Chlamydia (Chlamydial Genitourinary Infections) Workup

Updated: Mar 09, 2021
  • Author: Shahab Qureshi, MD, FACP; Chief Editor: Michael Stuart Bronze, MD  more...
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Approach Considerations

Because of the possibility of multiple sexually transmitted infections, all patients with any sexually transmitted disease (STD) should be evaluated for chlamydial infection.

Endocervical, urethral, rectal, or oropharyngeal specimens should be obtained and assayed for C trachomatis infection in both males and females based on the patient’s sexual practices obtained by history. [32] A voided urine sample, whether midstream or first-void, effectively captures the chlamydial organism for nucleic acid amplification testing (NAAT). [33] NAATs are the most sensitive tests for these specimens and are therefore recommended for detecting C trachomatis infection. [34, 35] Self-collected vaginal swab specimens are equivalent in sensitivity and specificity to those collected by a clinician using NAATs. [34, 36, 37]

In infants with suspected chlamydial pneumonia, perform a nasopharyngeal swab for Chlamydia culture. Currently available rapid tests [38] are not approved for use on such specimens. In severe or complicated cases, consider sending bronchoalveolar lavage fluid for chlamydial culture as well. A complete blood count (CBC) revealing peripheral eosinophilia in the appropriate clinical situation is additional evidence supporting C trachomatis pneumonia.

In infants with suspected chlamydial conjunctivitis, perform an antigen/DNA detection test, chlamydial culture, or both, using scrapings from the palpebral conjunctiva.

If the mother had a documented chlamydial infection during pregnancy that was untreated, presumptively treat the infant, even without confirmation of infection.


Basic Laboratory Studies

A complete blood count (CBC) can be performed for suspected pelvic inflammatory disease (PID). The following should also be considered:

  • HIV testing (coinfection is not uncommon)

  • In women, a Papanicolaou (Pap) smear (the risk of cervical cancer is increased 6.5-fold)

  • Testing sexual partners for Chlamydia

A pregnancy test is mandatory for females with suspected chlamydial infection. Obtaining a pregnancy test helps with early diagnosis and guidance of treatment. Because pregnancy is a contraindication for the use of doxycycline and ofloxacin, it is critical to obtain a pregnancy test before beginning treatment with these drugs.

Pap smear showing chlamydia in the vacuoles. Magni Pap smear showing chlamydia in the vacuoles. Magnification, 500x. Image courtesy of the National Institutes of Health, National Cancer Institute.

Cytology and Cell Culture

Cytology is used mainly for diagnosing infant inclusion conjunctivitis and ocular trachoma through the demonstration of intracytoplasmic C trachomatis inclusions in HeLa cells (ie, continuously cultured carcinoma cell line used for tissue cultures). Cytologic diagnosis also is used to evaluate endocervical scrapings, but interpretation is difficult, and sensitivity and specificity have been low.

C trachomatis grows well in a variety of cell lines (eg, McCoy and HeLa cells) that can be maintained in tissue culture. Incubation in tissue culture is 40-72 hours, depending on the cell type and specific biovar. Intracytoplasmic inclusions can be detected either by Giemsa stains or by immunofluorescent staining with monoclonal antibodies.

Cultures are difficult to obtain; many false-negative results are returned. They are also expensive to perform, because of the expertise and laboratory resources required. In addition, they are unsuitable for large numbers of patients (eg, in the emergency department [ED]). Nevertheless, in certain clinical situations, cultures are mandatory.

Because of its high specificity (100%) and sensitivity, cell culture is the only test that should be used to establish the presence or absence of infections in cases with legal implications, such as those involving rape or sexual abuse. Cell culture is also preferred for rectal specimens because nonculture test results are difficult to interpret in the presence of stool organisms.

This photomicrograph reveals McCoy cell monolayers This photomicrograph reveals McCoy cell monolayers with Chlamydia trachomatis inclusion bodies; magnified 200X. Image courtesy of the Centers for Disease Control and Prevention.

Molecular Techniques for Detecting Antigen, DNA, or RNA/Rapid Tests

Because C trachomatis grows only within columnar cells, obtaining a specimen that contains cells directly from the urethra or cervix, not on pooled vaginal secretions, is important. In obtaining cells along with discharge, attempt to apply pressure to the inside of the cervix or urethra. In males, insert collection swabs 1-2 cm into the urethra after the urethra is milked to bring down secretions. Always follow the directions of the manufacturer of the kit used for collection, and follow transport instructions.

Direct fluorescent antibody (DFA) testing is a laboratory assay for C trachomatis that has a sensitivity of 50-80% and a specificity of 99% specificity. It is the method of choice for confirming other assays. However, it is labor intensive and requires skilled personnel.

Enzyme-linked immunosorbent assay (ELISA) is a laboratory assay for C trachomatis that has a sensitivity of 40-60% and a specificity of 99%. Because it is both automatable and cost-effective, it is suitable for large numbers of patients. ELISA is the most commonly used test for Chlamydia in the emergency department (ED) and in outpatient clinics.

Detection of chlamydial DNA may be accomplished by using specific probes. Newer DNA probe kits currently are available that allow detection of C trachomatis and N gonorrhoeae from voided urine specimens, obviating the need for direct sampling in uncomplicated cases. These urine tests may also be appropriate for use in the evaluation of possible sexual abuse. [39]

The US Food and Drug Administration (FDA) recently cleared the Cepheid GeneXpert CT/NG (Xpert) rapid polymerase chain reaction (PCR) test as a moderate-complexity test. CT/NG GeneXpert is a real-time PCR assay that can be run on demand in less than 2 hours and has a test performance that is similar to that of existing nucleic acid amplification tests (NAATs) in both low- and high-prevalence populations. [40]

The C trachomatis nonculture tests have been largely replaced because of the superior performance of NAATs, even when performed on noninvasive specimens.


