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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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Rank abundance curves describing the microbial community (exclusiveof phage and plasmids) in infant #2.Colors correspond with those used in emergent self organizing maps (seeFigure 8 and Supplementary file3). Details are available in Supplementary file3. NEC: necrotizing enterocolitis.DOI:http://dx.doi.org/10.7554/eLife.05477.014
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fig8s1: Rank abundance curves describing the microbial community (exclusiveof phage and plasmids) in infant #2.Colors correspond with those used in emergent self organizing maps (seeFigure 8 and Supplementary file3). Details are available in Supplementary file3. NEC: necrotizing enterocolitis.DOI:http://dx.doi.org/10.7554/eLife.05477.014

Mentions: While no metabolic imbalance was found, many pathogens were detected in fecal samplesof infants who developed NEC. For example, Enterobacter cloacae isabundant in infant #2 and is predicted to have many toxin and type VIsecretion system genes and an extensive antibiotic resistance repertoire (Supplementary file 4). Theresistance genes may explain why E. cloacae remained abundant afterantibiotic treatment (sequence analyses indicate that the same genotype persistedthrough the treatments; Figure 2 and Figure 4—figure supplement 1). ESOMsused to validate the binning also provide an overview of the community composition,and in the case of infant #2, also highlight the almost complete dominance ofE. cloacae in response to antibiotics (Figure 8). Note that these maps do not reflect organismabundances, although very small areas can indicate genomes that were partiallysampled due to low sequence coverage (for abundance information see Supplementary file 3 andFigure 8—figure supplement 1).10.7554/eLife.05477.013Figure 8.Microbial community composition, community complexity, and anoverview of binning for samples from infant #2.


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)

Rank abundance curves describing the microbial community (exclusiveof phage and plasmids) in infant #2.Colors correspond with those used in emergent self organizing maps (seeFigure 8 and Supplementary file3). Details are available in Supplementary file3. NEC: necrotizing enterocolitis.DOI:http://dx.doi.org/10.7554/eLife.05477.014
© Copyright Policy
Related In: Results  -  Collection

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

fig8s1: Rank abundance curves describing the microbial community (exclusiveof phage and plasmids) in infant #2.Colors correspond with those used in emergent self organizing maps (seeFigure 8 and Supplementary file3). Details are available in Supplementary file3. NEC: necrotizing enterocolitis.DOI:http://dx.doi.org/10.7554/eLife.05477.014
Mentions: While no metabolic imbalance was found, many pathogens were detected in fecal samplesof infants who developed NEC. For example, Enterobacter cloacae isabundant in infant #2 and is predicted to have many toxin and type VIsecretion system genes and an extensive antibiotic resistance repertoire (Supplementary file 4). Theresistance genes may explain why E. cloacae remained abundant afterantibiotic treatment (sequence analyses indicate that the same genotype persistedthrough the treatments; Figure 2 and Figure 4—figure supplement 1). ESOMsused to validate the binning also provide an overview of the community composition,and in the case of infant #2, also highlight the almost complete dominance ofE. cloacae in response to antibiotics (Figure 8). Note that these maps do not reflect organismabundances, although very small areas can indicate genomes that were partiallysampled due to low sequence coverage (for abundance information see Supplementary file 3 andFigure 8—figure supplement 1).10.7554/eLife.05477.013Figure 8.Microbial community composition, community complexity, and anoverview of binning for samples from infant #2.

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