Introduction Utility of syndromic case management (SCM) in symptomatic women facing huge misdiagnosis/overtreatment problems due to lack of accurate and confirmed diagnosis. As a consequence antibiotic resistance has accelerated along with an increase in risk of infection to their partner.

Methods symptomatic women (18–56 years old) were recruited in the study and examined by clinician based on subjective judgment and treated vaginal discharge with various clinical symptoms causing microorganisms by NACO-NACP III Algorithms for STI/RTI and comparative analysis using PCR-based diagnostic assay.

Results We found that; 646/3200 (20.18%) female patients reported vaginal discharge and recommended treatment for either CT, NG, TV and Candida and/or co-infection using pre-packed STI/RTI kits under NACP III. Based on PCR, 48/646 (7.43%) subjects tested positive for infection with NG/TV/CT. Amongst 46 patents, 28 (60.86%) were correct and conformed diagnosis by PCR and SCM both. While 18/46 (39.14%) were incomplete treated and overtreatment due to poor diagnosis. Out of 600/646 (92.87) treated patients were uninfected of these three pathogens. Based on PCR and SCM, prevalence of TV, NG and CT were shows huge variations. As a result, SCM is inaccurate as infection caused by any of these pathogens showed similar symptoms: vaginitis, cervicitis, genital ulcers, AVD and LAP. The recent increases of misdiagnosis, overtreatment and antibiotic resistance are cause for public health concern. Here our results clearly demonstrate that prevalence of CT and NG is still significant among female patients.

Conclusion The study underpins the need to implement diagnostic assays for identification of causative pathogen before implementing antibiotic treatment to patients with vaginal discharge. It also divulges the need to review the use of SCM for controlling sexually transmitted diseases.