Bacteria Pathogen Distribution in Late-Onset Neonatal Sepsis: Trends from a South African Neonatal Intensive Care Unit

Late-onset sepsis (LOS) in neonates is defined as a bloodstream infection occurring after 72 hours of life and is primarily caused by bacterial pathogens, often associated with catheter use and prolonged hospitalization. Despite its clinical and policy relevance, limited data exist on the etiology of neonatal infections in sub-Saharan Africa. This 8-year retrospective study investigated microbial patterns and antibiotic trends of LOS in a South African neonatal unit to inform infection control and antibiotic stewardship strategies. Data from neonates weighing 500 to 2,500 g admitted to the neonatal unit of a public tertiary hospital in Johannesburg (2013-2020) were analyzed for culture-confirmed LOS. Microbial prevalence was stratified by birth weight and year, and temporal shifts were assessed using Joinpoint regression. Among 7,468 neonates, 1,454 LOS episodes occurred (194 per 1,000 live births), with males accounting for 51.1%. Gram-positive bacteria predominated (55.4%), mainly coagulase-negative staphylococci (CoNS; 37%), followed by Gram-negative bacteria (44.4%), notably extended-spectrum beta lactamase-producing Klebsiella (13.2%) and Acinetobacter baumannii (12.8%). A marked decline in CoNS incidence was observed in 2016 (annual percentage change: -17.6%). Meropenem (35%) and vancomycin (30.5%) were most frequently used, with extreme-low-birth-weight (ELBW) neonates disproportionately affected. Late-onset sepsis remains a persistent challenge, with CoNS as the leading pathogen and increasing multidrug-resistant Gram-negative infections, particularly in ELBW and very-low-birth-weight infants. The observed decline in CoNS may signal improved infection control, whereas reliance on last-line antibiotics underscores an urgent need for enhanced surveillance, prevention, and antimicrobial stewardship.