Factsheet for health professionals on chlamydia

Disclaimer: The information contained in this factsheet is intended for general information and should not substitute individual expert advice or judgement of healthcare professionals. 

Chlamydia is a sexually transmitted infection caused by Chlamydia trachomatis, a gram-negative obligate intracellular bacterium. It is the most commonly reported bacterial STI in Europe and particularly affects sexually active young people. Infection is often asymptomatic, which contributes to ongoing transmission and delayed diagnosis. Untreated infection may result in reproductive and neonatal complications, including pelvic inflammatory disease, ectopic pregnancy, infertility, chronic pelvic pain, and neonatal conjunctivitis or pneumonia. 

Case definition 

Chlamydia is notifiable in the European Union (EU) and European Economic Area (EEA). Member States report confirmed cases to the European Centre for Disease Prevention and Control (ECDC) on an annual basis according to the case definition established in Commission Implementing Regulation (EU) 2026/2097. If it is not possible to use the EU 2026 case definition, prior versions of the EU case definition or national case definitions may be accepted[13].

The EU 2026 case definition for chlamydial infection (non-LGV) is as follows:

Chlamydial Infection (non-LGV*)

Clinical criteria:

At least one of the following ten:

  1. Urethritis,
  2. Epididymitis,
  3. Pelvic inflammatory disease,
  4. Acute salpingitis,
  5. Acute endometritis,
  6. Cervicitis,
  7. Proctitis,
  8. Purulent conjunctivitis,
  9. Reactive arthritis,
  10. Perihepatitis.

In newborn children at least one of the following:

  1. Conjunctivitis,
  2. Pneumonia.

 Laboratory criteria: 

At least one of the following:

  1. Detection of Chlamydia trachomatis nucleic acid in a clinical specimen.
  2. Isolation of Chlamydia trachomatis from a clinical specimen.
  3. Detection of Chlamydia trachomatis by direct fluorescent antibody (DFA) test in a clinical specimen.

Epidemiological criteria:

An epidemiological link by human-to-human transmission (sexual contact or vertical transmission).

Case classification:

  • Possible case: NA,
  • Probable case: Any person meeting the clinical criteria with an epidemiological link,
  • Confirmed case: Any person meeting the laboratory criteria.

* Lymphogranuloma venereum (LGV), a Chlamydia trachomatis infection with genovar L1-3, is reported separately to ECDC (see LGV factsheet).  

The pathogen

Chlamydia trachomatis is a gram-negative obligate intracellular bacterium that only infects humans [1]. 

Chlamydia trachomatis has a unique biphasic developmental cycle, alternating between an infectious elementary body (EB) and a replicative reticulate body (RB) stage [1-3]. Infection begins when EBs attach to and enter epithelial cells of the urogenital tract, rectum or conjunctiva. Inside the host cell, EBs transform into RBs, which are metabolically active and replicate using host cell resources [1,3]. As replication progresses, RBs convert back into EBs, which are released to infect neighbouring cells and continue transmission [3]. Under certain conditions, the bacterium can enter a persistent, non-replicative state that may contribute to prolonged infection before resuming its normal developmental cycle [3,4].

C. trachomatis is classified into three groups of genovars with distinct clinical manifestations [2,4-6]:

  • Genovars A–C cause trachoma, an ocular infection. 
    • Genovars D–K are responsible for most sexually transmitted chlamydia infections. 
    • Genovars L1–L3 cause lymphogranuloma venereum (LGV), an invasive infection affecting the genital and anorectal tract.

Infection induces only partial and short-lived immunity, allowing for reinfection [5,6]. 

Clinical features and sequelae

Most chlamydia infections are asymptomatic or cause mild, non-specific symptoms [2]. When symptoms occur, they usually develop within 1-3 weeks after exposure [2,6]. Untreated asymptomatic infections may persist for months or, in some cases, years. Among women with asymptomatic infection, spontaneous clearance has been estimated at approximately 45-54% after one year, increasing to over 80% after two years [7].

Infections can occur at urogenital, anorectal, oropharyngeal and conjunctival mucosal sites [1,2,4,6]. 

Urogenital infection

  • Males

Approximately half of male urogenital infections are asymptomatic (with estimates ranging between 25-100%) [7]. Typical symptoms are caused by urethritis and include dysuria, urethral discharge, urethral irritation and testicular pain. Less frequently, epididymitis, epididymo-orchitis and prostatitis may occur [2,5,6]. Sexually acquired reactive arthritis (SARA) is an uncommon immune-mediated complication from urogenital infections including chlamydia [6].

