Background: Neonatal sepsis remains a major cause of morbidity and mortality globally, particularly in low-resource settings where antimicrobial resistance is increasing. This study aimed to identify microbial patterns, assess antibiotic resistance, and analyse their association with clinical outcomes among neonates treated for sepsis. Methods: A cross-sectional study was conducted on neonates aged 0–28 days with suspected sepsis and positive culture results admitted to the NICU and Perinatology Unit of Bali Mandara General Hospital from January to December 2024. Microbial isolates, antibiotic susceptibility, demographic characteristics, and clinical outcomes were analysed. Pearson’s Chi-square test was used to assess the association between Acinetobacter baumannii culture positivity and neonatal outcomes. Results: There were 75 samples There were 75 samples included in the final analysis. Gram-negative bacteria predominate, mainly carbapenem-resistant Acinetobacter baumannii (CRAB) (37.3%) and Klebsiella pneumoniae (24.0%). CRAB showed extensive antibiotic resistance, with residual susceptibility to amikacin and trimethoprim-sulfamethoxazole. Overall, 78.7% improved and 21.3% died. Mortality was higher in CRAB-positive neonates than in non-CRAB cases (35.8% vs. 12.8%; p = 0.019). Gestational age was significantly associated with outcomes (p = 0.006). Conclusion: Gram-negative bacteria, particularly A. baumannii and K. pneumoniae, were the leading causes of neonatal sepsis and demonstrated significant antimicrobial resistance. Although not statistically significant, A. baumannii infection showed a concerning trend toward higher mortality. Findings highlight the need for strengthened antimicrobial stewardship, updated empirical therapy, and enhanced infection-control practices in NICU settings.
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