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Chlamydia and Mycoplasmal Mucosal Infections


Sheldon R. Morris

, MD, MPH, University of California San Diego

Reviewed/Revised Jan 2023
Topic Resources

Sexually transmitted urethritis, cervicitis, proctitis, and pharyngitis (that are not due to gonorrhea) are caused predominantly by chlamydiae and less frequently by mycoplasmas. Chlamydiae may also cause salpingitis, epididymitis, perihepatitis, neonatal conjunctivitis, and infant pneumonia. Untreated chlamydial salpingitis can become chronic, causing minimal symptoms but having serious consequences. Diagnosis is by culture, immunoassay for antigens, or nucleic acid–based tests. Treatment is usually with doxycycline or azithromycin.

Several organisms can cause nongonococcal sexually transmitted cervicitis in women and urethritis, proctitis, and pharyngitis in both sexes. These organisms include

The imprecise term "nonspecific urethritis” can be used, but only if tests for chlamydiae and gonococci are negative and no other pathogen is identified.

Symptoms and Signs of Chlamydia

Men develop symptomatic urethritis after a 7- to 28-day incubation period, usually beginning with mild dysuria, discomfort in the urethra, and a clear to mucopurulent discharge. Discharge may be slight, and symptoms may be mild but are frequently more marked early in the morning; then, the urethral meatus is often red and blocked with dried secretions, which may also stain underclothes. Occasionally, onset is more acute and severe, with severe dysuria, frequency, and a copious, purulent discharge that simulates gonococcal urethritis. Infection may progress to epididymitis Epididymitis Epididymitis is inflammation of the epididymis, occasionally accompanied by inflammation of the testis (epididymo-orchitis). Scrotal pain and swelling usually occur unilaterally. Diagnosis is... read more Epididymitis . After rectal or orogenital contact with an infected person, proctitis Proctitis Proctitis is inflammation of the rectal mucosa, which may result from infection, inflammatory bowel disease, or radiation. Symptoms are rectal discomfort and bleeding. Diagnosis is by proctoscopy... read more or pharyngitis Tonsillopharyngitis Tonsillopharyngitis is acute infection of the pharynx, palatine tonsils, or both. Symptoms may include sore throat, odynophagia, cervical lymphadenopathy, and fever. Diagnosis is clinical, supplemented... read more Tonsillopharyngitis may develop.

Women are usually asymptomatic, although vaginal discharge, dysuria, increased urinary frequency and urgency, pelvic pain, dyspareunia, and symptoms of urethritis may occur. Cervicitis Cervicitis Cervicitis is infectious or noninfectious inflammation of the cervix. Findings may include cervical or vaginal discharge and cervical erythema and friability. Diagnosis is with tests for cervical... read more Cervicitis with yellow, mucopurulent exudate and cervical ectopy (expansion of the red endocervical epithelium onto the vaginal surfaces of the cervix) are characteristic. Pelvic inflammatory disease Pelvic Inflammatory Disease (PID) Pelvic inflammatory disease (PID) is a polymicrobial infection of the upper female genital tract: the cervix, uterus, fallopian tubes, and ovaries; abscess may occur. PID may be caused by sexually... read more (PID; salpingitis and pelvic peritonitis) may cause lower abdominal discomfort (typically bilateral) and marked tenderness when the abdomen, adnexa, and cervix are palpated. Long-term consequences of PID include ectopic pregnancy and infertility. Fitz-Hugh-Curtis syndrome (perihepatitis) may cause right upper quadrant pain, fever, and vomiting.

Images of Chlamydial Reactive Arthritis

Diagnosis of Chlamydia

  • Nucleic acid–based tests of cervical, urethral, pharyngeal, or rectal exudate or urine

Chlamydial or mycoplasmal infection is suspected in patients with symptoms of urethritis, salpingitis, cervicitis, or unexplained proctitis, but similar symptoms can also result from gonococcal infection.

If clinical evidence for urethritis is uncertain, the Centers for Disease Control and Prevention (CDC) 2021 Sexually Transmitted Infections Treatment Guidelines state that urethritis can be documented by any of the following:

  • Mucoid, mucopurulent, or purulent discharge observed during examination

  • ≥ 10 white blood cells per high-power field in spun first-void urine

  • A positive leukocyte esterase test on first-void urine

  • ≥ 2 white blood cells per oil immersion field in Gram-stained urethral secretions

Samples of cervical or vaginal specimens or male urethral or rectal exudates are obtained to check for chlamydiae. Urine samples can be used as an alternative to cervical or urethral specimens. Throat and rectal swabs are needed to test for infection at those sites.