  • Females

At least 70% of females with urogenital infection are asymptomatic [4]. When symptoms occur, they are due to urethritis and cervicitis, with mild symptoms including dysuria, vaginal discharge and bleeding and mild abdominal pain [2,4-6]. Untreated infection can lead to pelvic inflammatory disease (PID), including endometritis and salpingitis, as well as SARA [5,7]. Long term sequelae include chronic pelvic pain, tubal factor infertility and ectopic pregnancy [6,7]. The risk of sequelae following untreated infection is not well known, with recent evidence indicating the estimated risk may be lower than previously thought [7,8]. A UK study estimated that every 1 000 C. trachomatis infections in women aged 16–44 years result in an around 171 cases of PID and 73 cases of salpingitis, two ectopic pregnancies and five females with tubal factor infertility by the age 44 years [9].  

Rectal infection

Rectal chlamydia infections of non-LGV genovars (see ECDC LGV Factsheet for clinical features related to LGV genovars) are often asymptomatic. Rectal infections may manifest as proctitis, with anorectal pain, discharge, discomfort and rectal bleeding [2,5,6]. Among women with urogenital chlamydia, concurrent rectal infection is common in an estimated 70% of women [7]. This is often observed without reporting of anal sex, suggesting possible autoinoculation between genital and rectal sites [10]. 

Pharyngeal infection

Pharyngeal infections are uncommon and generally asymptomatic. Symptoms could include a mild sore throat [6,7]. Among women and gay, bisexual and other men who have sex with men attending STI services for testing, pharyngeal C. trachomatis positivity is estimated between 1-3% [7]. 

Conjunctival infection 

Ocular infections cause inclusion conjunctivitis, which untreated, can lead to chronic conjunctivitis lasting several months [4,7]. Adult inclusion conjunctivitis is often caused by autoinoculation from a genital tract infection [6].

Pregnancy 

Maternal infection has been associated with adverse pregnancy outcomes including premature membrane rupture, chorioamnionitis, preterm labour and low birth weight [2,6]. Vertical transmission during vaginal delivery can result in neonatal conjunctivitis and pneumonia, with approximately 30–50% of exposed infants developing conjunctivitis and 10–20% developing pneumonia [6,7]. 

Epidemiology 

Chlamydia is among the most common STIs worldwide. The World Health Organization estimated that approximately 128.5 million (90.0–173.8 million) new infections with C. trachomatis occurred globally among people aged 15 to 49 years in 2020. Global prevalence in this age group was estimated at 4.0% for women and 2.5% for men [11]. Sexually-active women have the highest burden of infection globally [11]. A meta-analysis estimated that the pooled prevalence of C. trachomatis infection within the general population between 2000-2019 was highest in the Americas (4.5%, 95% CI, 3.1–5.9%), followed by Europe (2.7%, 95% CI, 1.9–3.6%), Africa (2.6%, 95% CI, 1.4–3.9%) and the Western Pacific (2.6%, 95% CI, 1.8–3.5%), while the lowest pooled prevalence was in South-East Asia (0.8%, 95% CI, 0.3–1.3%). The difference in estimated prevalence between males and females was significant in the Americas and Africa [12]. 

In the EU/EEA, chlamydia is the most frequently reported bacterial STI under surveillance. Reported notification rates vary considerably across EU/EEA countries (from <3 to >300 cases per 100 000 persons), reflecting variations in testing, control policies, and surveillance systems [13].

Prevalence estimates based on studies published between 2019-2023 were at 2.8% (95% CI 1.7–3.9) among women and 2.6% (95% CI 0.6–4.7) among men in the European region [14]. Individuals aged 20–24 years consistently account for the largest proportion of reported cases, followed by those aged 25–34 years [13].

Among young people aged 15-24 years, the pooled estimated prevalence reached 5.5% (95% CI 4.6-6.5) among women and 3.3% (95% CI 2.0-4.6) among men [14]. Notification rates are consistently highest among young women, who are frequently targeted for screening. Besides young age, additional risk factors include condomless sex and having new or multiple sexual partners [7]. 

For updated epidemiological data and figures, please see ECDC’s most recent Annual Epidemiological Report.

Transmission

Transmission of C. trachomatis occurs primarily through direct mucosal contact during vaginal, anal or oral sex with a partner who has the infection [7]. The bacterium is transmitted through infected genital and rectal secretions. The risk of transmission increases through condomless sex, having new sexual partners and multiple concurrent relationships [7]. 

