Project Overview
Project title: Baby GERMS Surveillance
Summary: Neonatal deaths account for almost half of deaths in children under 5 years, with infections being the third largest contributor after prematurity and intrapartum complications.
Lancet Global Health PMID: PMID 35839815
BMJ PMID: PMID 35135762
Project title: Baby GERMS Outbreak
Summary:
Despite major global progress in reducing under-five mortality, neonatal deaths remained high, accounting for nearly half of all child deaths. Infectious diseases were among the leading causes of neonatal mortality, particularly in sub-Saharan Africa, where reliable population-level data on neonatal infections had been scarce. In South Africa, existing studies were largely limited to tertiary hospitals, leaving major knowledge gaps in the true burden, causes, and antimicrobial resistance (AMR) patterns of neonatal infections across different healthcare levels. Accurate national data were essential to measure progress toward South Africa’s goal of reducing neonatal sepsis by 84% by 2025.
The Baby GERMS-SA study aimed to improve understanding of the incidence, aetiology, and outcomes of neonatal bloodstream infections (BSI) and meningitis in South Africa.
Its objectives were to:
- Determine the bacterial and fungal causes and incidence of culture-confirmed neonatal infections from 2014–2021.
- Describe the prevalence of AMR in neonatal pathogens at secondary-level hospitals.
- Identify clinical characteristics and modifiable risk factors associated with neonatal mortality.
A two-tiered surveillance approach was used:
- Tier 1: Retrospective population-based surveillance of all culture-confirmed neonatal BSIs and meningitis in South Africa (2014–2021) using National Health Laboratory Service (NHLS) data to calculate provincial and facility-level incidence risks.
- Tier 2: Prospective enhanced surveillance at six sentinel regional hospitals (one per province) to collect detailed clinical, epidemiological, and laboratory data to identify risk factors for mortality and characterise resistant pathogens.
A complementary national survey of neonatal units assessed staffing, diagnostic capacity, and infection-prevention practices to support interpretation of surveillance findings.
Outcomes and Impact
The project generated the first national dataset describing the burden and trends of neonatal infections and AMR across all healthcare levels in South Africa. Findings guided the Department of Health in designing targeted antimicrobial stewardship and infection-prevention programmes. Sentinel hospitals received facility-specific feedback to inform empiric treatment protocols and local quality-improvement interventions.
By providing robust baseline data on neonatal sepsis burden and resistance trends, Baby GERMS-SA strengthened surveillance capacity, enabled evaluation of national interventions, and contributed to achieving Sustainable Development Goal 3—improving neonatal and child health outcomes.
Key Objectives
Baby GERMS is the first population-based surveillance programme on neonatal infections in Africa and was set up in the latter half of 2019 with funding from the Bill and Melinda Gates Foundation (BMGF). The aim was to provide a baseline description of the aetiology, antimicrobial susceptibility and clinical characteristics of culture-confirmed neonatal bloodstream infections and meningitis in South Africa.
Through this surveillance programme, we aimed to identify modifiable risk factors which could be targeted to reduce neonatal morbidity and mortality. Baby GERMS has been acknowledged as a major new source of strategic data by the National Neonatal Task Force, which was launched in September 2019 to provide technical advice and guidance on surveillance for neonatal sepsis, infection prevention and control, neonatal infection case management, antimicrobialstewardship and containment of neonatal unit outbreaks.
In 2021, data from approximately 45 000 laboratory-confirmed cases of neonatal meningitis and blood stream infections were collated and analysed and a publication was submitted to Lancet Global Health. This analysis was shared with stakeholders from the National Department of Health to inform neonatal sepsis prevention guidelines.
Isolates collected from 933 episodes of laboratory-confirmed neonatal meningitis and blood stream infections occurring at 6 provincial/regional hospitals between October 2019 and September 2020 underwent further genotypic and phenotypic analysis and results on the numerous Klebsiella pneumoniae infections have been shared with KlebNET, an international group looking at global genomics of Klebsiella K-loci.
Aspects of the sentinel surveillance data were shared at the International Symposium on Streptococcus Agalactiae Disease (ISSAD) and the World Symposium on Paediatric Infectious Diseases (WSPID).
Partners
Team Members
Publications
Culture-confirmed neonatal bloodstream infections and meningitis in South Africa, 2014-19: a cross-sectional study
Rudzani C Mashau, Susan T Meiring, Angela Dramowski, Rindidzani E Magobo, Vanessa C Quan, Olga Perovic, Anne von Gottberg, Cheryl Cohen, Sithembiso Velaphi, Erika van Schalkwyk, Nelesh P Govender
Pathogen aetiology and risk factors for death among neonates with bloodstream infections at lower-tier South African hospitals
Susan Meiring, Vanessa Quan, Rudzani Mashau, Olga Perovic, Rindidzani Magobo, Marshagne Smith, Ruth Mpembe, Anne von Gottberg, Linda de Gouveia, Sibongile Walaza, Cheryl Cohen, Constance Kapongo, Cheryl Mackay, Mphekwa Thomas Mailula, Omphile Mekgoe, Lerato Motjale, Rose Phayane, Angela Dramowski, Nelesh P Govender
Outbreak of NDM-1– and OXA-181–Producing Klebsiella pneumoniae Bloodstream Infections in a Neonatal Unit, South Africa
Rindidzani E Magobo, Husna Ismail, Michelle Lowe, Wilhelmina Strasheim, Ruth Mogokotleng, Olga Perovic, Stanford Kwenda, Arshad Ismail, Manala Makua, Abram Bore, Rose Phayane, Harishia Naidoo, Tanya Dennis, Makhosazane Ngobese, Wim Wijnant, Nelesh P Govender
Culture-confirmed neonatal bloodstream infections and meningitis in South Africa, 2014–19: a cross-sectional study
Rudzani C Mashau, Susan T Meiring, Angela Dramowski, Rindidzani E Magobo, Vanessa C Quan, Olga Perovic
Study protocol for a population-based observational surveillance study of culture-confirmed neonatal bloodstream infections and meningitis in South Africa: Baby GERMS-SA
Susan Meiring, Rudzani Mashau, Rindidzani Magobo, Olga Perovic, Vanessa Quan, Cheryl Cohen, Linda de Gouveia, Anne von Gottberg, Cheryl Mackay, Mphekwa Thomas Mailula, Rose Phayane, Angela Dramowski, Nelesh P Govender
Maternal-infant Characteristics of Preterm and Term Neonates With Bloodstream Infections in Lower-tier Hospitals in South Africa
Vanessa Quan, Susan Meiring, Rudzani Mashau, Olga Perovic, Rindidzani Magobo, Marshagne Smith, Ruth Mpembe, Anne von Gottberg, Linda de Gouveia, Sibongile Walaza, Cheryl Cohen, Constance Kapongo, Cheryl Mackay, Mphekwa Thomas Mailula, Omphile Mekgoe, Lerato Motjale, Rose Phayane, Angela Dramowski, Nelesh P Govender
