<p><strong>INTRODUCTION: </strong>Data from Africa reporting the epidemiology of infection in hospitalised neonates are limited.</p>

<p><strong>METHODOLOGY: </strong>A prospective study with convenience sampling was conducted to characterise neonates investigated with blood culture/s for suspected infection at a 132-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 suspected but blood culture-negative) or as potentially at risk of infection (maternal risk factors at birth).</p>

<p><strong>RESULTS: </strong>Of 1299 hospitalised neonates with &gt;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 &lt; 0.001). Median onset of proven BSI versus presumed infection was at 8 (IQR = 5-13) and 1 (IQR = 0-5) days respectively (p &lt; 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 &lt; 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).</p>

<p><strong>CONCLUSIONS: </strong>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.</p>