In short, chlamydia is not typically present in urine. Chlamydia is caused by the bacteria Chlamydia trachomatis and is a common sexually transmitted infection (STI). The infection usually affects the urethra in males and the cervix in females, but it can also infect the throat and rectum. While chlamydia bacteria may be present in the urinary tract, the bacteria are not normally found in urine samples.
What is chlamydia?
Chlamydia is an STI caused by infection with the bacteria Chlamydia trachomatis. There are multiple strains or serovars of C. trachomatis that can cause different conditions:
- Serovars D-K: Cause genital tract infections in men and women (urethritis, cervicitis, pelvic inflammatory disease)
- Serovars L1-L3: Cause lymphogranuloma venereum, an infection of the lymph nodes
- Serovars A-C: Cause trachoma, an eye infection that can lead to blindness
Genital infections with chlamydia are extremely common, especially among young people aged 15-24 years old. The Centers for Disease Control and Prevention (CDC) estimates that in 2018, over 1.7 million cases of chlamydia were reported in the United States. However, many infections go undiagnosed and unreported, so the actual number of annual cases may be closer to 2.9 million.
Where does chlamydia infection occur?
In men, chlamydia most commonly infects the urethra, the tube that carries urine from the bladder out of the penis. The bacteria can also infect the epididymis, a coiled tube located behind each testicle where sperm mature.
In women, the most common site of infection is the endocervix, the narrow end of the uterus that opens into the vagina. Chlamydia can spread into the uterus and Fallopian tubes, causing pelvic inflammatory disease (PID).
Chlamydia can also infect the rectum, throat, and eyes if infected secretions come into contact with these areas.
Symptoms of chlamydia
Many people with chlamydia are asymptomatic and do not develop any symptoms. When symptoms do occur, they may include:
- Men: Discharge from penis, burning urination, swollen/painful testicles
- Women: Vaginal discharge, burning urination, bleeding between periods, abdominal pain
- Rectal infection: Rectal discharge, pain, bleeding
- Throat infection: Sore throat
Without treatment, chlamydia can persist for months or even years. Long-term infection can cause permanent damage and serious complications like infertility and ectopic pregnancy in women.
How do you get infected with chlamydia?
Chlamydia is spread through unprotected vaginal, anal, or oral sex with an infected partner. It can also be passed from an infected mother to her baby during childbirth.
The bacteria infect and multiply inside the epithelial cells that line the urethra, cervix, rectum, throat, and eyelids. The infected cells eventually rupture and release bacteria that can spread to new sites in the body.
Risk factors for chlamydia infection include:
- Having unprotected sex, especially with multiple partners
- Having another STI, like gonorrhea
- Having sex at an early age (less than 25 years old)
- Exchanging sex for money or drugs
Can chlamydia be found in urine?
Typically, chlamydia bacteria are not present in urine. The bacteria live inside the cells that line the reproductive tract and urinary system, not freely floating in urine. So urine alone is generally not a suitable specimen for diagnosing chlamydial infections.
Why chlamydia is not usually detectable in urine
There are a few reasons why chlamydia bacteria are not readily found in urine samples:
- Chlamydia lives inside cells, not in urine. The bacteria infect epithelial cells and take up residence inside them. Shed bacteria are then released when these infected cells rupture.
- Urine flushes out the urethra. As urine passes through the urethra, it washes away any infected cells or free floating bacteria.
- The bladder is usually not infected. Chlamydia typically only infects the urethra and does not reach further into the bladder.
- Urine is hostile to chlamydia. The bacteria are sensitive to the acidic, salty environment of urine and cannot survive for long when excreted.
For these reasons, urine specimens are generally inadequate for detecting chlamydia. Urine testing will mainly pick up infections that have spread to the upper genital tract and bladder. More invasive sampling of the urethra or cervix is needed to accurately diagnose chlamydia.
When can chlamydia be found in urine?
