Background: Data from Africa reporting the epidemiology of infection in hospitalised neonates are limited. Methods: We conducted a cross-sectional study with convenience sampling to characterise neonates investigated with blood culture/s for suspected infection at a 124-bed neonatal unit in Cape Town, South Africa (1 February-31 October 2018). Enrolled neonates were classified as having proven bloodstream infection (BSI) (blood culture-positive with a pathogen) or presumed infection (clinically

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... suspected but blood culture-negative) or potentially at risk of infection (maternal risk factors at birth). Results: Of 1299 hospitalised neonates with >1 blood culture sampling episode, 712 (55%) were enrolled: 126 (17.7%) had proven BSI; 299 (42%) had presumed infection and 287 (40.3%) were potentially at risk of infection. Neonates with proven BSI had lower birth weight and higher rates of co-existing surgical conditions versus the presumed/potential infection groups (p<0.001). Median onset of proven BSI versus presumed infection was at 8 (IQR 5-13) and 1 (IQR 0-5) days respectively (p<0.001). Most proven BSI were healthcare-associated (114/126; 90.5%), with Klebsiella pneumoniae (80.6% extended-spectrum β-lactamase producers) and Staphylococcus aureus (66.7% methicillin-resistant) predominating. Mortality from proven BSI (34/126; 27%) was substantially higher than that observed in presumed (8/299; 2.7%) and potential infections (3/287; 1.0%) (p<0.001). The odds of death from proven BSI was 3-fold higher for Gram-negatives than for Gram-positive/fungal pathogens (OR 3.23; 95%CI 1.17-8.92). Conclusion: Proven BSI episodes were predominantly healthcare-associated and associated with a high case fatality rate. Most neonates with presumed infection or at potential risk of infection had favourable 30-day outcomes.