FATAL acute febrile illness (fAFI) is a major contributor to infant mortality in low-resource settings. Yet, the biological warning signs that precede these severe infections remain poorly defined. New research from Zambia has identified distinct nasopharyngeal microbiome patterns that may help predict which infants are most at risk of developing deadly infections.
Tracking the Microbiome from Birth
In this longitudinal study, researchers analysed nasopharyngeal samples collected from Zambian infants between 1 and 14 weeks of age. The study compared 26 samples from nine infants who later developed fAFI with 69 samples from ten healthy controls. Using 16S rRNA gene sequencing, the team examined how the infants’ nasopharyngeal microbiota developed over time and whether early microbial imbalances were linked to severe illness.
Loss of Key Microbes and Early Dysbiosis
Infants who developed fatal febrile illness (fAFI+) had markedly lower microbial diversity than healthy infants (fAFI−). Their nasopharyngeal microbiomes showed reduced levels of beneficial bacteria such as Dolosigranulum, Haemophilus, Streptococcus, and Corynebacterium, alongside increased presence of potentially harmful Pseudomonas. This microbial imbalance, or dysbiosis, was observed before the onset of illness, suggesting a predictive role.
Implications for Infant Health and Survival
These findings highlight that early nasopharyngeal microbiome disruption may act as a biomarker for fatal infections in infancy. Identifying microbial warning patterns could help clinicians intervene earlier, particularly in low-resource settings where infectious diseases are a leading cause of infant death.
Towards Precision Paediatric Care
By linking microbial composition to illness risk, this study provides a foundation for developing microbiome-based screening tools. With further validation, such tools could enable precision paediatric interventions, improving early diagnosis, treatment, and survival outcomes for vulnerable newborns worldwide.
Reference
Odom AR et al. Longitudinal Analysis of Nasopharyngeal Microbial Risk Markers for Fatal Acute Febrile Illness in a Zambian Birth Cohort. J Infect Dis. 2025;232(15): 779–89.
