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A cross-sectional molecular epidemiological study of Entamoeba species was conducted among asymptomatic Kenyan children with (n = 123) and without (n = 111) HIV infection. The prevalence of E. histolytica was low (0.4%). Entamoeba species infection was inversely related with HIV infection [HIV(+): 29.3% vs. HIV(−): 55.0%, P < 0.001]: multiple-species infection was related to higher CD4+ T-cell counts. Thus, HIV infection is not a risk factor for amebic infection, and multiple-species infection can be an indicator of better immune status.