Commercially available nucleic acid amplification tests (NAATs) are highly sensitive and specific for chlamydia and can also be done on self-collected urine or vaginal specimens, eliminating the need for doing an uncomfortable swab of the urethra or cervix. Point-of-care NAAT platforms are available and can provide same-visit results. In general, samples from the throat and rectum should be tested only in laboratories that have verified the use of these tests for those anatomic sites.

Because other STIs (particularly gonococcal infection) often coexist, patients who have symptomatic urethritis should also be tested for gonorrhea Diagnosis Gonorrhea is caused by the bacterium Neisseria gonorrhoeae. It typically infects epithelia of the urethra, cervix, rectum, pharynx, or conjunctivae, causing irritation or pain and purulent... read more Diagnosis . All patients who receive a diagnosis of gonorrhea or chlamydia should be tested for other STIs, including syphilis and HIV.

Mycoplasma genitalium can be detected using commercial NAAT assays, but those may not be widely available.

In the US, confirmed cases of chlamydial infection, gonorrhea, and syphilis must be reported to the public health system.

Screening for Chlamydia

Testing urine or self-collected vaginal swabs using NAAT is especially useful for screening asymptomatic people at high risk of STIs because genital examination is not necessary. Screening recommendations vary by sex, age, sexual practices, and setting. The following are based on the CDC's Sexually Transmitted Infections (STI) Treatment Guidelines, 2021.

Women are screened annually if they are sexually active and < 25 years of age or if they are ≥ 25 years of age, sexually active, and have one or more of the following risk factors:

  • Have a history of a prior STI

  • Engage in high-risk sexual behavior (eg, have a new sex partner or multiple sex partners; engage in sex work; or use condoms inconsistently when not in a mutually monogamous relationship)

  • Have a partner who has an STI or engages in high-risk behavior (eg, a sex partner who has concurrent partners)

  • Have a history of incarceration

Pregnant women who are < 25 years or who are ≥ 25 years with one or more of the risk factors are screened during their first prenatal visit and again during their 3rd trimester if risk remains high.

The American College of Obstetrics and Gynecology (ACOG) recommends that all pregnant women be tested for chlamydia early in pregnancy, with a repeat test in the 3rd trimester for women with risk factors. It recommends testing for gonorrhea in pregnant women ≤ 25 years and for those living in an area where gonorrhea is common. (See ACOG: Routine Tests During Pregnancy.)

Heterosexually active men are not routinely screened except for those in clinical settings with a high prevalence of chlamydial infection (eg, adolescent clinics, STI clinics, correctional facilities).

Men who have sex with men are screened at least annually if they have been sexually active within the previous year (for insertive intercourse, urine screen; for receptive intercourse, rectal swab; and for oral intercourse, pharyngeal swab), regardless of condom use. Those at increased risk (eg, with HIV infection, receive preexposure prophylaxis with antiretrovirals, have multiple sex partners, or whose partner has multiple partners) should be screened more frequently, at 3 to 6-month intervals.

Transgender and gender diverse people are screened if they are sexually active on the basis of sexual practices and anatomy (eg, annual screening for all people with a cervix who are < 25 years old; if ≥ 25 years old, people with a cervix should be screened annually if at increased risk; rectal swab based on reported sexual behaviors and exposure).

(See also the US Preventive Services Task Force’s summary of recommendations regarding screening for chlamydial infection.)

Treatment of Chlamydia

  • Oral antibiotics (preferably azithromycin)

  • Empiric treatment for gonorrhea if it has not been excluded

  • Treatment of sex partners

Uncomplicated documented or suspected chlamydial infections are treated with one of the following:

  • A single dose of azithromycin 1 g orally

  • Doxycycline 100 mg orally twice a day for 7 days

  • Levofloxacin 500 mg orally once a day for 7 days

Azithromycin (given as a single dose) is preferred to medications that require multiple doses over 7 days, although there is some evidence that doxycycline may be preferable for rectal chlamydia (1 Treatment references Sexually transmitted urethritis, cervicitis, proctitis, and pharyngitis (that are not due to gonorrhea) are caused predominantly by chlamydiae and less frequently by mycoplasmas. Chlamydiae... read more Treatment references ).

