We performed a secondary analysis of data from two longitudinal cohorts of individuals on long-term ART: the ART cohort of The Infectious Diseases Institute (IDI) of the College of Health Sciences at Makerere University in Kampala, Uganda  and the ART cohort of The AIDS Support Organization (TASO) in Jinja, Uganda .
The IDI urban ART cohort in Kampala
The adult IDI clinic is a center of excellence for HIV care and treatment  located in Mulago Teaching Hospital in Kampala-Uganda. The out-patient clinic has over 30,000 patients ever enrolled and cares for people living in five Kampala municipalities. ART is provided free of charge, initially though the Global Fund and later mainly through the US President’s Emergency Plan for AIDS Relief (PEPFAR).
Following written informed consent, adults (age ≥ 18 years) starting ART between April 2004 and April 2005 were enrolled in a cohort study and followed up for 10 years (hereafter referred to as the urban cohort). ART was started in patients with WHO Stage 4 or CD4 count ≤200 cells/ml, (according to national treatment guidelines implemented at that time), and consisted of stavudine (weight-adjusted, but discontinued in 2013 in Uganda), lamivudine and nevirapine (fixed-dose combination) or zidovudine, lamivudine (fixed-dose combination) and efavirenz. A doctor or clinician and adherence counselor evaluated cohort participants at study enrolment and every three months thereafter while they attended the clinic for ART medication refills . At each study visit, a physical examination was performed and information was recorded about HIV status of the partner(s), social support, sexual history in the past month including STIs screening, diagnosis and treatment. At each clinic visit, the study Doctor asked if the participant experienced any of the syndromic symptoms read to the participant since the last visit, a syphilis serology was done for selected participants based on presenting symptoms. ART was monitored every 6 months through viral load (VL) testing. Participants with a VL ≥1000 copies/ml were offered enhanced adherence counseling and support. Patients with two consecutive viral loads ≥1000 copies/ml were eligible for second-line ART.
The TASO rural ART cohort in Jinja
TASO was the first and is one of the largest non-governmental organizations in sub-Saharan Africa (SSA), providing treatment to over 98,000 patients through 11 TASO care facilities in Uganda. Since 2004, TASO Jinja facility has cared for people living with HIV in Jinja district within a radius of 75 km and currently provides ART to over 5000 people. In 2015, A world bank report on development indicators categorized 83.9% of Jinja population as rural. In this study, 81% of the study participants resided outside Jinja municipality.
In June 2012, TASO Jinja initiated a prospective longitudinal cohort study (the Long-Term Outcomes on ART in Uganda Study) of adults who had been receiving first-line ART for a minimum of 4 years (hereafter referred to as the rural cohort) [20, 21]. Between July 1, 2012, and December 31, 2013, all individuals receiving first-line ART for at least 4 years were eligible to participate in the cohort study. From August 2014 until January 2015, enrollment was restricted to patients on ART for at least 4 years with CD4 cell count ≤450 cells/mm3 in order to over-sample participants who may have had virologic failure. All participants continued to receive routine comprehensive HIV care from TASO service providers. All participants received a VL test at enrollment. Participants with a VL ≥1000 copies/ml were offered enhanced adherence counseling and VL was re-assessed after three months.
Patients were followed up for an additional 3–3.5 years. Every six months, cohort participants completed an interviewer-administered standardized questionnaire (adapted from the HAARP study)  to collect behavioral and treatment outcomes. Clinical care was provided by doctors and clinicians and included STI syndromic screening and management. At each clinic visit the study nurse asked if the participant experienced lower abdominal pain with abnormal vaginal discharge, sores or pus in the penis and vagina since the last visit. and a syphilis serology done for selected participants based on symptoms. Laboratory monitoring included CD4 counts and VL every 6 months. CD4 counts were performed at the Jinja referral hospital regional laboratory. Plasma samples were stored in liquid nitrogen and shipped to the Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) laboratory in Entebbe, Uganda for VL testing and resistance assays.
Data management and statistical analysis
The urban cohort data were directly collected into an electronic medical record by medical doctors who provided clinical care. Data were periodically validated by a senior Data Manager as part of routine quality control checks. The rural cohort data were double entered using Epi-Info and imported into Microsoft Access for data management and storage. Laboratory test results were transmitted electronically from the MRC laboratory to the data center at TASO Jinja and manually entered into the study database.
For this analysis, data extracted from TASO and IDI database included socio-demographic information, ART start date, ART regimen, sexual behavior, ART adherence at enrolment and at subsequent clinic visits. Clinical data at enrollment and during follow up including information on STI syndromic symptoms and management, CD4 cell counts, and viral load testing were also extracted. Risky sexual behavior was defined as sexual intercourse with ≥2 partners or inconsistent or no condom use in previous 6 months.
In this analysis, baseline was defined as the time of enrollment into the cohort (rural cohort) or the 4-year visit on ART (urban cohort). We described baseline participant characteristics overall and by gender and cohort (urban and rural) using means and frequencies.
The primary outcome of interest was STI incidence rate, defined as the number of new diagnoses per study population at risk during the follow-up (up to additional 3.5 years for both cohorts taking time of enrollment into the cohort (rural cohort) or the 4-year visit on ART (urban cohort) as the baseline. The primary endpoint (STI diagnosis) was defined as syndromic diagnosis (urethral discharge, genital ulcer disease, abnormal vaginal discharge) and a laboratory diagnosis of syphilis. We focused on first STI during follow, only 0.9% of study participants had more than one STI diagnosed during follow up. In time-to-event analysis, all participants contributed person-time from baseline until occurrence of event (STI diagnosis), death, lost to follow up, and transferred out, withdrawal of consent or completion of 3.5 years of follow up, whichever occurred first. A Kaplan-Meier analysis was performed to estimate time to first STI. Using a Cox proportional hazards regression model, we evaluated for associations between STIs and covariates (urban/rural residence, age, CD4 cell count, viral load, gender, education level, marital status, occupation, and time on ART). Covariates were included in the initial Cox model based on prior knowledge and results of the bivariable association and removed using a backward elimination procedure to identify factors independently associated with STI incidence.