Background Studies assessing algorithms for management of ano-rectal discharge (ARD) syndrome among men who have sex with men (MSM) are scarce. Performance of ARD management flow charts for the diagnosis of Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) was evaluated.

Methods Between 2008 and 2009, four MSM dedicated clinics, located in two Indian cities, enrolled attendees consecutively and provided follow-up visit during four months. Data collected at each visit included behavioural information, clinical data, and rectal swabs tested for NG and CT using Roche Amplicor. Eight ARD algorithms were assessed. Data were used to construct the best performing flowchart.

Results The 508 participants made a total of 868 clinic visits including 127 instances of rectal NG and/or CT. Among those instances of NG/CT, only one (0.8%) had ano-rectal complaint(s) and 12 (9.5%) had ano-rectal discharge, observed at clinical examination. And on rectal smear microscopy, 31.5% had pus cells (OR 2.16, p < 0.001) and 44.1% had gramme negative diplococci with/without pus cells (OR 1.60, p = 0.016).

Algorithms using ano-rectal symptom as entry point had poor sensitivity (0.8%). The algorithm using receptive anal sex and/or complaint of ano-rectal discharge as the entry point, and subsequently using proctoscopic and/or rectal smear findings had a sensitivity, specificity and positive predictive value of 41.7, 66.3 and 17.5, respectively. By adding risk assessment, the algorithm performance values changed to 81.9, 20.1 and 14.9, respectively.

Conclusion Effectiveness of flow-charts for syndromic management of ARD is constrained by the asymptomatic nature of rectal NG/CT. Algorithms including receptive anal sex at entry point and applying risk assessment, clinical and rectal smear examination may be useful for management of rectal NG/CT in resource limited settings, until cheaper, reliable and feasible laboratory tests are made available.