Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.
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. 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.
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Tali
T
Raveh-Sadka
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Brian
B
Firek
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Itai
I
Sharon
Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Robyn
R
Baker
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Christopher T
0000-0002-7758-6447
CT
Brown
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Brian C
BC
Thomas
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Michael J
MJ
Morowitz
Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
Jillian F
JF
Banfield
D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D015331:Cohort Studies; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007234:Infant, Premature; D008297:Male