For pregnant women, azithromycin 1 g orally once should be used. Amoxicillin 500 mg orally 3 times a day for 7 days is an alternative therapy for pregnant women. Pregnant women should have a test of cure 4 weeks after treatment and be retested within 3 months.

For mycoplasma, preferred treatment is doxycycline 100 mg orally twice a day for 7 days, followed by moxifloxacin 400 mg orally once a day for 7 days for those with unknown azithromycin susceptibility or known azithromycin resistance (2 Treatment references Sexually transmitted urethritis, cervicitis, proctitis, and pharyngitis (that are not due to gonorrhea) are caused predominantly by chlamydiae and less frequently by mycoplasmas. Chlamydiae... read more Treatment references ). If there is known azithromycin susceptibility, treatment is doxycycline 100 mg orally twice a day for 7 days followed by azithromycin 1g orally initial dose followed by 500 mg orally once a day for 3 additional days.

These regimens do not reliably treat gonorrhea, which coexists in many patients with chlamydial infections. Therefore, treatment should include a single dose of ceftriaxone 500 mg IM (1 g IM for patients weighing ≥ 150 kg) if gonorrhea has not been excluded.

Patients who relapse (about 10%) are usually coinfected with microbes that do not respond to antichlamydial therapy, or they were reinfected since treatment.

They should be retested for chlamydial infection and gonorrhea and, if possible, for mycoplasma and trichomoniasis.

In areas where trichomoniasis Trichomoniasis Trichomoniasis is infection of the vagina or male genital tract with Trichomonas vaginalis. It can be asymptomatic or cause urethritis, vaginitis, or occasionally cystitis, epididymitis... read more is prevalent, empiric treatment with metronidazole is recommended unless polymerase chain reaction (PCR) testing indicates patients are negative for trichomoniasis.

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

If chlamydial genital infections are untreated, symptoms and signs subside within 4 weeks in about two thirds of patients. However, in women, asymptomatic cervical infection may persist, resulting in chronic endometritis, salpingitis, or pelvic peritonitis and their sequelae—pelvic pain, infertility, and increased risk of ectopic pregnancy. Because chlamydial infections can have serious long-term consequences for women, even when symptoms are mild or absent, detecting the infection in women and treating them and their sex partners is crucial.

Treatment references

Key Points

  • Sexually acquired chlamydial and mycoplasmal infections may affect the urethra, cervix, adnexa, throat, or rectum.

  • Diagnose using nucleic acid amplification tests.

  • Also test for coinfection with other STIs, including gonorrhea, syphilis, and HIV infection.

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

  • Use an antibiotic regimen that also treats gonorrhea if it has not been excluded.

More Information

The following English-language resources may be useful. Please note that THE MANUAL is not responsible for the content of these resources.

Drugs Mentioned In This Article

Drug Name Select Trade
Acticlate, Adoxa, Adoxa Pak, Avidoxy, Doryx, Doxal, Doxy 100, LYMEPAK, Mondoxyne NL, Monodox, Morgidox 1x, Morgidox 2x , Okebo, Oracea, Oraxyl, Periostat, TARGADOX, Vibramycin, Vibra-Tabs
Azasite, Zithromax, Zithromax Powder, Zithromax Single-Dose , Zithromax Tri-Pak, Zithromax Z-Pak, Zmax, Zmax Pediatric
Iquix, Levaquin, Levaquin Leva-Pak, Quixin
Amoxil, Dispermox, Moxatag, Moxilin , Sumox, Trimox
Avelox, Avelox ABC Pack, Avelox I.V., MOXEZA, Vigamox
Ceftrisol Plus, Rocephin
Flagyl, Flagyl ER, Flagyl RTU, LIKMEZ, MetroCream, MetroGel, MetroGel Vaginal, MetroLotion, Noritate, NUVESSA, Nydamax, Rosadan, Rozex, Vandazole, Vitazol
NOTE: This is the Professional Version. CONSUMERS: View Consumer Version
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