In some cases, chlamydia bacteria can end up in urine samples:
- Widespread infection: If the infection has spread extensively in the urinary tract, infected cells containing chlamydia may be shed into urine.
- Advanced infection: Chronic, untreated infections lasting months to years are more likely to disseminate into the bladder.
- Persistent discharge: Pus or discharge from the urethra or cervix can mix with urine and contain trace amounts of chlamydia.
- First-catch urine: The initial urine stream may pick up contaminated cells from the urethral opening.
These scenarios represent more extensive infections with a higher burden of bacteria in the urinary system. The chlamydia bacterial load is still lower than sampling directly from the genital tract.
When is urine testing appropriate for chlamydia?
Urine testing for chlamydia can be appropriate in certain situations:
- Screening sexually active women under 25 years old
- Testing in community settings or outreach programs
- Home sample collection instead of invasive swabs
- Retesting to confirm treatment effectiveness
- Routine testing for infections during pregnancy
For routine screening, urine nucleic acid amplification tests (NAAT) are reasonably sensitive in women. However, urine testing is not recommended for detecting chlamydia in heterosexual men, who more often have localized urethral infections.
How is chlamydia typically diagnosed?
The recommended methods for diagnosing chlamydia infection are:
- Women: Vaginal swab, endocervical swab, urine
- Men: Urethral swab, first-catch urine
- Rectal infection: Rectal swab
- Throat infection: Throat swab
Culture testing was previously the gold standard, but NAATs are now the preferred technique. NAAT detects bacterial genetic material rather than requiring viable organisms. Commonly used NAAT platforms include PCR, TMA, and SDA.
Compared to urine samples, genital samples like cervical and urethral swabs contain more chlamydia bacteria and cellular material, leading to higher test sensitivity. But urine and self-collected vaginal swabs are suitable options for screening programs given their convenience and non-invasive collection.
Tips for urine-based testing
If urine testing is performed, the CDC recommends:
- First-catch urine (first 10-30 ml)
- Use NAAT to maximize sensitivity
- Re-test with a genital specimen if urine is negative but symptoms persist
Can you detect chlamydia in urine through a microscopy?
Looking for chlamydia in urine under a microscope is not a reliable diagnostic method. There are two main reasons this technique does not work well:
- No visible bacteria. Chlamydia cannot be seen under routine microscopy. The small elementary bodies are difficult to visualize unless special stains are used.
- Low concentration. Even if present, only small numbers of chlamydia bacteria are shed into urine. Their concentration gets diluted in the large urine volume.
Microscopy is also prone to human error and has poor sensitivity compared to NAATs. So urine microscopy is not recommended for chlamydia diagnosis and has been replaced by molecular techniques.
Can you do a urine culture for chlamydia?
Urine culture is not the optimal specimen type for isolating chlamydia bacteria. Culturing urine for chlamydia suffers from similar drawbacks as microscopy:
- Low bacterial concentration and heavy dilution in urine
- Overgrowth by contaminating microbes
- Slow turnaround time of several days to weeks
- Labor intensive cell culture techniques
Urine cultures can sometimes detect chlamydia in cases of disseminated infection with complications like cystitis and urethritis. But the sensitivity is low compared to cervical and urethral swabs.
NAAT is faster, more sensitive, and preferred for urine testing. Urine culture for chlamydia diagnosis is now reserved for special cases like legal purposes or antibiotic resistance testing.
Can a chlamydia urine test come back negative and be wrong?
Yes, it is possible for a chlamydia urine test to come back negative but be incorrect. Some reasons for false negative urine tests include:
- Low bacterial load in urine specimen
- Urine collected too early or late during infection
- Improper urine sample storage/transport
- Not first-catch urine or small sample volume
- Low-sensitivity test method like microscopy
- Lab error or equipment malfunction
- Antibiotics taken recently lowered bacterial concentration
A meta-analysis found that NAAT urine tests can produce false negatives in up to 5% of chlamydia cases in women. The false negative rate is higher in men.
