Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.
Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. Thus, spread of potential pathogens among hospitalized infants is of great concern. Here, we reconstructed hundreds of high-quality genomes of microorganisms that colonized co-hospitalized premature infants, assessed their metabolic potential, and tracked them over time to evaluate bacterial strain dispersal among infants. We compared microbial communities in infants who did and did not develop necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, our genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants who developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to the spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Tali
T
Raveh-Sadka
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Brian C
BC
Thomas
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Andrea
A
Singh
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States.
Brian
B
Firek
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Brandon
B
Brooks
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Cindy J
CJ
Castelle
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Itai
I
Sharon
Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States.
Robyn
R
Baker
Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States.
Misty
M
Good
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, United States.
Michael J
MJ
Morowitz
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.
Jillian F
JF
Banfield
D001419:Bacteria / Q000302:isolation & purification*; D020345:Enterocolitis, Necrotizing / Q000382:microbiology*; D006760:Hospitalization; D006801:Humans; D007231:Infant, Newborn; D007234:Infant, Premature; D007422:Intestines / Q000382:microbiology*
Microbiota; evolutionary biology; genomics; gut microbial colonization; infectious disease; metagenomics; microbiology; necrotizing enterocolitis; nosocomial infections; preterm infants