Receiving a positive Chlamydia test result while your partner tests negative can be a confusing and upsetting experience. Chlamydia is a common bacterial infection, Chlamydia trachomatis, transmitted through sexual contact. A difference in test results might understandably raise questions about infidelity or testing accuracy. However, a discordant result—one positive, one negative—frequently reflects complex biological and technical factors inherent in infection and diagnostic testing. The detection of this specific bacterium depends on variables, including when the test was taken, how the sample was collected, and where the infection is located in the body.
Differences in Diagnostic Testing and Sample Collection
The gold standard for detecting Chlamydia trachomatis is the Nucleic Acid Amplification Test (NAAT), which works by identifying the genetic material (DNA or RNA) of the bacteria. NAATs are highly sensitive, but even these advanced tests are not 100% accurate and are susceptible to false-negative results. A false negative means the test indicates no infection even though the bacteria are present in the body, which is a common explanation for a partner’s negative result.
The quality of the sample collected significantly affects the accuracy of the NAAT. For instance, in men, an accurate test relies on a “first-catch” urine sample, meaning the initial stream of urine must be collected because it contains the highest concentration of cells shed from the urethra. If the partner was tested with a midstream urine sample, the bacterial load could be diluted and fall below the test’s detection threshold, leading to an inaccurate negative result. Similarly, a poorly collected or insufficient vaginal swab in women can also cause the test to miss an existing infection.
Other technical issues can compromise test sensitivity. These include the use of certain lubricants or antiseptics during sample collection, which may inhibit the amplification process in the lab. Additionally, rare genetic variants of C. trachomatis exist that possess a deletion in a specific part of their DNA, and if the particular NAAT used targets that deleted region, it can fail to detect the infection. Issues with sample transport, storage, or processing can also degrade the quality of the sample, potentially causing a false-negative outcome for the partner.
Biological Factors and Infection Timing
The biological timeline of the infection itself can also explain the disparity in results between partners. The C. trachomatis bacterium requires a certain amount of time to multiply within the body to a level high enough to be reliably detected by a NAAT; this period is known as the incubation or “window period.” Chlamydia tests typically become positive about one to two weeks after exposure, but if the partner was tested too soon, their bacterial load may have been too low to register, resulting in a negative test.
The infectious load of the bacteria can also fluctuate over time, a phenomenon known as intermittent shedding. The concentration of C. trachomatis organisms may vary dramatically in the genital or other infected areas. This means the bacteria might be detectable one day and then temporarily drop below the test’s threshold the next, coinciding with a low-shedding period for the partner who tested negative.
Differences in individual immune response also play a role in how the infection progresses and how detectable it becomes. Some individuals may mount a faster immune response that keeps the bacterial population suppressed, leading to a significantly lower, harder-to-detect load. One person may develop a high enough concentration for a positive result, while the other maintains a bacterial load that the test cannot reliably pick up.
The Impact of Site-Specific Infection
The location of the Chlamydia infection relative to the site of sample collection is another major cause of discordant results. C. trachomatis can infect multiple anatomical sites, including the urogenital tract (cervix or urethra), the rectum, and the throat (pharynx). Standard screening often focuses only on the urogenital site, typically using a urine sample or a genital swab.
If the partner’s infection is located at an extragenital site, such as the rectum or pharynx, but they were only tested with a genital swab or urine sample, the result will be negative. Rectal and pharyngeal infections are often asymptomatic, meaning the partner may be infected and contagious without any noticeable symptoms. This is particularly common among individuals who engage in receptive anal or oral sex, as the bacteria can be transmitted to those sites.
For example, a person may have a rectal Chlamydia infection, but if the healthcare provider only collected a urine sample, the NAAT would correctly detect no bacteria in the urine, leading to a misleading negative result. Comprehensive screening requires that samples are taken from all potentially exposed sites—genital, rectal, and pharyngeal—based on the patient’s sexual history. This practice is not always followed during routine testing.
Necessary Steps Following Discordant Results
The most immediate step following a positive Chlamydia result is for the infected partner to begin antibiotic treatment as prescribed by a healthcare provider. The positive partner must follow the instructions carefully and complete the entire course of medication to ensure the infection is cured. During treatment and until seven days after completion of the regimen, both partners should abstain from all sexual contact to prevent re-infection or transmission.
For the partner who tested negative, the medical protocol often involves presumptive treatment, also known as empirical therapy, because of the high likelihood of a false-negative result or an incubating infection. Treating the negative partner prevents them from developing complications, stops the cycle of transmission, and eliminates the risk associated with a potential undetected infection. If presumptive treatment is not immediately given, the negative partner should be retested, typically two weeks after the potential exposure or their initial test to ensure the infection has passed the window period for detection.
Both individuals must understand that retesting is necessary for the positive partner three months after finishing treatment, as repeat infections are common. The focus should remain on open communication, partner notification, and ensuring that both individuals are either treated or confirmed negative to safeguard their health. Discussing the results with a healthcare professional can help determine the most appropriate course of action based on the specific circumstances of the discordant results.