Prevalence of multidrug-resistant organisms colonizing neonates at a tertiary hospital in Johannesburg, South Africa

Neonatal mortality remains a global health challenge, particularly in sub-Saharan Africa, where infections often caused by multidrug-resistant (MDR) organisms are a leading cause of death. This study aimed to assess the prevalence of MDR ESKAPE pathogens and Candida auris colonization among hospitalized neonates in a non-outbreak setting, identify associated risk factors, and characterize antimicrobial resistance patterns. A cross-sectional sub-study was conducted at a tertiary hospital in South Africa between November and December 2020. A total of 258 rectal and skin swabs were collected from 86 neonates and cultured for ESKAPE organisms and C. auris. Isolated MDR organisms underwent further characterization. Of the 135 ESKAPE + C. auris isolates identified, 70.4% (95/135) were MDR. Colonization with ESBL-producing Klebsiella pneumoniae was most common (65%, 56/86), followed by XDR Acinetobacter baumannii. NDM-producing A. baumannii (5.8%) was more frequently detected than carbapenemase-producing Enterobacterales (3.9%). A prolonged hospital stay (median 14 days, P < .001) was significantly associated with MDR colonization. Rectal and skin swabs provided comparable yields for Gram-negative MDR organisms. The high prevalence of MDR ESKAPE + C. auris colonization highlights the value of routine, non-invasive screening for surveillance in neonatal units. Enhanced infection control strategies and improved surveillance systems incorporating colonization swabs and clinical risk profiling are urgently needed.