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Non-Invasive Model of Neuropathogenic Escherichia coli Infection in the Neonatal Rat
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Metagenomic survey of pathogen prevalence in the infant gut

Nienke van Beek1,2, Ahmed Bargheet3,4, Ching Jian1

  • 1Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland.

Scientific Reports
|May 22, 2026
PubMed

Insights

Infant gut opportunistic pathogens are influenced by breastfeeding, antibiotics, and delivery mode. Targeted interventions can modify their prevalence, potentially reducing early life infections.

Area of Science:

  • Microbiome research
  • Pediatric infectious diseases
  • Human gut ecology

Background:

  • The human microbiota plays a crucial role in health from infancy.
  • Infants are susceptible to opportunistic pathogens due to immature immune systems and low microbial diversity.
  • Understanding factors influencing pathogen colonization is vital for infant health.

Purpose of the Study:

  • To investigate associations between opportunistic pathogen prevalence in infants and factors like breastfeeding, antibiotic use, and birth mode.
  • To identify specific bacterial taxa linked to opportunistic pathogen colonization in the infant gut.
  • To explore the impact of medical and caregiving practices on infant gut microbiota composition.

Main Methods:

  • Analysis of 3981 publicly available infant and mother shotgun metagenomes from 10 countries.
  • Identification of opportunistic pathogen species within the infant gut microbiome.
  • Statistical analysis to determine correlations between pathogen prevalence and various influencing factors.

Main Results:

  • Clostridioides difficile prevalence decreased with breastfeeding and presence of Faecalibacterium and Dorea spp.
  • Staphylococcus aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding.
  • Klebsiella pneumoniae acquisition was later, more prevalent in premature infants, and less common in non-antibiotic vaginal births.

Conclusions:

  • Opportunistic pathogen prevalence in the infant gut is significantly influenced by medical interventions and caregiving practices.
  • Findings suggest that targeted interventions could modify pathogen colonization and reduce early life infections.
  • Reducing the spread of infant gut pathogens may contribute to global efforts against pediatric infections.

Keywords:
Antimicrobial resistanceGut microbiotaInfant gutInfectious diseaseOpportunistic pathogen colonisation

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