If suspicious symptoms persist after a negative urine test, follow up testing with a cervical/urethral swab is recommended to rule out infection.
Improving urine test accuracy
Ways to potentially decrease false negatives from urine chlamydia testing include:
- Use NAAT instead of culture or microscopy
- Collect first-catch urine sample
- Take large urine volume (30-40 ml)
- Standardize sample handling protocols
- Retest with a genital swab if symptoms continue
Does chlamydia cause cloudy urine?
Chlamydia does not typically cause cloudy or milky-appearing urine, known as pyuria. Cloudy urine suggests inflammation in the urinary tract and the presence of discharge, usually from a bacterial infection.
Common causes of cloudy urine include:
- Urinary tract infection (UTI)
- Kidney infection (pyelonephritis)
- Urethritis or cystitis
- Bladder fistula
- STDs like gonorrhea and trichomoniasis
- Urinary stones
- Encapsulated bacterial colonies (emphysematous cystitis)
But in most uncomplicated cases of urethral or cervical chlamydia infection, cloudy urine is not seen. Reasons why cloudy urine is uncommon with chlamydia:
- Minimal lower urinary tract inflammation
- Low bacterial burden shed into urine
- Urine flushing action helps prevent ascending infection
- More common STDs cause discharge and pyuria
However, some cases of pelvic inflammatory disease, epididymitis, or ascending bladder infection from untreated chlamydia can present with cloudy urine. If discharge, pain, or other urinary symptoms accompany chlamydia, urine testing and additional evaluation is warranted.
Does chlamydia cause hematuria?
Hematuria, or blood in the urine, is uncommon with uncomplicated chlamydial infections. Typical urethral infection in males and endocervical infection in females does not cause bleeding or detectable blood in urine.
However, some rarer complications of advanced chlamydia infection can lead to hematuria, including:
- Cystitis: Bladder infection can cause bladder inflammation and bleeding.
- Urethritis: Severe urethral inflammation may cause penile discharge tinged with blood.
- Pyelonephritis: Kidney infection can cause inflammation and kidney damage.
- PID: Pelvic inflammatory disease advancing to the upper genital tract.
If hematuria occurs along with pelvic pain in women or painful urination in men, it may signal serious ascending infection in the urinary tract. Evaluation for cystitis, urethritis, epididymitis, or PID is recommended in these cases.
Causes of hematuria
Some other common causes of blood in urine besides chlamydia complications include:
- Kidney stones
- Urinary tract infection
- Vigorous exercise
- Trauma or injury to kidneys or bladder
- Benign prostatic hyperplasia (enlarged prostate)
- Urinary tract malignancies like bladder cancer
- Blood clotting disorders
- Catheter irritation
Not all cases of hematuria require aggressive evaluation, but persistent or recurrent bleeding with pain warrants medical investigation. Sometimes no cause is found on workup.
Summary: Key Points
- Chlamydia is a common sexually transmitted infection caused by Chlamydia trachomatis bacteria.
- It typically infects the urethra in males and cervix in females.
- Chlamydia bacteria live inside mucosal cells and are not freely present in urine.
- Urine testing has lower sensitivity than genital specimens for diagnosis.
- First-catch urine with NAAT is appropriate for screening in some populations.
- Ascending urinary tract infections may shed more bacteria into urine.
- Cloudy urine and hematuria are uncommon findings with uncomplicated chlamydia.
The takeaway
While chlamydia may infect the urinary tract, the bacteria are not normally detectable in urine during routine screening. This is because chlamydia lives inside cells lining the genital tract rather than floating freely in urine. Cervical and urethral swabs are best for diagnosis. But urine NAAT is appropriate for screening young, sexually active women given its non-invasiveness. Persistent or worsening genitourinary symptoms despite a negative urine test warrant follow up testing with a genital specimen.