ByMargaret R. Hammerschlag, MD, State University of New York Downstate Medical Center
Reviewed/Revised Apr 2023
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Three species of Chlamydia cause human disease, including sexually transmitted infections and respiratory infections. Diagnosis depends on species; culture, nucleic acid amplification tests (NAATs), or serologic tests may be done. Treatment is with doxycycline for nonpregnant people and with azithromycin for pregnant women.

Chlamydiae are nonmotile, obligate intracellular bacteria. They contain DNA, RNA, and ribosomes and make their own proteins and nucleic acids. However, they depend on the host cell for 3 of their 4 nucleoside triphosphates and use host adenosine triphosphate (ATP) to synthesize chlamydial protein.

The genus Chlamydia now contains 12 species; 3 of them cause human disease:

  • Chlamydia trachomatis

  • Chlamydia pneumoniae

  • Chlamydia psittaci

Chlamydial species can cause persistent infection, which is often subclinical.

Chlamydia trachomatis

C. trachomatis has 18 immunologically defined serovars:

  • A, B, Ba, and C cause the eye disease trachoma.

  • D through K cause sexually transmitted infections (STIs) localized to mucosal surfaces.

  • L1, L2, and L3 cause STIs that lead to invasive lymph node disease (lymphogranuloma venereum).

In the United States, C. trachomatis is the most common bacterial cause of STIs, including

Maternal transmission of C. trachomatis causes neonatal conjunctivitis and neonatal pneumonia. Universal prenatal screening and treatment of pregnant women have greatly reduced the incidence of infant C. trachomatis infection in the United States (1).

The organism can be isolated from the rectum and throat in adults (usually in men who have sex with men [MSM]). Rectal infection with L2 strains can cause severe proctocolitis that can mimic acute inflammatory bowel disease in MSM who are HIV-positive.

Chlamydia pneumoniae

C. pneumoniae can cause pneumonia (especially in children and young adults) that may be clinically indistinguishable from pneumonia caused by Mycoplasma pneumoniae. In some patients with C. pneumoniae, pneumonia, hoarseness, and sore throat may precede coughing, which may be persistent and complicated by bronchospasm.

Approximately 6 to 19% of community-acquired pneumonia cases are due to C. pneumoniae. Outbreaks of C. pneumoniae pneumonia pose a particular risk for people in congregate settings (eg, nursing homes, schools, military installations, prisons). No seasonal variations in occurrence have been observed.

C. pneumoniae has also been implicated as an infectious trigger of reactive airway disease.

Chlamydia psittaci

(See also the Centers for Disease Control and Prevention's [CDC] Psittacosis: For Clinicians and Laboratorians.)

C. psittaci causes psittacosis. Strains causing human disease are usually acquired from psittacine birds (eg, parrots), causing a disease characterized by pneumonitis. Patients may have severe headache and abnormal liver blood tests.

Psittacosis is a rare infection. Since 2010, typically < 10 cases/year are reported to the CDC (see also the CDC's Psittacosis). However, psittacosis might be underdiagnosed because mild cases do happen. History of epidemiologic exposure is very important, eg, pet bird owners, veterinarians, and workers in the poultry industry. Outbreaks have occurred among workers who handle turkeys and ducks in poultry processing plants.

General reference

  1. 1. Kohlhoff S, Roblin PM, Clement S, et al: Universal prenatal screening and testing and Chlamydia trachomatis conjunctivitis in infants. Sex Transm Dis 48(9):e122–e123, 2021. doi: 10.1097/OLQ.0000000000001344

Diagnosis of Chlamydia

  • For C. trachomatis, nucleic acid–based testing

  • For C. pneumoniae, culture or nucleic acid–based testing

  • For C. psittaci, serologic tests or polymerase chain reaction (PCR; where available)

(See also the CDC's 2021 Sexually Transmitted Infections Treatment Guidelines: Chlamydial Infections.)

C. trachomatis STIs are best identified in genital samples using nucleic acid amplification tests (NAATs) because these tests are more sensitive than cell culture and have less stringent sample handling requirements. Currently, NAATs are available for testing genital and urine specimens from adults and adolescents. NAATs for genital infection can be done using urine or vaginal swabs obtained by the patient or clinician. Several commercially available NAATs have been approved for extragenital infections (eg, those in the rectum or pharynx).

Serologic tests are of limited value except for diagnosing lymphogranuloma venereum and psittacosis.