Nucleic Acid Amplification Tests

NAATs have become the preferred diagnostic and screening test for C trachomatis genital infection in the United States because they are sensitive and can be used for noninvasive testing without the need for a pelvic examination or a urethral swab. [41, 42, 43] NAATs target and amplify conserved nucleic acid sequences that are present in almost all clinical strains of C trachomatis, including the genital, LGV, and ocular serovars.

The APTIMA Combo 2 Assay for ribosomal RNA (rRNA) can be used on ThinPrep liquid-based Pap smear specimens. [44] This has the advantage of being relatively simple and inexpensive. Most studies report sensitivities greater than 70% and specificities of 97-99% in populations of men and women with a prevalence of infection of 5% or more. If a definitive diagnostic test is required, antigen detection may well be the most appropriate diagnostic test for a primary care setting in the United States.

The main disadvantage of this approach is that it is less sensitive than tissue culture. In populations with a low (< 5%) prevalence of chlamydial infection, a highly significant percentage of positive test results are false positives. Accordingly, verification of a positive test result is desirable in certain cases. Such verification can be achieved by means of culture (eg, a second nonculture test that identifies a different chlamydial antigen or nucleic acid sequence from that identified in the first test), a blocking antibody, or a competitive probe.

NAATs that are cleared by the FDA are recommended for detection of genital tract infections caused by C trachomatis and N gonorrhoeae in men and women with or without symptoms. [45] Older nonculture tests and non-NAATs have inferior sensitivity and specificity characteristics and are no longer recommended.

NAATs have not been cleared by FDA for the detection of rectal and oropharyngeal infections caused by C trachomatis. The Centers for Disease Control and Prevention (CDC) recommends NAATs to test for these extragenital infections based on increased sensitivity, ease of specimen transport, and processing. Routine repeat testing of NAAT-positive genital tract specimens is not recommended because the practice does not improve the positive predictive value of the test. C trachomatis and N gonorrhoeae culture capacity might still be needed in instances of child sexual assault in boys and extragenital infections in girls. [45]

Although NAATs are sensitive, numerous disadvantages have been discussed. The first is that they are expensive and thus may not be affordable by health departments for comprehensive screening. [46] Another disadvantage is that the FDA-approved NAATs cannot distinguish LGV from non-LGV strains, which is important because the duration of treatment is longer for LGV infections. In addition, NAATs detect chlamydial DNA or RNA rather than live organisms, and positive NAAT results are not uncommon 3 weeks after completion of antibiotic therapy. [47] Thus, NAATs should not be used as a test-of-cure assay, except in pregnant women in whom it is justified to document cure at 3-4 weeks after completion of therapy in an effort to prevent infection in the infant. [41]



On a complement fixation test, all patients with lymphogranuloma venereum (LGV) have complement-fixing antibody titers higher than 1:16. Fifteen percent of men with urethritis and 45% of women with endocervical infection have titers of 1:16 or greater. The microimmunofluorescence test is more sensitive than the complement fixation test. Results are positive in at least 99% of women with cervicitis and in 80-90% of men with urethritis.

Antichlamydia immunoglobulin M (IgM) is uncommon in adults with genital tract infection. The prevalence of antichlamydial immunoglobulin G (IgG) is high in sexually active adults, even in those who do not have an active infection, and it likely is due to past infection. A statistically significant association exists between chlamydia-specific serum immunoglobulin A (IgA) and active disease.

The sensitivity, specificity, and predictive values of serologic studies for Chlamydia are not high enough to make any of them clinically useful in the diagnosis of active disease. Therefore, chlamydial serologies are not recommended for diagnosis of genital tract disease. The choice of the most appropriate test depends on the clinical setting, the facilities available, and the relative cost.


CT, Radiography, and Ultrasonography

Imaging studies are usually not required for patients with uncomplicated genital chlamydial infections. However, computed tomography (CT) and ultrasonography are useful diagnostic adjuncts in cases of complicated (upper tract) infection. For example, CT may identify Fitz-Hugh-Curtis syndrome (perihepatitis; see the images below). Ultrasonography may be performed to look for tubo-ovarian abscess.

CT scan of adolescent with chlamydial Fitz-Hugh-Cu CT scan of adolescent with chlamydial Fitz-Hugh-Curtis syndrome demonstrating perihepatic fluid collection anterior to liver.
CT scan of adolescent with chlamydial Fitz-Hugh-Cu CT scan of adolescent with chlamydial Fitz-Hugh-Curtis syndrome demonstrating free peritoneal fluid.

Obtain a chest radiograph for infants with suspected pneumonia. Chlamydial pneumonia may appear as a lobar or interstitial pneumonia in infants.



The US Preventive Services Task Force recommends routine Chlamydia screening for sexually active young women to prevent consequences of untreated chlamydial infection (eg, PID, infertility, ectopic pregnancy, and chronic pelvic pain). [5] Less than 50% of young, sexually active females in the United States are screened for Chlamydia. Nationally, the annual screening rate increased from 25.3% in 2000 to 43.6% in 2006, then decreased slightly to 41.6% in 2007. [5]

A guideline synthesis that addresses screening recommendations is also available from the National Guideline Clearinghouse. [8]

As a screening measure for asymptomatic males only, obtain urine for a leukocyte esterase test. This looks for white blood cells (WBCs), which are virtually diagnostic of chlamydial infection or gonorrhea in the absence of urinary tract infection (UTI) symptoms. If the leukocyte esterase test result is positive, proceed with the usual diagnostic tests.