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Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

Author

Listed:
  • Brandon Brooks

    (University of California)

  • Matthew R. Olm

    (University of California)

  • Brian A. Firek

    (University of Pittsburgh School of Medicine)

  • Robyn Baker

    (Division of Newborn Medicine, Magee-Womens Hospital of Pittsburgh of UPMC)

  • Brian C. Thomas

    (University of California)

  • Michael J. Morowitz

    (University of Pittsburgh School of Medicine)

  • Jillian F. Banfield

    (University of California)

Abstract

Preterm infants exhibit different microbiome colonization patterns relative to full-term infants, and it is speculated that the hospital room environment may contribute to infant microbiome development. Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastrointestinal tracts of infants and from the neonatal intensive care unit (NICU) room environment. Some strains detected in hospitalized infants also occur in sinks and on surfaces, and belong to species such as Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa, and Klebsiella pneumoniae, which are frequently implicated in nosocomial infection and preterm infant gut colonization. Of the 15 K. pneumoniae strains detected in the study, four were detected in both infant gut and room samples. Time series experiments showed that nearly all strains associated with infant gut colonization can be detected in the room after, and often before, detection in the gut. Thus, we conclude that a component of premature infant gut colonization is the cycle of microbial exchange between the room and the occupant.

Suggested Citation

  • Brandon Brooks & Matthew R. Olm & Brian A. Firek & Robyn Baker & Brian C. Thomas & Michael J. Morowitz & Jillian F. Banfield, 2017. "Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome," Nature Communications, Nature, vol. 8(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-02018-w
    DOI: 10.1038/s41467-017-02018-w
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    Cited by:

    1. Mohammad H. Mirhakkak & Xiuqiang Chen & Yueqiong Ni & Thorsten Heinekamp & Tongta Sae-Ong & Lin-Lin Xu & Oliver Kurzai & Amelia E. Barber & Axel A. Brakhage & Sebastien Boutin & Sascha Schäuble & Gian, 2023. "Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Shuqin Zeng & Dhrati Patangia & Alexandre Almeida & Zhemin Zhou & Dezhi Mu & R. Paul Ross & Catherine Stanton & Shaopu Wang, 2022. "A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Manoshi S. Datta & Idan Yelin & Ori Hochwald & Imad Kassis & Liron Borenstein-Levin & Amir Kugelman & Roy Kishony, 2021. "Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    4. Li Zhang & Karen R. Jonscher & Zuyuan Zhang & Yi Xiong & Ryan S. Mueller & Jacob E. Friedman & Chongle Pan, 2022. "Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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