Abstract:

Background: Urogenital pathogens such as Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis have been reported to cause pus in urine; however with the use of routine urine culture media they cannot be captured. This had led to the delay in diagnosis and miss-management of these patients which lead to complications like cervicitis, urethritis, infertility and pelvic inflammatory disease.

Objective: To determine microbiological patterns of culture negative pyuria, associated factors and utility of rapid test in detecting C. trachomatis using Polymerase Chain Reaction as gold standard in selected areas of Tanzania.

Methods: This was a cross sectional laboratory based study. The study involved 227 archived urine samples collected from patients with pyuria but bacteria culture negative results. These samples were used for detection of not-routinely cultured bacteria using PCR. DNA extraction was done using Cetyltrimethlammonium bromide (CTAB) modified Phenol –chloroform method. PCR was performed using specific primers of each bacteria. Rapid test for detection of Chlamydia trachomatis antigen from urine sample was performed following manufacturer instructions.

Results: Of the 227 samples, 62 (27.3%) were positive for at least one or more urogenital pathogens. The most prevalent pathogen was Neisseria gonorrhoeae 25 (11.0%), followed by Trichomonas vaginalis 24 (10.6%), Mycoplasma genitalium 13(5.7%) and Chlamydia trachomatis 11 (4.9%). Of the 62 positive samples, 10 (16%) were co-infected with two or three urogenital pathogens. The sensitivity, specificity, positive and negative predictive value of the rapid for detection of Chlamydia trachomatis were 27.3%, 99.1%, 60.0% and 96.4% respectively. Following multivariate logistic regression analysis factors predictive of PCR positive for urogenital pathogen were being female (OR 2.4; 95% CI: 1.1 – 5.5; p-value =0.039) and having history of using antibiotics in the past two weeks (OR 1.9; 95% CI: 1.1 – 3.6; p-value=0.036).

Conclusion: The burden of not-routinely cultured urogenital pathogens among patients with pyuria but bacteria culture negative is high with the most common urogenital pathogens being Neisseria gonorrhea followed by Trichomonas vaginalis. Independent factors predictive of PCR positive for urogenital pathogens were being female and having history of using antibiotics in the past two weeks. PCR assay should be done among all patients with pyuria but bacteria culture negative results. The rapid test for detection of Chlamydia trachomatis has low sensitivity which may be attributed to use of urine sample which is not recommended.