Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

Raveh-Sadka, Tali; Firek, Brian; Sharon, Itai; Baker, Robyn; Brown, Christopher T.; Thomas, Brian C.; Morowitz, Michael J.; Banfield, Jillian F.

doi:10.1038/ismej.2016.83

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

Journal Article · Fri Jun 03 00:00:00 EDT 2016 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2016.83· OSTI ID:1581584

Raveh-Sadka, Tali ^[1]; Firek, Brian ^[2]; Sharon, Itai ^[1]; Baker, Robyn ^[2]; ^[1]; Thomas, Brian C. ^[1]; Morowitz, Michael J. ^[2]; Banfield, Jillian F. ^[1]

Univ. of California, Berkeley, CA (United States)
Univ. of Pittsburgh School of Medicine, PA (United States)

The potentially critical stage of initial gut colonization in premature infants occurs in the hospital environment, where infants are exposed to a variety of hospital-associated bacteria. Because few studies of microbial communities are strain-resolved, we know little about the extent to which specific strains persist in the hospital environment and disperse among infants. To study this, we compared 304 near-complete genomes reconstructed from fecal samples of 21 infants hospitalized in the same intensive care unit in two cohorts, over 3 years apart. The genomes represent 159 distinct bacterial strains, only 14 of which occurred in multiple infants. Enterococcus faecalis and Staphylococcus epidermidis, common infant gut colonists, exhibit diversity comparable to that of reference strains, inline with introduction of strains from infant-specific sources rather than a hospital strain pool. Unlike other infants, a pair of sibling infants shared multiple strains, even after extensive antibiotic administration, suggesting overlapping strain-sources and/or genetic selection drive microbiota similarities. Interestingly, however, five strains were detected in infants hospitalized three years apart. Three of these were also detected in multiple infants in the same year. Finally, this finding of a few widely dispersed and persistent bacterial colonizers despite overall low potential for strain dispersal among infants has implications for understanding and directing healthy colonization.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC02-05CH11231; SC0004918

OSTI ID:: 1581584

Alternate ID(s):: OSTI ID: 1535035

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 12 Vol. 10; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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