More than 80% of infection-linked newborn deaths in South Africa may be preventable

A study published in The Lancet Infectious Diseases Journal has identified that the vast majority of neonatal (newborn infant in the first 28 days of life) deaths caused by infections in South Africa and other low-and-middle-income countries could be prevented through improved clinical care and targeted medical interventions.

The research, conducted by the Child Health and Mortality Prevention Surveillance (CHAMPS) network, utilized innovative post-mortem techniques that enable accurate identification of causes of death in low-resource settings. To provide the most granular look to date at what is killing newborns in these regions, more than 2,600 neonatal deaths were analyzed using minimally invasive tissue sampling (MITS).

The study, titled “Post-mortem characterization of pathogen-specific causes of infection-related deaths in African and South Asian neonates: a prospective, observational, multicentre study which included a major surveillance site in Soweto, South Africa,” has revealed that infections are involved in 44% of neonatal deaths across multiple sites in Africa and South Asia, underscoring an urgent need to strengthen infection prevention, diagnosis, and treatment strategies. Crucially, an expert panel determined that over 80% of these infection-related deaths were preventable under current or improved facility-based conditions.

Key findings for South Africa

• Dominant hospital pathogens: In South Africa, Acinetobacter baumannii was the overwhelming driver of hospital-acquired infections, contributing to 74.3% of presumed hospital-acquired neonatal deaths.
• Community-acquired threats: Group B Streptococcus (GBS) was identified as the leading cause of community-acquired neonatal deaths in South Africa, accounting for 30.6% of such cases, followed by Escherichia coli at 24.7%.
• Emerging fungal risks: South Africa was the only site to report specific life-threatening fungal infections, including Candidozyma auris and Nakaseomyces glabratus, in the causal pathway to death.
• Preventability: The modifiable factors identified to reduce these deaths include improvements in infection prevention and control (50.8%), clinical care (50.7%), and antenatal and obstetric care (42.2%).

The findings reveal that current empirical antibiotic treatments may be insufficient, particularly in high-burden settings where antimicrobial resistance is rising. The study also shows that infections often occur alongside other conditions such as prematurity and birth complications, indicating that neonatal deaths are driven by multiple, interconnected factors.

“These findings indicate an urgent need to review empirical antibiotic treatment for neonatal infections,” said Prof. Shabir A. Madhi, Director of the South African Medical Research Council Vaccines and Infectious Diseases Analytics Research (Wits VIDA) Unit and lead author of the study. “The high prevalence of multidrug-resistant pathogens like K. pneumoniae and A. baumannii suggests our current standard protocols may no longer be sufficient. Alarmingly, some of these bacteria are resistant to all classes of antibiotics currently available.”

Nearly half of all deaths in children under five occur in the neonatal period, with the highest burden in Africa and South Asia. Importantly, local data further underscores the urgency of action. Within the Soweto and Thembelihle surveillance population, the neonatal mortality rate is estimated at 16.0 deaths per 1,000 live births, significantly higher than both South Africa’s national estimate of 10 per 1,000 and the Sustainable Development Goal (SDG) 2030 target of 12 per 1,000 live births.

These findings highlight persistent inequalities in maternal and child health outcomes, even within urban settings, and reinforce the need for targeted, evidence-based interventions.

The MITS technique used at Wits VIDA uses needle biopsies rather than full autopsies to collect biological specimens. This method proved far more effective than traditional antemortem diagnostics, which failed to identify a pathogen in up to 73% of suspected sepsis cases in South Africa.

The study provides one of the most comprehensive, pathogen-specific analyses of neonatal deaths to date and ultimately, the study highlights a powerful opportunity: Most infection-related neonatal deaths are preventable. The CHAMPS consortium concludes that prioritizing new maternal vaccines and strengthening hospital infection control are essential steps to reducing the high burden of neonatal mortality.

CHAMPS South Africa consistently shares its granular research findings with the National Department of Health (NDoH) through various channels to ensure this detailed evidence assists in developing targeted strategies to prevent neonatal infections. These data, which provide a precise look at the pathogens responsible for mortality, are intended to help the NDoH refine empirical antibiotic protocols and strengthen hospital infection control measures.

Beyond policy-level engagement, CHAMPS collaborates with local communities to raise awareness regarding prevention strategies, specifically emphasizing the importance of early antenatal care booking and consistent attendance. By focusing on these modifiable factors, the initiative seeks to improve obstetric care and reduce the number of babies born “too soon or too small,” addressing the preterm birth complications that frequently underlie neonatal deaths.

Who’s behind this story?

Stephanie Baum

Master’s in TESOL from The New School. Passionate about language learning and editing science news on biology and space exploration.

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Robert Egan

Bachelor’s in mathematical biology, Master’s in creative writing. Well-traveled with unique perspectives on science and language.

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