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Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF - Elife (2015)

Bottom Line: Thus, spread of potential pathogens among hospitalized infants is of great concern.We compared microbial communities in infants who did and did not develop necrotizing enterocolitis.Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.

ABSTRACT
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.

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Related in: MedlinePlus

An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).White boxes indicate that the strain was absent; shading intensity increaseswith increased organism abundance. Note the persistence of specificgenotypes within infants and the almost complete lack of overlap in strainsbetween infants. The few strains shared between infants are highlighted inred. Colors associated with organism names indicate the broader organismclassification: green are Firmicutes, orange are Gammaproteobacteria, redare Epsilonproteobacteria, pink are Betaproteobacteria, and blue areActinobacteria. Red lines indicate antibiotic administration associated withnecrotizing enterocolitis diagnoses, blue lines indicate antibioticadministration for other reasons.DOI:http://dx.doi.org/10.7554/eLife.05477.004
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fig2: An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).White boxes indicate that the strain was absent; shading intensity increaseswith increased organism abundance. Note the persistence of specificgenotypes within infants and the almost complete lack of overlap in strainsbetween infants. The few strains shared between infants are highlighted inred. Colors associated with organism names indicate the broader organismclassification: green are Firmicutes, orange are Gammaproteobacteria, redare Epsilonproteobacteria, pink are Betaproteobacteria, and blue areActinobacteria. Red lines indicate antibiotic administration associated withnecrotizing enterocolitis diagnoses, blue lines indicate antibioticadministration for other reasons.DOI:http://dx.doi.org/10.7554/eLife.05477.004

Mentions: Remarkably, very few bacterial strains occurred in more than one infant and no strainwas shared by all infants who developed NEC (Figure2). In contrast, and as could be expected, identical genotypes were almostalways detected in samples from the same infant, providing reassurance regarding thevalidity of our methods (Figure 2).10.7554/eLife.05477.004Figure 2.An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).


Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF - Elife (2015)

An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).White boxes indicate that the strain was absent; shading intensity increaseswith increased organism abundance. Note the persistence of specificgenotypes within infants and the almost complete lack of overlap in strainsbetween infants. The few strains shared between infants are highlighted inred. Colors associated with organism names indicate the broader organismclassification: green are Firmicutes, orange are Gammaproteobacteria, redare Epsilonproteobacteria, pink are Betaproteobacteria, and blue areActinobacteria. Red lines indicate antibiotic administration associated withnecrotizing enterocolitis diagnoses, blue lines indicate antibioticadministration for other reasons.DOI:http://dx.doi.org/10.7554/eLife.05477.004
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384745&req=5

fig2: An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).White boxes indicate that the strain was absent; shading intensity increaseswith increased organism abundance. Note the persistence of specificgenotypes within infants and the almost complete lack of overlap in strainsbetween infants. The few strains shared between infants are highlighted inred. Colors associated with organism names indicate the broader organismclassification: green are Firmicutes, orange are Gammaproteobacteria, redare Epsilonproteobacteria, pink are Betaproteobacteria, and blue areActinobacteria. Red lines indicate antibiotic administration associated withnecrotizing enterocolitis diagnoses, blue lines indicate antibioticadministration for other reasons.DOI:http://dx.doi.org/10.7554/eLife.05477.004
Mentions: Remarkably, very few bacterial strains occurred in more than one infant and no strainwas shared by all infants who developed NEC (Figure2). In contrast, and as could be expected, identical genotypes were almostalways detected in samples from the same infant, providing reassurance regarding thevalidity of our methods (Figure 2).10.7554/eLife.05477.004Figure 2.An overview of the distribution of 144 of the 149 tracked strains in the55 samples from 10 infants (five rare organisms were not included for spacereasons).

Bottom Line: Thus, spread of potential pathogens among hospitalized infants is of great concern.We compared microbial communities in infants who did and did not develop necrotizing enterocolitis.Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically relevant time scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, United States.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus