost of pelvic inflammatory disease and how much could be prevented by screening for chlamydia trachomatis? Cost analysis of the Prevention of Pelvic Infection (POPI) trial. Sex Transm Infect 2011;87(4):312–7.
3. Schoeman SA, et al. Assessment of best single sample for finding chlamydia in women with and without symptoms: a diagnostic test study. BMJ 2012;345:e8013.
4. Chandra NL, et al. Detection of Chlamydia trachomatis in rectal specimens in women and its association with anal intercourse: a systematic review and meta-analysis. Sex Transm Infect 2018;94(5):320–6.
5. Fajardo-Bernal L, et al. Home-based versus clinic-based specimen collection in the management of Chlamydia trachomatis and Neisseria gonorrhoeae infections. Cochrane Database Syst Rev 2015;9:CD011317. Available from: http://dx.doi.org/10.1002/14651858.CD011317.pub2
6. Public Health England. National Chlamydia Screening Programme standards. 7th edn. October 2016. Available from: https://www.gov.uk/government/publications/ncsp-standards
7. Nwokolo NC, et al. 2015 UK national guideline for the management of infection with Chlamydia trachomatis. Int J STD AIDS 2016;27(4):251–67.
8. BASHH Clinical Effectiveness Group. Update on the treatment of Chlamydia trachomatis (CT) infection. September 2018. Available from: https://www.bashhguidelines.org/media/1191/update-on-the-treatment-of-chlamydia-trachomatis-infection-final-16-9-18.pdf

Diagnosis and management of chlamydia: a guide for GPs

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