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OBJECTIVE: To evaluate the pneumonia specific case fatality rate over time following the implementation of a Child Lung Health Programme (CLHP) within the existing government health services in Malawi to improve delivery of pneumonia case management. METHODS: A prospective, nationwide public health intervention was studied to evaluate the impact on pneumonia specific case fatality rate (CFR) in infants and young children (0 to 59 months of age) following the implementation of the CLHP. The implementation was step-wise from October 1st 2000 until 31st December 2005 within paediatric inpatient wards in 24 of 25 district hospitals in Malawi. Data analysis compared recorded outcomes in the first three months of the intervention (the control period) to the period after that, looking at trend over time and variation by calendar month, age group, severity of disease and region of the country. The analysis was repeated standardizing the follow-up period by using only the first 15 months after implementation at each district hospital. FINDINGS: Following implementation, 47,228 children were admitted to hospital for severe/very severe pneumonia with an overall CFR of 9.8%. In both analyses, the highest CFR was in the children 2 to 11 months, and those with very severe pneumonia. The majority (64%) of cases, 2-59 months, had severe pneumonia. In this group there was a significant effect of the intervention Odds Ratio (OR) 0.70 (95%CI: 0.50-0.98); p = 0.036), while in the same age group children treated for very severe pneumonia there was no interventional benefit (OR 0.97 (95%CI: 0.72-1.30); p = 0.8). No benefit was observed for neonates (OR 0.83 (95%CI: 0.56-1.22); p = 0.335). CONCLUSIONS: The nationwide implementation of the CLHP significantly reduced CFR in Malawian infants and children (2-59 months) treated for severe pneumonia. Reasons for the lack of benefit for neonates, infants and children with very severe pneumonia requires further research.