Microbial etiology and antimicrobial resistance patterns in neonates admitted to a tertiary neonatal intensive care unit in Mogadishu, Somalia

Abstract

Objective Neonatal sepsis continues to be one of the leading causes of morbidity and death, particularly in low- and middle-income countries (LMICs). This study aimed to evaluate the microbiological etiology, temporal trends, and antibiotic resistance patterns in a tertiary neonatal intensive care unit (NICU) over a six-year period. Methods This retrospective study included neonates admitted to a tertiary neonatal intensive care unit between 2018 and 2024. Early-onset infections were defined as infections occurring within the first 72 hours of life, while late-onset infections were defined as infections occurring after 72 hours. Logistic regression analysis was used to assess temporal trends and identify factors associated with multidrug-resistant infection. Results Microbial growth was observed in 891 (30.0%) of the total samples. A total of 891 isolates (30.0% of all samples) with complete data were included in the final study after duplicate and contaminated isolates were removed. Among these isolates, 472 (53.0%) were Gram-positive bacteria , 366 (41.1%) were Gram-negative bacteria , and 53 (5.9%) were Candida spp. isolates . isolates. In addition to a greater proportion of Gram-negative organisms (43.6% vs. 35.4%) and Candida species (7.5% vs. 2.6%), late-onset infections showed considerably higher culture-positive rates (37.7% vs. 20.7%, p < 0.001) than early-onset infections. On the other hand, Gram-positive organisms predominated in early-onset infections (62.0% vs. 48.9%, p < 0.001). In Multivariate logistic regression analysis, study year was not independently associated with MDR after adjustment (aOR: 1.06, 95% CI: 0.98–1.14, p = 0.169), whereas late-onset infection was still independently linked with MDR infection (aOR: 2.53, 95% CI: 1.84–3.47, p < 0.001). Despite changes in MDR rates throughout the course of the research years, carbapenem resistance demonstrated a significant growing trend over time ( p for trend = 0.004). Notably, none of the commonly used empirical antibiotics met the recommended susceptibility level of ≥80%. Conclusion This six-year study reveals a significant burden of neonatal infections in the NICU, with Candida spp. and Gram-negative organisms predominating in late-onset infections and Gram-positive organisms in early-onset infections. Carbapenem resistance dramatically increased over time, and late-onset infection was independently linked to multidrug resistance. These results highlight the necessity of stronger IPC, localized antimicrobial stewardship, updated empirical treatment guidelines, and regular AMR surveillance.