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Background  East and South Africa contributes 59% of all pediatric HIV infections globally. In Uganda, HIV prevalence among HIV exposed infants was estimated at 5.3% in 2014. Understanding the remaining bottlenecks to elimination of mother-to-child transmission (eMTCT) is critical to accelerating efforts towards eMTCT. This study determined factors associated with HIV positive sero-status among exposed infants attending mother-baby care clinics in rural Kasese so as to inform enhancement of interventions to further reduce MTCT.    Methods  This was a cross-sectional mixed methods study. Quantitative data was derived from routine service data from the mother’s HIV care card and exposed infant clinical chart. Key informant interviews were conducted with health workers and in-depth interviews with HIV infected mothers. Quantitative data was analyzed using Stata version 12. Logistic regression was used to determine factors associated with HIV sero-status. Latent content analysis was used to analyse qualitative data.    Results  Overall, 32 of the 493 exposed infants (6.5%) were HIV infected. Infants who did not receive ART prophylaxis at birth (AOR = 4.9, 95% CI: 1.901–13.051, p=0.001) and those delivered outside of a health facility (AOR = 5.1, 95% CI: 1.038 – 24.742,  p  = 0.045) were five times more likely to be HIV infected than those who received prophylaxis and those delivered in health facilities, respectively. Based on the qualitative findings, health system factors affecting eMTCT were long waiting time, understaffing, weak community follow up system, stock outs of Neverapine syrup and lack of HIV testing kits.    Conclusion  Increasing facility based deliveries and addressing underlying health system challenges related to staffing and availability of the required commodities may further accelerate eMTCT.

Factors associated with HIV positive sero-status among exposed infants attending care at health facilities: a cross sectional study in rural Uganda