Prevalence and bacterial etiology of culture-confirmed neonatal sepsis in sub-Saharan Africa: a systematic review and meta-analysis

Neonatal sepsis is a life-threatening clinical syndrome caused by systemic infection during the first 28 days of life. Data on its pooled prevalence and bacterial pathogen distribution in sub-Saharan Africa remain limited. We conducted a systematic review and meta-analysis to estimate the pooled prevalence of neonatal sepsis and describe the distribution of causative bacterial pathogens in sub-Saharan Africa. This PRISMA 2020-guided systematic review and meta-analysis included observational studies published between January 2020 and December 2025 that evaluated neonates aged 0–28 days in SSA and reported culture-confirmed bacterial sepsis and pathogen data. The pooled prevalence of neonatal sepsis was estimated using the DerSimonian and Laird random-effects model with corresponding 95% confidence intervals (CIs). Statistical heterogeneity was assessed using Cochran’s Q test and the I² statistic. The pooled proportions of bacterial pathogens isolated from blood cultures were also estimated using random-effects models. Publication bias was assessed using funnel plot inspection and Egger’s regression test. Twenty-one studies from seven SSA countries involving 7,993 neonates were included. Most studies were conducted in neonatal intensive care. The pooled prevalence of neonatal sepsis among neonates evaluated for suspected sepsis was 35.2% (95% CI: 27.4–43.5%), with substantial heterogeneity between studies (I² = 98.3%, p < 0.001). Subgroup analysis showed no significant difference in prevalence between studies published during 2020–2022 (36.1%, 95% CI: 26.9–45.7%) and 2023–2025 (33.8%, 95% CI: 19.3–50.1%) ( p = 0.8129). Among culture-confirmed bacterial isolates, Staphylococcus aureus was the most frequently identified pathogen (23.0%, 95% CI: 17.3–29.3%), followed by coagulase-negative staphylococci (20.6%, 95% CI: 13.8–28.3%), Klebsiella pneumoniae (15.2%, 95% CI: 10.5–20.6%), Escherichia coli (9.3%, 95% CI: 5.9–13.3%), and Streptococcus spp. (8.1%, 95% CI: 3.1–14.9%). No evidence of publication bias was detected (Egger’s test, p = 0.827). Neonatal sepsis remains a substantial burden among neonates evaluated for suspected sepsis in sub-Saharan Africa, with diverse Gram-positive and Gram-negative bacterial pathogens, particularly Staphylococcus aureus , coagulase-negative staphylococci, and Klebsiella pneumoniae . These findings highlight the need to strengthen microbiological surveillance, diagnostic capacity, and infection prevention and control measures in the region.