Background: Trends in prevalence of opportunistic infections (OIs) associated with the human immunodeficiency virus (HIV) in resource poor settings have previously not been well documented. The objective of this study was to describe the trends in prevalence of Diarrhoea, Bacterial pneumonia, Kaposi’s sarcoma, Malaria and Geohelminths among HIV positive individuals over a 12 year period in Uganda.

Methods: Observation data for 5972 HIV positive individuals enrolled with the AIDS support organisation (TASO) in Uganda were analysed. Study participants were drawn from three HIV clinics located in different geographical areas of Uganda and followed from January 2002 to December 2013. The prevalence trends for the above OIs were plotted using the Box Jenkins moving average technique. X2-test for trend was used to test for the significance of the trends and Pearson’s correlation coefficient used to test for the strength of linear relationship between OI prevalence and calendar time. Mixed effect linear regression was used to estimate average monthly change in prevalence with monthly variation modelled as a random effect.

Results: A total of 204,871 monthly medical reports were retrieved and analysed. 73 % (4301/5972) were female with a median age of 32 years (inter-quartile range 26–39). Overall, significant decreasing mean annual prevalence trends (p < 0.05, X2 trend) were observed for Diarrhoea (<1 month) with Pearson’s correlation coefficient (r = -0.89), Malaria (r = -0.75), Bacterial Pneumonia (r = -0.52), and Geohelminth (r = -0.32). Non-significant increasing mean annual prevalence trend was observed for Kaposis sarcoma (p = 0.20, X2 trend; r = +0.26). After adjusting for age, sex and clinic in a mixed effects linear regression model, average monthly prevalence declined significantly at a rate of 0.4 % for Kaposis sarcoma, 0.3 % for Geohelminths, 2 % for Malaria, 1 % for Bacterial Pneumonia and 3 % for Diarrhoea(<1 month). However, the rate of decline per month differed significantly (p < 0.05) by HIV clinic for Diarrhoea (<1 month), and age, sex and clinic for malaria.

Conclusions and recommendations: Overall, decreasing trends were observed in the above OIs. However the trends differed significantly by OI, geographical location and demographic characteristics. There is urgent need to integrate interventions targeting malaria and geohelminths in HIV programmes.