Vertical transmission can occur during vaginal delivery when an infant passes through an infected cervical canal, causing infection in infants born to mothers with urogenital chlamydia [2,6]. 

Among EU/EEA countries reporting transmission type to ECDC, most reported infections occurred through sex between men and women while around a fifth of transmission also occurred in sex between men, and very infrequently cases were reported through vertical transmission [13]. 

Diagnostics 

A confirmed case of chlamydia requires laboratory confirmation since clinical manifestations alone are neither sufficiently sensitive nor specific for diagnosis.  

Nucleic acid amplification tests

Nucleic acid amplification tests (NAATs) are the recommended diagnostic method for C. trachomatis, due to their high sensitivity, specificity, and quick results [4]. They detect C. trachomatis DNA directly from clinical specimens. Laboratories should use NAATs capable of detecting all known C. trachomatis variants, including two targets, one of which should be chromosomal [7].

The recommended specimens include [4,7]:

  • Males: first-void urine or meatal swabs when urine samples are not possible,
  • Females: vulvo-vaginal swabs. First-void urine and pap-smear samples are not recommended when other samples are available,
  • Rectal and pharyngeal swabs only when indicated based on symptoms or sexual exposures.

Self-collected vulvo-vaginal, pharyngeal and rectal swabs demonstrate similar accuracy compared to clinician-collected samples and are acceptable for both males and females [7].

Culture and direct fluorescence assays

Culture and direct fluorescence assays may be used where NAATs are unavailable, although they are less sensitive and no longer preferred in routine clinical practice [7,15].

Serology

Serological testing is not recommended for screening or diagnosing acute, uncomplicated anogenital C. trachomatis infections due to its limited sensitivity and specificity in detecting current infections [15]. However, it may support PID or infertility investigations by identifying recent or past invasive infections [4,7,15].    

Point-of-care tests

As of 2025, available non-NAAT rapid tests lack the accuracy and reliability to meet the quality and performance standards necessary for recommendation in Europe [7]. However, testing sites may consider using multiplex NAAT-based point-of-care tests (POCTs), such as those for chlamydia and gonorrhea [15].

Case management and treatment 

The objectives of case management and treatment for C. trachomatis cases are to prevent complications and interrupt onward transmission.

For uncomplicated urogenital, rectal and pharyngeal infections, 2025 European guidelines suggest [7]:

  • first-line regimen is doxycycline 100 mg twice daily for seven days, 
  • second-line regimen is azithromycin 1 g as a single dose, 
  • third-line regimes include erythromycin, levofloxacin or ofloxacin.

Routine test of cure (TOC) is not recommended for patients who are treated with the first-line regimen but may be considered in cases diagnosed and treated during pregnancy, with clinical complications, persistent symptoms, use of second- or third-line treatment regimens, suspected non-adherence or risk of re-exposure from an untreated partner. In these cases, a NAAT should be performed at least four weeks after completion of therapy [7]. Please refer to updated European clinical guidelines for further information [7].

Prompt diagnosis and treatment after symptom onset are important to prevent complications and onward transmission. Patients should receive instructions on treatment administration, partner notification and partner management. Where indicated by national guidelines, expedited partner therapy or patient-delivered partner treatment can be considered to ensure timely treatment of partners and reduce risk of reinfection [7].

Patients diagnosed with chlamydia should also be assessed for other STIs, including gonorrhoea, syphilis and HIV, according to national recommendations. Gay, bisexual and other men who have sex with men who test positive for rectal chlamydia should be tested for LGV and considered for HIV pre-exposure prophylaxis (PrEP) if they are not already taking it or known to be living with HIV [16,17]. 

Current evidence suggests that antimicrobial resistance in C. trachomatis remains uncommon [18]. Nevertheless, ongoing surveillance is important given reports of variable treatment effectiveness and occasional treatment failures of single-dose azithromycin [7,19].

Prevention

Prevention for all sexually transmitted infections comprises primary prevention, which aims to reduce the risk of acquiring infections, and secondary prevention, which focuses on early detection and treatment to prevent complications and further transmission. 

A key aspect of both primary and secondary prevention of STIs is comprehensive sex education in schools and provision of sexual health information by healthcare providers. This includes knowledge of safe sexual practices, facilitating access to barrier protection and testing services, as well as integrating STI prevention into routine care pathways wherever feasible [20].

A large proportion of STIs are asymptomatic and natural immunity is short-lived, meaning individuals are often unaware of their infection status and can unknowingly transmit the infection and easily become (re-)infected. 

