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Updated: May 31, 2026
Microbiological Rapid On-Site Evaluation for Pulmonary Infectious Diseases
Published on: March 1, 2024
PCR improves diagnostic yield from lung aspiration in Malawian children with radiologically confirmed pneumonia
Enitan D Carrol1, Limangeni A Mankhambo, Malcolm Guiver
1Department of Women's and Children's Health, The University of Liverpool, Institute of Child Health, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom. edcarrol@liv.ac.uk
Insights
Polymerase chain reaction (PCR) on lung aspirates significantly improves childhood pneumonia diagnosis in Africa. This method identifies more bacterial and viral pathogens, including Streptococcus pneumoniae, than traditional blood cultures.
Area of Science:
- Pediatric Infectious Diseases
- Microbiology
- Molecular Diagnostics
Background:
- Accurate childhood pneumonia aetiology data is crucial for high-mortality regions.
- Blood culture has low diagnostic yield for pneumonia pathogens.
- Lung aspirate culture offers higher yield, but further improvements are explored.
Purpose of the Study:
- To enhance diagnostic yield for childhood pneumonia in African children.
- To evaluate the utility of polymerase chain reaction (PCR) on lung aspirates.
- To identify bacterial and viral aetiologies, including Streptococcus pneumoniae and Haemophilus influenzae b.
Main Methods:
- 95 children with radiological pneumonia underwent lung aspirate collection.
- Samples were analyzed using bacterial culture and PCR for bacteria, viruses, and Pneumocystis jirovecii.
- Bacterial loads were quantified in blood and lung aspirates for pneumococcal cases.
Main Results:
- PCR on lung aspirates increased pathogen identification to 62% (59/95) from 8% (8/95) with blood culture alone.
- Streptococcus pneumoniae was the most common bacterial pathogen (41%).
- Adenovirus (16%) and human bocavirus (4%) were the most frequent viral pathogens identified.
Conclusions:
- Lung aspirate PCR significantly enhances the diagnostic yield in a select group of African children with pneumonia.
- The study confirms a substantial role for Streptococcus pneumoniae and viruses in childhood pneumonia aetiology in Africa.
Background:
Accurate data on childhood pneumonia aetiology are essential especially from regions where mortality is high, in order to inform case-management guidelines and the potential of prevention strategies such as bacterial conjugate vaccines. Yield from blood culture is low, but lung aspirate culture provides a higher diagnostic yield. We aimed to determine if diagnostic yield could be increased further by polymerase chain reaction (PCR) detection of bacteria (Streptococcus pneumoniae and Haemophilus influenzae b) and viruses in lung aspirate fluid.
Methods:
A total of 95 children with radiological focal, lobar or segmental consolidation had lung aspirate performed and sent for bacterial culture and for PCR for detection of bacteria, viruses and Pneumocystis jirovecii. In children with a pneumococcal aetiology, pneumococcal bacterial loads were calculated in blood and lung aspirate fluid.
Results:
Blood culture identified a bacterial pathogen in only 8 patients (8%). With the addition of PCR on lung aspirate samples, causative pathogens (bacterial, viral, pneumocystis) were identified singly or as co-infections in 59 children (62%). The commonest bacterial organism was S.pneumoniae (41%), followed by H. influenzae b (6%), and the commonest virus identified was adenovirus (16%), followed by human bocavirus (HBoV) (4%), either as single or co-infection.
Conclusions:
In a select group of African children, lung aspirate PCR significantly improves diagnostic yield. Our study confirms a major role of S.pneumoniae and viruses in the aetiology of childhood pneumonia in Africa.
