Fungal cutaneous microbiome and host determinants in preterm and term neonates

Pediatr Res. 2020 Aug;88(2):225-233. doi: 10.1038/s41390-019-0719-7. Epub 2019 Dec 9.


Background: The neonatal cutaneous mycobiome has not been characterized in preterm infants. Invasive fungal infections in preterm neonates are associated with high mortality. The immaturity of the preterm skin predisposes neonates to invasive infection by skin colonizers. We report the clinical and host determinants that influence the skin mycobiome.

Methods: Skin swabs from the antecubital fossa, forehead, and gluteal region of 15 preterm and 15 term neonates were obtained during the first 5 weeks of life. The mycobiome was sequenced using the conserved pan-fungal ITS2 region. Blood samples were used to genotype immune modulating genes. Clinical metadata was collected to determine the clinical predictors of the abundance and diversity of the skin mycobiome.

Results: The neonatal mycobiome is characterized by few taxa. Alpha diversity of the mycobiome is influenced by antibiotic exposure, the forehead body site, and the neonatal intensive care unit (NICU) environment. Beta diversity varies with mode of delivery, diet, and body site. The host determinants of the cutaneous microbiome include single-nucleotide polymorphisms in TLR4, NLRP3,CARD8, and NOD2.

Conclusion: The neonatal cutaneous mycobiome is composed of few genera and is influenced by clinical factors and host genetics, the understanding of which will inform preventive strategies against invasive fungal infections.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • CARD Signaling Adaptor Proteins / genetics
  • Female
  • Fungi / classification
  • Genotype
  • Humans
  • Infant, Premature
  • Intensive Care Units, Neonatal*
  • Intensive Care, Neonatal
  • Longitudinal Studies
  • Male
  • Microbiota*
  • Mycobiome*
  • NLR Family, Pyrin Domain-Containing 3 Protein / genetics
  • Neoplasm Proteins / genetics
  • Nod2 Signaling Adaptor Protein / genetics
  • Polymorphism, Single Nucleotide
  • Prospective Studies
  • Skin / metabolism
  • Skin / microbiology*
  • Toll-Like Receptor 4 / genetics


  • Anti-Bacterial Agents
  • CARD Signaling Adaptor Proteins
  • CARD8 protein, human
  • NLR Family, Pyrin Domain-Containing 3 Protein
  • NLRP3 protein, human
  • NOD2 protein, human
  • Neoplasm Proteins
  • Nod2 Signaling Adaptor Protein
  • TLR4 protein, human
  • Toll-Like Receptor 4