C. pneumoniae is diagnosed by culture of respiratory tract specimens or by NAAT testing. Two NAATs for C. pneumoniae are available as part of panels that simultaneously test for multiple respiratory pathogens.

A primary clue to the diagnosis of C. psittaci infection is close contact with birds, typically pet birds such as parrots or parakeets, including veterinarians and workers in turkey and duck processing plants. Diagnosis is confirmed by serologic tests. Culture is not generally available. There are no commercially available NAATs for C. psittaci, but PCR can be done by the Centers for Disease Control and Prevention (CDC) and some specialty laboratories. (See also the CDC's different methods for diagnosing psittacosis.)

Diagnosis reference

  1. 1. Kohlhoff S, Roblin PM, Clement S, et al: Universal prenatal screening and testing and Chlamydia trachomatis conjunctivitis in infants. Sex Transm Dis 48(9):e122–e123, 2021. doi: 10.1097/OLQ.0000000000001344


Because chlamydial genital infection is so common and often asymptomatic or causes only mild or nonspecific symptoms (particularly in women), routine screening of asymptomatic people at high risk of STIs is recommended by the CDC (see the 2021 Sexually Transmitted Infections Treatment Guidelines: Screening Recommendations and Considerations Referenced in Treatment Guidelines and Original Sources: Chlamydia).

See also Screening for Chlamydia for a summary of screening recommendations.

Treatment of Chlamydia

  • For nonpregnant people, doxycycline

  • For pregnant women, azithromycin

1). A review of randomized trials that compared doxycycline and azithromycin for treating urogenital chlamydial infection found that microbiologic treatment failure among men was higher for azithromycin than for doxycycline (2). The recommendation also is based on studies that showed a 7-day course of doxycycline was superior to a single dose of azithromycin for treatment of rectal infection in men who have sex with men (3). The recommendations for use of doxycycline were expanded to include women because rectal infection is not routinely screened for in this population.

Azithromycin may be useful in populations that may have problems with compliance and may not be able to tolerate a 7-day course of multidose doxycycline.

Current sex partners should be treated. Patients should abstain from sexual intercourse until they and their partners have been treated for ≥ 1 week.

When gonorrhea is present and chlamydial infection has not been excluded (uncommon, because all currently available NAATs for gonococcal infection are duplexed with a test for C. trachomatis), concurrent treatment for gonorrhea is recommended.

Screening and treatment of pregnant women is the most effective way to prevent neonatal chlamydial infection, including conjunctivitis and pneumonia. Neonatal ocular prophylaxis with erythromycin or other preparations does not prevent neonatal chlamydial conjunctivitis.

Azithromycin and doxycycline are first-line antibiotics for treatment of C. pneumoniae and psittacosis.

Specific infections are discussed elsewhere in THE MANUAL: Lymphogranuloma venereum and urethritis, pelvic inflammatory disease, epididymitis, reactive arthritis, neonatal conjunctivitis and neonatal pneumonia, trachoma, and inclusion conjunctivitis.

Treatment references

  1. 1. Centers for Disease Control and Prevention: Sexually Transmitted Infections Treatment Guidelines, 2021: Chlamydial Infections: Chlamydial Infection Among Adolescents and Adults. Accessed 03/30/2023.

  2. 2. Páez-Canro C, Alzate JP, González LM, et al: Antibiotics for treating urogenital Chlamydia trachomatis infection in men and non-pregnant women. Cochrane Database Syst Rev 1(1):CD010871, 2019. doi: 10.1002/14651858.CD010871.pub2

  3. 3. Dombrowski JC, Wierzbicki MR, Newman LM, et al: Doxycycline versus azithromycin for the treatment of rectal chlamydia in men who have sex with men: A randomized controlled trial. Clin Infect Dis 73(5):824–831, 2021. doi: 10.1093/cid/ciab153

Key Points

  • C. trachomatis causes trachoma or STIs; maternal transmission can cause neonatal conjunctivitis and/or pneumonia.

  • C. pneumoniae can cause pneumonia (especially in children and young adults and in enclosed populations).

  • C. psittaci is a rare cause of pneumonia (psittacosis) that is usually acquired from psittacine birds (eg, parrots).

  • Diagnose C. trachomatis and C. pneumoniae infections using nucleic acid amplification tests.

  • Screen high-risk, asymptomatic patients for sexually transmitted chlamydial infection.

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