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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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Overview community composition for infant #8, who developednecrotizing enterocolitis 1 day after collection of the lastsample.(A) Time series + GC content emergent self organizingmaps (ESOMs) were used to fine-tune binning and provide an overview ofcommunity composition. Points in the ESOM are color coded to indicategenome bin, the name for which is given to the right. (B)Time series abundance patterns for the relatively well-sampled bacteria;brown shading over numbers indicates sample pairs collected on the sameday. The communities were dominated by bacteria closely related toEnterobacter cloacae (yellow) and Klebsiellapneumoniae (brown). (C) Expanded view of the lowabundance part of B. Several organisms were present at lowabundance; some appeared a few days prior to the necrotizingenterocolitis diagnosis. Clostridium was detected but the genome samplingwas so low that it was not included in the figure (see Supplementary file3). DOL: day of life.DOI:http://dx.doi.org/10.7554/eLife.05477.016
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fig8s3: Overview community composition for infant #8, who developednecrotizing enterocolitis 1 day after collection of the lastsample.(A) Time series + GC content emergent self organizingmaps (ESOMs) were used to fine-tune binning and provide an overview ofcommunity composition. Points in the ESOM are color coded to indicategenome bin, the name for which is given to the right. (B)Time series abundance patterns for the relatively well-sampled bacteria;brown shading over numbers indicates sample pairs collected on the sameday. The communities were dominated by bacteria closely related toEnterobacter cloacae (yellow) and Klebsiellapneumoniae (brown). (C) Expanded view of the lowabundance part of B. Several organisms were present at lowabundance; some appeared a few days prior to the necrotizingenterocolitis diagnosis. Clostridium was detected but the genome samplingwas so low that it was not included in the figure (see Supplementary file3). DOL: day of life.DOI:http://dx.doi.org/10.7554/eLife.05477.016

Mentions: Infant #8 developed NEC 1 day after collection of the last sample. Thecommunities in the two pairs of samples from different times on the same day (Figure 8—figure supplement 3) containgenerally similar organisms, but rapid abundance shifts occur, consistent withgeneral observations over whole day periods. Especially prominent in samples frominfant #8 were a Klebsiella pneumoniae-related strain (Figure 4—figure supplement 2) and anE. cloacae (Figure4—figure supplement 1) strain. C. perfringens has anotable inventory of predicted pathogenicity-related genes. E. coli,present in the three samples collected prior to diagnosis, may have contributed tointestinal inflammation, given that it has a large inventory of type III and type VIsecretion system genes and many toxin-encoding genes (Supplementary file 4).


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)

Overview community composition for infant #8, who developednecrotizing enterocolitis 1 day after collection of the lastsample.(A) Time series + GC content emergent self organizingmaps (ESOMs) were used to fine-tune binning and provide an overview ofcommunity composition. Points in the ESOM are color coded to indicategenome bin, the name for which is given to the right. (B)Time series abundance patterns for the relatively well-sampled bacteria;brown shading over numbers indicates sample pairs collected on the sameday. The communities were dominated by bacteria closely related toEnterobacter cloacae (yellow) and Klebsiellapneumoniae (brown). (C) Expanded view of the lowabundance part of B. Several organisms were present at lowabundance; some appeared a few days prior to the necrotizingenterocolitis diagnosis. Clostridium was detected but the genome samplingwas so low that it was not included in the figure (see Supplementary file3). DOL: day of life.DOI:http://dx.doi.org/10.7554/eLife.05477.016
© Copyright Policy
Related In: Results  -  Collection

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

fig8s3: Overview community composition for infant #8, who developednecrotizing enterocolitis 1 day after collection of the lastsample.(A) Time series + GC content emergent self organizingmaps (ESOMs) were used to fine-tune binning and provide an overview ofcommunity composition. Points in the ESOM are color coded to indicategenome bin, the name for which is given to the right. (B)Time series abundance patterns for the relatively well-sampled bacteria;brown shading over numbers indicates sample pairs collected on the sameday. The communities were dominated by bacteria closely related toEnterobacter cloacae (yellow) and Klebsiellapneumoniae (brown). (C) Expanded view of the lowabundance part of B. Several organisms were present at lowabundance; some appeared a few days prior to the necrotizingenterocolitis diagnosis. Clostridium was detected but the genome samplingwas so low that it was not included in the figure (see Supplementary file3). DOL: day of life.DOI:http://dx.doi.org/10.7554/eLife.05477.016
Mentions: Infant #8 developed NEC 1 day after collection of the last sample. Thecommunities in the two pairs of samples from different times on the same day (Figure 8—figure supplement 3) containgenerally similar organisms, but rapid abundance shifts occur, consistent withgeneral observations over whole day periods. Especially prominent in samples frominfant #8 were a Klebsiella pneumoniae-related strain (Figure 4—figure supplement 2) and anE. cloacae (Figure4—figure supplement 1) strain. C. perfringens has anotable inventory of predicted pathogenicity-related genes. E. coli,present in the three samples collected prior to diagnosis, may have contributed tointestinal inflammation, given that it has a large inventory of type III and type VIsecretion system genes and many toxin-encoding genes (Supplementary file 4).

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