Chlamydia is one of the most common bacterial sexually transmitted infections, relying heavily on laboratory testing for diagnosis. While modern diagnostic methods are highly accurate, they are not infallible, and misdiagnosis is possible. Understanding the circumstances under which a test result can be incorrect—either reporting a false positive or a false negative—is important for patients and healthcare providers. The reliability of the result depends on the technology used, the timing of the test, and the quality of the sample collected.
How Chlamydia is Typically Tested
Chlamydia diagnosis relies on Nucleic Acid Amplification Tests (NAATs). These tests detect the unique genetic material (DNA or RNA) of the Chlamydia trachomatis bacteria in a patient sample. NAATs are highly sensitive, allowing them to detect very low concentrations of the bacteria.
The type of sample used depends on the patient’s anatomy and sexual history. For women, a vaginal swab is often the preferred and most sensitive sample type, which can sometimes be collected privately by the patient. For men, a first-void urine sample—the initial stream of urine—is typically used for testing the urogenital tract.
Testing is also possible from non-genital sites, such as the throat and rectum, using mucosal swabs. This is recommended for individuals with specific risk factors to detect localized infections. The use of non-invasive samples like urine and self-collected swabs has significantly improved the accessibility of chlamydia screening.
Factors Leading to False Negative Results
A false negative result occurs when an infected person is incorrectly reported as negative. One common cause is testing too soon after exposure, known as the “window period.” The bacteria need time, typically one to three weeks, to multiply to a detectable level in the body; testing earlier can miss a nascent infection.
The quality of the specimen collected significantly influences accuracy. If a swab is improperly collected or lacks sufficient infected cells, the bacterial load may be too low for the NAAT to amplify the genetic material. For men, collecting a mid-stream urine sample instead of the required first-void can dilute the bacterial concentration, potentially causing a false negative.
Technical issues can also arise from substances in the sample that interfere with the laboratory process. These “inhibitors” can block the NAAT amplification step, preventing detection of the bacterial DNA. Additionally, rare genetic mutations in the Chlamydia trachomatis DNA sequence may cause certain NAATs to fail to recognize the target sequence, resulting in an inaccurate reading.
Factors Leading to False Positive Results
A false positive result indicates an infection in a person who is actually uninfected, though this is less common than a false negative. Laboratory contamination is a primary cause, occurring if a positive sample is accidentally mixed with a negative one during processing. Because NAATs are extremely sensitive, minute traces of genetic material can be amplified, leading to an incorrect result.
Administrative errors, such as mislabeling a sample, can also result in a false positive diagnosis. Technical issues with the test kit itself are infrequent but possible. Furthermore, the test may detect residual bacterial DNA from a successfully treated prior infection, which is not an active infection but can still trigger a positive result.
Cross-reactivity with non-chlamydial bacteria is a rare consideration. While certain bacteria, such as those causing bacterial vaginosis or urinary tract infections, could theoretically interfere, modern diagnostic technologies minimize this risk. Statistically, in populations where the actual rate of infection is very low (low-prevalence), the chance that a positive result is a false positive increases.
Health Consequences of Misdiagnosis
A false negative is medically concerning because it leaves an active infection untreated. In women, untreated chlamydia can ascend from the cervix into the upper reproductive tract, causing Pelvic Inflammatory Disease (PID). PID can result in long-term complications, including chronic pelvic pain, tubal factor infertility, and an increased risk of ectopic pregnancy.
In men, untreated infection can lead to epididymitis, a painful inflammation of the tube that stores and carries sperm, which may rarely cause infertility. Additionally, an undiagnosed infection allows the bacteria to be unknowingly transmitted to sexual partners.
A false positive result leads to unnecessary antibiotic treatment. This exposes the uninfected individual to potential medication side effects and contributes to antibiotic resistance. Beyond physical risks, receiving a false diagnosis of a sexually transmitted infection can cause significant psychological distress and strain on personal relationships.
Steps for Seeking Diagnostic Confirmation
If a misdiagnosis is suspected, such as a positive result in a low-risk individual, retesting is the most practical next step. A healthcare provider may recommend retesting if the initial test was performed within the window period following potential exposure. If the initial result was positive, a second test, potentially using a different NAAT platform or specimen type, can be requested for confirmation.
For patients with a negative result who still have symptoms or a high-risk exposure, retesting is advised after the recommended window period has passed. Discussing the result’s context with a healthcare provider is important, as they assess the test’s predictive value based on individual risk factors. In specific situations, such as when the positive predictive value is low, specialized confirmatory testing, like a culture, may be necessary due to its near-perfect specificity.