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Background  Chlamydia is a bacterial infection that has long plagued humanity as the most commonly contracted STD and is caused by  Chlamydia trachomatis . With the emergence of HIV/AIDS, sexually transmitted diseases have also re-emerged as a grave public health problem, particularly in developing countries. Updated Information about the relative frequencies in developing countries is sparse. This study aims at establishing the relative occurrence of chlamydia using real time PCR technique in the Vhembe District of South Africa where reports on the prevalence of chlamydia are not available.    Methods  A total of 243 Urine samples were collected from patients attending different ARV clinics in the Vhembe District and genomic DNA was purified using blood genomic DNA kit from Sigma-Aldrich. Real-Time PCR protocol targeting the 16S rRNA gene of  C. trachomatis  was used to confirm the presence of chlamydia among these patients. Demographic information as well as clinical data was collected as well.    Results  Of all the participants, 70.4 % were females. The age varied from 19 to 72 years. The overall prevalence of chlamydia was 32.1 %. The prevalence was significantly higher among females (39.2 %) compared to males (15.5 %) patients (P = 0.001) and was highest among pregnant women followed by patients who had reported any allergic reaction. Among the HIV positive patients, the prevalence was higher among those who were not taking ARV (38.1 %) compared to those who were taking them (28.5 %). The age group within which the highest prevalence was found was between 26–45 years.    Conclusions  The present study shows a high prevalence of chlamydia among HIV and AIDS patients in the Vhembe District emphasizing the need to enhance STI control and particularly chlamydia among all young people. The particularly high prevalence of chlamydia among pregnant women is of great concern as this predisposes them to complications, while allergy migh predispose people to chlamydia infections. Further studies are needed in the general population both HIV positive and HIV negative persons to further determine the impact of these infections in the community.

Prevalence of chlamydia among HIV positive and HIV negative patients in the Vhembe District as detected by real time PCR from urine samples