Primary prevention: reducing risk of STI acquisition

Primary prevention strategies aim to reduce the likelihood of infection during sexual contact. Key measures include:

  • Promotion and provision of barrier protection: Consistent and correct use of condoms, internal condoms and dental dams significantly lowers transmission risk. Access to these should be promoted. 

  • Sexual health education and counselling: Counselling should be tailored to individual needs to support informed decision-making and safer sexual practices. This may include discussion of factors associated with increased STI risk, including multiple or concurrent sexual relationships, mixing across sexual networks and engaging in activities that increase susceptibility to transmission.

  • Risk reduction during symptomatic periods: In the presence of lesions or symptoms including ulcers, discharge, and rashes, individuals should be advised to avoid sexual contact or use appropriate protective measures until  symptoms are managed as these are associated with higher infectiousness.

  • Awareness of reinfection and ongoing prevention needs: Since most STIs do not confer lasting immunity after infection, individuals should be aware of the risk of re-infection and encouraged to maintain preventive behaviours post-treatment.

Secondary prevention: early detection and treatment

Secondary prevention aims to shorten the infectious period and prevent complications. Key actions include:

  • Timely healthcare-seeking: Early recognition of symptoms and prompt access to testing and treatment are important. Accessible and integrated services including free or low cost, on demand testing is recommended.

  • Testing: Regular testing in populations at increased risk of infection according to evidence-based national or international guidelines is recommended, as well as provider-initiated testing based on sexual history and assessed risk facilitates early detection. 

  • Effective treatment: Completed course of evidence-based regimens reduce individual morbidity, risk of complications, and community transmission.

  • Partner notification and management: Contact tracing and partner management approaches are useful to prevent reinfection and interrupt transmission chains.

Screening 

Targeted testing strategies are generally recommended for populations at increased risk of acquiring chlamydia, including sexually active young women under 25 years of age, gay, bisexual and other men who have sex with men, people who use HIV PrEP and those who are pregnant [7]. 

A few countries implement routine asymptomatic screening of these populations who are at increased risk of contracting chlamydia, such as young people. However, there is an ongoing debate regarding the population-level benefits of widespread testing of asymptomatic individuals [22,23]. While testing remains a central component of STI control, evidence on its impact for reducing overall chlamydia prevalence and long-term complications remains under evaluation.

Doxycycline postexposure prophylaxis (doxyPEP)

DoxyPEP is a single 200 mg dose of doxycycline taken within 24−72 hours after sexual exposure, for the prevention of bacterial STIs [27].DoxyPEP use has shown significant efficacy in reducing chlamydia incidence among gay, bisexual and other men who have sex with men, and transgender women. However, current evidence does not support its use in cisgender women [24]. ECDC advises that decisions regarding doxyPEP use should be made at an individual level, based on the individual risk of infection as assessed by a clinician (see ECDC 2026 guidance for further information). Its use is not recommended as a population-level intervention for chlamydia prevention due to concerns for the development of antimicrobial resistance [24].

Vaccination

There is currently no licensed vaccine against Chlamydia trachomatis.

National strategy 

ECDC recommends that EU/EEA countries maintain a national strategy or action plan for the control of STIs, including [21]:

  • access to primary prevention interventions for individuals and groups at increased risk of acquiring the infection,
  • implementation of evidence-based case management guidelines for each setting in which chlamydia may be diagnosed,
  • robust surveillance of diagnosed infections,
  • a plan for monitoring and evaluation of the national strategy’s effectiveness.

Advice to travellers 

Travellers should be advised to use protection when having sex with new partners during travel. They should pack reliable barrier protection and seek testing if they develop symptoms or if sexual activity during travel posed an increased risk for chlamydia infection.

References

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  2. Holmes KK, Sparling FP, Stamm WE, Piot P, Stamm WE. Sexually Transmitted Diseases. New York, USA: McGraw-Hill Professional Publishing; 2008.
  3. Stelzner K, Vollmuth N, Rudel T. Intracellular lifestyle of Chlamydia trachomatis and host–pathogen interactions. Nature Reviews Microbiology. 2023 2023/07/01;21(7):448-62. Available at: https://doi.org/10.1038/s41579-023-00860-y
  4. Black CM. Chlamydial infection : a clinical and public health perspective. Basel: Karger; 2013.
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  11. Organization WH. Updated recommendations for the treatment of Neisseria gonorrhoeae, Chlamydia trachomatis, and Treponema pallidum (syphilis) and new recommendations on syphilis testing and partner services. 2024 
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