Introduction Trichomonas vaginalis (TV) is a protozoan parasite that infects the genitourinary tract of 250 million individuals annually, leading to trichomoniasis. The Infection is associated with preterm delivery, low foetus birth weight and increased susceptibility to other STDs as well as increased HIV acquisition. Infection with Trichomonas is globally underestimated because of ineffective screening protocols and under equipped pathological laboratories especially in developing countries. As a consequence, trichomoniasis is associated with poor reproductive health, with numerous clinical squeal and complications. In developing countries like India, due to forbidden cost of commercial kits, syndromic management is preffered. Hence, a cost effective and quick diagnostic assay is urgently required. The present study is an attempt to develop an inexpensive, specific and sensitive quantitative assay for Trichomonas vaginalis.

Methods Specimens were retrieved consecutively from patients with vaginal complaints. In-house primers and molecular TV beacon (Tv-B) were designed to detect the presence of unique regions in the genome of Trichomonas in clinical isolates. The sensitivity and specificity of the inhouse primers were evaluated against published primers and the method was validated against qPCR based commercial kit using DNA isolated from 802 dry clinical swabs.

Results In-house designed PCR based assay for detection of trichomonas was highly sensitive as could detect as low as 10fg of genomic DNA (3–5 pathogens). Using molecular beacon, Tv-B, 83 women (10.3%) tested positive for trichomonas out of 802 women (age 15 yrs –55 yrs). The assay was extremely specific and sensitive (99.25% and 94.64% respectively). The PPV was found to be 94% and NPV was 99%. The assay could be used for quantification of load of infection.

Conclusion The results demonstrated that in housed developed test for TV is highly specific, sensitive, pocket and user friendly.