Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.

Summary

In febrile term infants, 63% of extraintestinal infections had an intestinal strain essentially identical to the invasive pathogen (>99.999% ANI), supporting the gut as a reservoir. E. coli cases showed higher gut E. coli abundance, enrichment of phylogroup B2, and virulence loci in isogenic colonized infants.

Key Findings

• In 63% of EBI cases, a gut strain was presumptively isogenic to the invasive pathogen (>99.999% ANI).
• E. coli EBIs were associated with increased gut E. coli relative abundance versus controls.
• Isogenic E. coli colonization correlated with higher phylogroup B2 abundance and enrichment of virulence factor loci.

Clinical Implications

Consider targeted surveillance/decolonization among colonized infants (e.g., high-risk E. coli B2 carriers) and refine risk stratification beyond clinical signs by incorporating gut microbiome signatures.

Limitations

• Moderate sample size and observational design limit causal inference.
• Single-country ED network; timing between stool sampling and infection onset may affect detectability.

Future Directions

Prospective interventional studies testing surveillance, decolonization, or microbiome-modulating strategies in colonized infants; validation in diverse populations and preterm cohorts.