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Epidemiological data on neonatal bloodstream infections (BSI) in sub-Saharan Africa are extremely limited. A comparative analysis of laboratory-confirmed neonatal BSI episodes was conducted retrospectively in two large neonatal units in Botswana and South Africa (January 1 to December 31, 2017). Routine laboratory and ward register data were used to determine BSI rates, the pathogen spectrum, and BSI outcomes. In 2017, the Princess Marina Hospital (PMH) and Tygerberg Hospital (TBH) neonatal units admitted 1187 and 2826 neonates, respect